int main ( int argc, /* number of input arguments */ char ** argv /* array of input arguments */ ) { /*----- Identify software -----*/ #if 0 printf ("\n\n"); printf ("Program: %s \n", PROGRAM_NAME); printf ("Author: %s \n", PROGRAM_AUTHOR); printf ("Date: %s \n", PROGRAM_DATE); printf ("\n"); #endif PRINT_VERSION("3destpdf") ; AUTHOR(PROGRAM_AUTHOR) ;mainENTRY("3destpdf main") ; machdep() ; /*----- Program initialization -----*/ initialize_program (argc, argv); }
/*--------------- main routine ---------------*/ int main( int argc, char *argv[] ) { options_t * opts = &g_opts; int rv; if( argc < 2 ) { show_help(); return 0; } mainENTRY("3dTto1D main"); machdep(); AFNI_logger("3dTto1D",argc,argv); /* process command line arguments (and read dataset and mask) */ rv = process_opts(opts, argc, argv); if( rv ) RETURN(rv < 0); /* only a negative return is considered failure */ if( check_dims(opts) ) RETURN(1); /* evaluation of rv now depends on the method, usually non-zero is bad */ rv = compute_results(opts); /* for 4095_warn, return now, regardless */ if( opts->method == T21_METH_4095_WARN ) RETURN(rv); /* otherwise, any non-zero return is a failure */ if ( rv ) RETURN(1); if( write_results(opts) ) RETURN(1); RETURN(0); }
int main( int argc , char * argv[] ) { THD_3dim_dataset * dset ; int iarg ; MCW_idcode idc ; char str[256] ; if( argc < 2 || strncmp(argv[1],"-help",4) == 0 ) Syntax() ; iarg = 1 ; mainENTRY("3dnewid main"); machdep(); if( strcmp(argv[1],"-fun") == 0 ){ /* 22 May 2000: for fun */ int nid=0 , ii ; char *eee = getenv("UUID") ; if( argc > 2 ) nid = strtol(argv[2],NULL,10) ; if( nid <= 0 ) nid = 1 ; if( eee == NULL ){ for( ii=0 ; ii < nid ; ii++ ){ idc = MCW_new_idcode() ; printf("%s\n",idc.str) ; } } else { /* 20 Aug 2002: test of niml.c */ for( ii=0 ; ii < nid ; ii++ ){ eee = UUID_idcode(); printf("%s\n",eee); free(eee); } } exit(0) ; } else if ( strcmp(argv[1],"-hash") == 0 ){ /* Oct. 2011:for repeatable fun */ if( argc != 3 ) { ERROR_message("You need a string following -hash"); exit(1); } printf("%s\n", UNIQ_hashcode(argv[2])); exit(0) ; } /*-- OK, not for fun --*/ AFNI_logger("3dnewid",argc,argv) ; for( ; iarg < argc ; iarg++ ){ dset = THD_open_one_dataset( argv[iarg] ) ; if( dset == NULL ){ fprintf(stderr,"** Skipping dataset %s\n",argv[iarg]) ; continue ; } dset->idcode = MCW_new_idcode() ; sprintf(str,"3dnewid %s\n",argv[iarg]) ; tross_Append_History( dset , str) ; putenv("AFNI_DECONFLICT=OVERWRITE") ; THD_write_3dim_dataset( NULL , NULL , dset , False ) ; THD_delete_3dim_dataset( dset , False ) ; } exit(0) ; }
/*--------------- main routine ---------------*/ int main( int argc, char *argv[] ) { THD_3dim_dataset * countset=NULL; param_t * params = &g_params; int rv, limit; if( argc < 1 ) { show_help(); return 0; } /* general stuff */ mainENTRY("3dmask_tool"); machdep(); AFNI_logger("3dmask_tool",argc,argv); enable_mcw_malloc(); /* process options: a negative return is considered an error */ rv = process_opts(params, argc, argv); if( rv ) RETURN(rv < 0); /* open, convert to byte, zeropad, dilate, unzeropad */ if( process_input_dsets(params) ) RETURN(1); /* create mask count dataset and return num volumes (delete old dsets) */ if( count_masks(params->dsets, params->ndsets, params->verb, &countset, ¶ms->nvols) ) RETURN(1); /* limit to frac of nvols (if not counting, convert to 0/1 mask) */ limit = ceil((params->frac>1) ? params->frac : params->nvols*params->frac ); if( params->verb ) INFO_message("frac %g over %d volumes gives min count %d\n", params->frac, params->nvols, limit); if( limit <= 0 ) limit = 1; /* if not counting, result is binary 0/1 */ if( limit_to_frac(countset, limit, params->count, params->verb) ) RETURN(1); /* maybe apply dilations to output */ if( params->RESD.num > 0 ) { countset = apply_dilations(countset, ¶ms->RESD, 0, params->verb); if( !countset ) RETURN(1); } /* maybe fill any remaining holes */ if( params->fill ) if ( fill_holes(countset, params->verb) ) RETURN(1); /* create output */ if( write_result(params, countset, argc, argv) ) RETURN(1); /* clean up a little memory */ DSET_delete(countset); free(params->dsets); RETURN(0); }
int main( int argc , char *argv[] ) { line_opt opt ; /* holds data constructed from command line */ THD_3dim_dataset * new_dset; /* functional data set to be calculated */ Boolean ok; /* true if 3d write is successful */ /*----- Identify software -----*/ #if 0 printf ("\n\n"); printf ("Program: %s \n", PROGRAM_NAME); printf ("Author: %s \n", PROGRAM_AUTHOR); printf ("Initial Release: %s \n", PROGRAM_INITIAL); printf ("Latest Revision: %s \n", PROGRAM_LATEST); printf ("\n"); #endif PRINT_VERSION("3dfim") ; AUTHOR(PROGRAM_AUTHOR) ; mainENTRY("3dfim main") ; machdep() ; /*-- 20 Apr 2001: addto the arglist, if user wants to [RWCox] --*/ { int new_argc ; char ** new_argv ; addto_args( argc , argv , &new_argc , &new_argv ) ; if( new_argv != NULL ){ argc = new_argc ; argv = new_argv ; } } /* --- read command line --- */ get_line_opt( argc , argv , &opt ) ; /* --- calculate functional image --- */ new_dset = fim3d_fimmer_compute (opt.dset, opt.idts, opt.ortts, opt.first_im, opt.prefix_name, opt.max_percent); /* 19 May 1997 */ /*----- Record history of dataset -----*/ tross_Copy_History( opt.dset , new_dset ) ; tross_Make_History( PROGRAM_NAME , argc , argv , new_dset ) ; /* --- write 3d functional image data --- */ ok = THD_write_3dim_dataset ("", opt.prefix_name, new_dset, TRUE); if (!ok) Syntax ("Failure to write functional data set."); /* --- cleanup --- */ THD_delete_3dim_dataset (new_dset, FALSE); return (0); }
int main( int argc , char *argv[] ) { int ndset=0 , ii ; THD_3dim_dataset **dset ; if( argc < 3 || strcasecmp(argv[1],"-help") == 0 ){ printf( "** Program 3dConformist reads in a collection of datasets and\n" " zero pads them to the same size.\n" "** The output volume size is the smallest region that includes\n" " all datasets (i.e., the minimal covering box).\n" "** If the datasets cannot be processed (e.g., different grid\n" " spacings), then nothing will happen except for error messages.\n" "** The purpose of this program is to be used in scripts that\n" " process lots of datasets and needs to make them all conform\n" " to the same size for collective voxel-wise analyses.\n" "** The input datasets ARE ALTERED (embiggened)! <<<<<<------******\n" " Therefore, don't use this program casually.\n" ) ; exit(0) ; } mainENTRY("3dConformist") ; machdep() ; PRINT_VERSION("3dConformist") ; ndset = argc-1 ; dset = (THD_3dim_dataset **)malloc(sizeof(THD_3dim_dataset *)*ndset) ; for( ii=0 ; ii < ndset ; ii++ ){ dset[ii] = THD_open_dataset(argv[ii+1]) ; CHECK_OPEN_ERROR(dset[ii],argv[ii+1]) ; } ii = THD_conformist(ndset,dset,CONFORM_REWRITE,NULL) ; switch(ii){ default: INFO_message ("3dConformist: Re-wrote %d datasets",ii) ; break ; case 0: INFO_message ("3dConformist: all datasets matched OK") ; break ; case -1: ERROR_message("3dConformist: bad input") ; break ; case -2: ERROR_message("3dConformist: bad inputs") ; break ; case -3: ERROR_message("3dConformist: can't match grids") ; break ; } exit(0) ; }
int main( int argc , char * argv[] ) { THD_3dim_dataset * new_dset = NULL; /* output bucket dataset */ /*----- Identify software -----*/ #if 0 printf ("\n\n"); printf ("Program: %s \n", PROGRAM_NAME); printf ("Author: %s \n", PROGRAM_AUTHOR); printf ("Initial Release: %s \n", PROGRAM_INITIAL); printf ("Latest Revision: %s \n", PROGRAM_LATEST); printf ("\n"); #endif PRINT_VERSION("3dFDR") ; AUTHOR(PROGRAM_AUTHOR); mainENTRY("3dFDR main") ; machdep() ; /*----- Initialize program: get all operator inputs; create mask for voxels above mask threshold -----*/ initialize_program (argc, argv); if (FDR_input1D_filename != NULL) { /*----- Process list of p-values -----*/ process_1ddata (); } else { /*----- Process 3d dataset -----*/ new_dset = process_dataset (); /*----- Output the results as a bucket dataset -----*/ output_results (new_dset); } exit(0) ; }
int main( int argc , char *argv[] ) { THD_3dim_dataset *inset=NULL , *outset=NULL ; MCW_cluster *nbhd=NULL ; byte *mask=NULL ; int mask_nx,mask_ny,mask_nz , automask=0 ; char *prefix="./LocalCormat" ; int iarg=1 , verb=1 , ntype=0 , kk,nx,ny,nz,nxy,nxyz,nt , xx,yy,zz, vstep ; float na,nb,nc , dx,dy,dz ; MRI_IMARR *imar=NULL ; MRI_IMAGE *pim=NULL ; int mmlag=10 , ii,jj , do_arma=0 , nvout ; MRI_IMAGE *concim=NULL ; float *concar=NULL ; if( argc < 2 || strcmp(argv[1],"-help") == 0 ){ printf( "Usage: 3dLocalCORMAT [options] inputdataset\n" "\n" "Compute the correlation matrix (in time) of the input dataset,\n" "up to lag given by -maxlag. The matrix is averaged over the\n" "neighborhood specified by the -nbhd option, and then the entries\n" "are output at each voxel in a new dataset.\n" "\n" "Normally, the input to this program would be the -errts output\n" "from 3dDeconvolve, or the equivalent residuals from some other\n" "analysis. If you input a non-residual time series file, you at\n" "least should use an appropriate -polort level for detrending!\n" "\n" "Options:\n" " -input inputdataset\n" " -prefix ppp\n" " -mask mset {these 2 options are}\n" " -automask {mutually exclusive.}\n" " -nbhd nnn [e.g., 'SPHERE(9)' for 9 mm radius]\n" " -polort ppp [default = 0, which is reasonable for -errts output]\n" " -concat ccc [as in 3dDeconvolve]\n" " -maxlag mmm [default = 10]\n" " -ARMA [estimate ARMA(1,1) parameters into last 2 sub-bricks]\n" "\n" "A quick hack for my own benignant purposes -- RWCox -- June 2008\n" ) ; PRINT_COMPILE_DATE ; exit(0) ; } /*---- official startup ---*/ PRINT_VERSION("3dLocalCormat"); mainENTRY("3dLocalCormat main"); machdep(); AFNI_logger("3dLocalCormat",argc,argv); AUTHOR("Zhark the Toeplitzer"); /*---- loop over options ----*/ while( iarg < argc && argv[iarg][0] == '-' ){ #if 0 fprintf(stderr,"argv[%d] = %s\n",iarg,argv[iarg]) ; #endif if( strcmp(argv[iarg],"-ARMA") == 0 ){ do_arma = 1 ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-polort") == 0 ){ char *cpt ; if( ++iarg >= argc ) ERROR_exit("Need argument after option %s",argv[iarg-1]) ; pport = (int)strtod(argv[iarg],&cpt) ; if( *cpt != '\0' ) WARNING_message("Illegal non-numeric value after -polort") ; if( pport > 3 ){ pport = 3 ; WARNING_message("-polort set to 3 == max implemented") ; } else if( pport < 0 ){ pport = 0 ; WARNING_message("-polort set to 0 == min implemented") ; } iarg++ ; continue ; } if( strcmp(argv[iarg],"-input") == 0 ){ if( inset != NULL ) ERROR_exit("Can't have two -input options") ; if( ++iarg >= argc ) ERROR_exit("Need argument after '-input'") ; inset = THD_open_dataset( argv[iarg] ) ; CHECK_OPEN_ERROR(inset,argv[iarg]) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-prefix") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '-prefix'") ; prefix = strdup(argv[iarg]) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-mask") == 0 ){ THD_3dim_dataset *mset ; int mmm ; if( ++iarg >= argc ) ERROR_exit("Need argument after '-mask'") ; if( mask != NULL || automask ) ERROR_exit("Can't have two mask inputs") ; mset = THD_open_dataset( argv[iarg] ) ; CHECK_OPEN_ERROR(mset,argv[iarg]) ; DSET_load(mset) ; CHECK_LOAD_ERROR(mset) ; mask_nx = DSET_NX(mset); mask_ny = DSET_NY(mset); mask_nz = DSET_NZ(mset); mask = THD_makemask( mset , 0 , 0.5f, 0.0f ) ; DSET_delete(mset) ; if( mask == NULL ) ERROR_exit("Can't make mask from dataset '%s'",argv[iarg]) ; mmm = THD_countmask( mask_nx*mask_ny*mask_nz , mask ) ; INFO_message("Number of voxels in mask = %d",mmm) ; if( mmm < 2 ) ERROR_exit("Mask is too small to process") ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-automask") == 0 ){ if( mask != NULL ) ERROR_exit("Can't have -automask and -mask") ; automask = 1 ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-nbhd") == 0 ){ char *cpt ; if( ntype > 0 ) ERROR_exit("Can't have 2 '-nbhd' options") ; if( ++iarg >= argc ) ERROR_exit("Need argument after '-nbhd'") ; cpt = argv[iarg] ; if( strncasecmp(cpt,"SPHERE",6) == 0 ){ sscanf( cpt+7 , "%f" , &na ) ; if( na == 0.0f ) ERROR_exit("Can't have a SPHERE of radius 0") ; ntype = NTYPE_SPHERE ; } else if( strncasecmp(cpt,"RECT",4) == 0 ){ sscanf( cpt+5 , "%f,%f,%f" , &na,&nb,&nc ) ; if( na == 0.0f && nb == 0.0f && nc == 0.0f ) ERROR_exit("'RECT(0,0,0)' is not a legal neighborhood") ; ntype = NTYPE_RECT ; } else if( strncasecmp(cpt,"RHDD",4) == 0 ){ sscanf( cpt+5 , "%f" , &na ) ; if( na == 0.0f ) ERROR_exit("Can't have a RHDD of radius 0") ; ntype = NTYPE_RHDD ; } else { ERROR_exit("Unknown -nbhd shape: '%s'",cpt) ; } iarg++ ; continue ; } if( strcmp(argv[iarg],"-maxlag") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after option %s",argv[iarg-1]) ; mmlag = (int)strtod(argv[iarg],NULL) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-concat") == 0 ){ if( concim != NULL ) ERROR_exit("Can't have two %s options!",argv[iarg]) ; if( ++iarg >= argc ) ERROR_exit("Need argument after option %s",argv[iarg-1]) ; concim = mri_read_1D( argv[iarg] ) ; if( concim == NULL ) ERROR_exit("Can't read -concat file '%s'",argv[iarg]) ; if( concim->nx < 2 ) ERROR_exit("-concat file '%s' must have at least 2 entries!", argv[iarg]) ; concar = MRI_FLOAT_PTR(concim) ; for( ii=1 ; ii < concim->nx ; ii++ ) if( (int)concar[ii-1] >= (int)concar[ii] ) ERROR_exit("-concat file '%s' is not ordered increasingly!", argv[iarg]) ; iarg++ ; continue ; } ERROR_exit("Unknown option '%s'",argv[iarg]) ; } /*--- end of loop over options ---*/ if( do_arma && mmlag > 0 && mmlag < 5 ) ERROR_exit("Can't do -ARMA with -maxlag %d",mmlag) ; /*---- deal with input dataset ----*/ if( inset == NULL ){ if( iarg >= argc ) ERROR_exit("No input dataset on command line?") ; inset = THD_open_dataset( argv[iarg] ) ; CHECK_OPEN_ERROR(inset,argv[iarg]) ; } ntime = DSET_NVALS(inset) ; if( ntime < 9 ) ERROR_exit("Must have at least 9 values per voxel") ; DSET_load(inset) ; CHECK_LOAD_ERROR(inset) ; if( mask != NULL ){ if( mask_nx != DSET_NX(inset) || mask_ny != DSET_NY(inset) || mask_nz != DSET_NZ(inset) ) ERROR_exit("-mask dataset grid doesn't match input dataset") ; } else if( automask ){ int mmm ; mask = THD_automask( inset ) ; if( mask == NULL ) ERROR_message("Can't create -automask from input dataset?") ; mmm = THD_countmask( DSET_NVOX(inset) , mask ) ; INFO_message("Number of voxels in automask = %d",mmm) ; if( mmm < 2 ) ERROR_exit("Automask is too small to process") ; } /*-- set up blocks of continuous time data --*/ if( DSET_IS_TCAT(inset) ){ if( concim != NULL ){ WARNING_message("Ignoring -concat, since dataset is auto-catenated") ; mri_free(concim) ; } concim = mri_new(inset->tcat_num,1,MRI_float) ; concar = MRI_FLOAT_PTR(concim) ; concar[0] = 0.0 ; for( ii=0 ; ii < inset->tcat_num-1 ; ii++ ) concar[ii+1] = concar[ii] + inset->tcat_len[ii] ; } else if( concim == NULL ){ concim = mri_new(1,1,MRI_float) ; concar = MRI_FLOAT_PTR(concim) ; concar[0] = 0 ; } nbk = concim->nx ; bk = (int *)malloc(sizeof(int)*(nbk+1)) ; for( ii=0 ; ii < nbk ; ii++ ) bk[ii] = (int)concar[ii] ; bk[nbk] = ntime ; mri_free(concim) ; mlag = DSET_NVALS(inset) ; for( ii=0 ; ii < nbk ; ii++ ){ jj = bk[ii+1]-bk[ii] ; if( jj < mlag ) mlag = jj ; if( bk[ii] < 0 || jj < 9 ) ERROR_exit("something is rotten in the dataset run lengths") ; } mlag-- ; if( mmlag > 0 && mlag > mmlag ) mlag = mmlag ; else INFO_message("Max lag set to %d",mlag) ; if( do_arma && mlag < 5 ) ERROR_exit("Can't do -ARMA with maxlag=%d",mlag) ; /*---- create neighborhood (as a cluster) -----*/ if( ntype <= 0 ){ /* default neighborhood */ ntype = NTYPE_SPHERE ; na = -1.01f ; INFO_message("Using default neighborhood = self + 6 neighbors") ; } switch( ntype ){ default: ERROR_exit("WTF? ntype=%d",ntype) ; case NTYPE_SPHERE:{ if( na < 0.0f ){ dx = dy = dz = 1.0f ; na = -na ; } else { dx = fabsf(DSET_DX(inset)) ; dy = fabsf(DSET_DY(inset)) ; dz = fabsf(DSET_DZ(inset)) ; } nbhd = MCW_spheremask( dx,dy,dz , na ) ; } break ; case NTYPE_RECT:{ if( na < 0.0f ){ dx = 1.0f; na = -na; } else dx = fabsf(DSET_DX(inset)); if( nb < 0.0f ){ dy = 1.0f; nb = -nb; } else dy = fabsf(DSET_DY(inset)); if( nc < 0.0f ){ dz = 1.0f; nc = -nc; } else dz = fabsf(DSET_DZ(inset)); nbhd = MCW_rectmask( dx,dy,dz , na,nb,nc ) ; } break ; case NTYPE_RHDD:{ if( na < 0.0f ){ dx = dy = dz = 1.0f ; na = -na ; } else { dx = fabsf(DSET_DX(inset)) ; dy = fabsf(DSET_DY(inset)) ; dz = fabsf(DSET_DZ(inset)) ; } nbhd = MCW_rhddmask( dx,dy,dz , na ) ; } break ; } MCW_radsort_cluster( nbhd , dx,dy,dz ) ; /* 26 Feb 2008 */ INFO_message("Neighborhood comprises %d voxels",nbhd->num_pt) ; /** create output dataset **/ outset = EDIT_empty_copy(inset) ; nvout = mlag ; if( do_arma ) nvout += 2 ; EDIT_dset_items( outset, ADN_prefix , prefix, ADN_brick_fac, NULL , ADN_nvals , nvout , ADN_ntt , nvout , ADN_none ); tross_Copy_History( inset , outset ) ; tross_Make_History( "3dLocalCormat" , argc,argv , outset ) ; for( kk=0 ; kk < nvout ; kk++ ) EDIT_substitute_brick( outset , kk , MRI_float , NULL ) ; nx = DSET_NX(outset) ; ny = DSET_NY(outset) ; nxy = nx*ny ; nz = DSET_NZ(outset) ; nxyz = nxy*nz ; vstep = (verb && nxyz > 999) ? nxyz/50 : 0 ; if( vstep ) fprintf(stderr,"++ voxel loop: ") ; /** actually do the long long slog through all voxels **/ for( kk=0 ; kk < nxyz ; kk++ ){ if( vstep && kk%vstep==vstep-1 ) vstep_print() ; if( !INMASK(kk) ) continue ; IJK_TO_THREE( kk , xx,yy,zz , nx,nxy ) ; imar = THD_get_dset_nbhd_array( inset , mask , xx,yy,zz , nbhd ) ; if( imar == NULL ) continue ; pim = mri_cormat_vector(imar) ; DESTROY_IMARR(imar) ; if( pim == NULL ) continue ; THD_insert_series( kk, outset, pim->nx, MRI_float, MRI_FLOAT_PTR(pim), 0 ) ; if( do_arma ){ /* estimate ARMA(1,1) params and store those, too */ float_pair ab ; float *aa=DSET_ARRAY(outset,mlag), *bb=DSET_ARRAY(outset,mlag+1) ; ab = estimate_arma11( pim->nx , MRI_FLOAT_PTR(pim) ) ; aa[kk] = ab.a ; bb[kk] = ab.b ; } mri_free(pim) ; } if( vstep ) fprintf(stderr,"\n") ; DSET_delete(inset) ; DSET_write(outset) ; WROTE_DSET(outset) ; exit(0) ; }
int main( int argc , char *argv[] ) { THD_3dim_dataset *xset , *cset, *mset=NULL ; int nopt=1 , method=PEARSON , do_autoclip=0 ; int nvox , nvals , ii, jj, kout, kin, polort=1 ; int ix1,jy1,kz1, ix2, jy2, kz2 ; char *prefix = "degree_centrality" ; byte *mask=NULL; int nmask , abuc=1 ; int all_source=0; /* output all source voxels 25 Jun 2010 [rickr] */ char str[32] , *cpt ; int *imap = NULL ; MRI_vectim *xvectim ; float (*corfun)(int,float *,float*) = NULL ; /* djc - add 1d file output for similarity matrix */ FILE *fout1D=NULL; /* CC - we will have two subbricks: binary and weighted centrality */ int nsubbriks = 2; int subbrik = 0; float * bodset; float * wodset; int nb_ctr = 0; /* CC - added flags for thresholding correlations */ double thresh = 0.0; double othresh = 0.0; int dothresh = 0; double sparsity = 0.0; int dosparsity = 0; /* variables for calculating degree centrality */ long * binaryDC = NULL; double * weightedDC = NULL; /* variables for histogram */ hist_node_head* histogram=NULL; hist_node* hptr=NULL; hist_node* pptr=NULL; int bottom_node_idx = 0; int totNumCor = 0; long totPosCor = 0; int ngoal = 0; int nretain = 0; float binwidth = 0.0; int nhistnodes = 50; /*----*/ AFNI_SETUP_OMP(0) ; /* 24 Jun 2013 */ if( argc < 2 || strcmp(argv[1],"-help") == 0 ){ printf( "Usage: 3dDegreeCentrality [options] dset\n" " Computes voxelwise weighted and binary degree centrality and\n" " stores the result in a new 3D bucket dataset as floats to\n" " preserve their values. Degree centrality reflects the strength and\n" " extent of the correlation of a voxel with every other voxel in\n" " the brain.\n\n" " Conceptually the process involves: \n" " 1. Calculating the correlation between voxel time series for\n" " every pair of voxels in the brain (as determined by masking)\n" " 2. Applying a threshold to the resulting correlations to exclude\n" " those that might have arisen by chance, or to sparsify the\n" " connectivity graph.\n" " 3. At each voxel, summarizing its correlation with other voxels\n" " in the brain, by either counting the number of voxels correlated\n" " with the seed voxel (binary) or by summing the correlation \n" " coefficients (weighted).\n" " Practically the algorithm is ordered differently to optimize for\n" " computational time and memory usage.\n\n" " The threshold can be supplied as a correlation coefficient, \n" " or a sparsity threshold. The sparsity threshold reflects the fraction\n" " of connections that should be retained after the threshold has been\n" " applied. To minimize resource consumption, using a sparsity threshold\n" " involves a two-step procedure. In the first step, a correlation\n" " coefficient threshold is applied to substantially reduce the number\n" " of correlations. Next, the remaining correlations are sorted and a\n" " threshold is calculated so that only the specified fraction of \n" " possible correlations are above threshold. Due to ties between\n" " correlations, the fraction of correlations that pass the sparsity\n" " threshold might be slightly more than the number specified.\n\n" " Regardless of the thresholding procedure employed, negative \n" " correlations are excluded from the calculations.\n" "\n" "Options:\n" " -pearson = Correlation is the normal Pearson (product moment)\n" " correlation coefficient [default].\n" #if 0 " -spearman = Correlation is the Spearman (rank) correlation\n" " coefficient.\n" " -quadrant = Correlation is the quadrant correlation coefficient.\n" #else " -spearman AND -quadrant are disabled at this time :-(\n" #endif "\n" " -thresh r = exclude correlations <= r from calculations\n" " -sparsity s = only use top s percent of correlations in calculations\n" " s should be an integer between 0 and 100. Uses an\n" " an adaptive thresholding procedure to reduce memory.\n" " The speed of determining the adaptive threshold can\n" " be improved by specifying an initial threshold with\n" " the -thresh flag.\n" "\n" " -polort m = Remove polynomical trend of order 'm', for m=-1..3.\n" " [default is m=1; removal is by least squares].\n" " Using m=-1 means no detrending; this is only useful\n" " for data/information that has been pre-processed.\n" "\n" " -autoclip = Clip off low-intensity regions in the dataset,\n" " -automask = so that the correlation is only computed between\n" " high-intensity (presumably brain) voxels. The\n" " mask is determined the same way that 3dAutomask works.\n" "\n" " -mask mmm = Mask to define 'in-brain' voxels. Reducing the number\n" " the number of voxels included in the calculation will\n" " significantly speedup the calculation. Consider using\n" " a mask to constrain the calculations to the grey matter\n" " rather than the whole brain. This is also preferrable\n" " to using -autoclip or -automask.\n" "\n" " -prefix p = Save output into dataset with prefix 'p', this file will\n" " contain bricks for both 'weighted' or 'degree' centrality\n" " [default prefix is 'deg_centrality'].\n" "\n" " -out1D f = Save information about the above threshold correlations to\n" " 1D file 'f'. Each row of this file will contain:\n" " Voxel1 Voxel2 i1 j1 k1 i2 j2 k2 Corr\n" " Where voxel1 and voxel2 are the 1D indices of the pair of\n" " voxels, i j k correspond to their 3D coordinates, and Corr\n" " is the value of the correlation between the voxel time courses.\n" "\n" "Notes:\n" " * The output dataset is a bucket type of floats.\n" " * The program prints out an estimate of its memory used\n" " when it ends. It also prints out a progress 'meter'\n" " to keep you pacified.\n" "\n" "-- RWCox - 31 Jan 2002 and 16 Jul 2010\n" "-- Cameron Craddock - 26 Sept 2015 \n" ) ; PRINT_AFNI_OMP_USAGE("3dDegreeCentrality",NULL) ; PRINT_COMPILE_DATE ; exit(0) ; } mainENTRY("3dDegreeCentrality main"); machdep(); PRINT_VERSION("3dDegreeCentrality"); AFNI_logger("3dDegreeCentrality",argc,argv); /*-- option processing --*/ while( nopt < argc && argv[nopt][0] == '-' ){ if( strcmp(argv[nopt],"-time") == 0 ){ abuc = 0 ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-autoclip") == 0 || strcmp(argv[nopt],"-automask") == 0 ){ do_autoclip = 1 ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-mask") == 0 ){ mset = THD_open_dataset(argv[++nopt]); CHECK_OPEN_ERROR(mset,argv[nopt]); nopt++ ; continue ; } if( strcmp(argv[nopt],"-pearson") == 0 ){ method = PEARSON ; nopt++ ; continue ; } #if 0 if( strcmp(argv[nopt],"-spearman") == 0 ){ method = SPEARMAN ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-quadrant") == 0 ){ method = QUADRANT ; nopt++ ; continue ; } #endif if( strcmp(argv[nopt],"-eta2") == 0 ){ method = ETA2 ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-prefix") == 0 ){ prefix = strdup(argv[++nopt]) ; if( !THD_filename_ok(prefix) ){ ERROR_exit("Illegal value after -prefix!") ; } nopt++ ; continue ; } if( strcmp(argv[nopt],"-thresh") == 0 ){ double val = (double)strtod(argv[++nopt],&cpt) ; if( *cpt != '\0' || val >= 1.0 || val < 0.0 ){ ERROR_exit("Illegal value (%f) after -thresh!", val) ; } dothresh = 1; thresh = val ; othresh = val ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-sparsity") == 0 ){ double val = (double)strtod(argv[++nopt],&cpt) ; if( *cpt != '\0' || val > 100 || val <= 0 ){ ERROR_exit("Illegal value (%f) after -sparsity!", val) ; } if( val > 5.0 ) { WARNING_message("Sparsity %3.2f%% is large and will require alot of memory and time, consider using a smaller value. ", val); } dosparsity = 1 ; sparsity = val ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-polort") == 0 ){ int val = (int)strtod(argv[++nopt],&cpt) ; if( *cpt != '\0' || val < -1 || val > 3 ){ ERROR_exit("Illegal value after -polort!") ; } polort = val ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-mem_stat") == 0 ){ MEM_STAT = 1 ; nopt++ ; continue ; } if( strncmp(argv[nopt],"-mem_profile",8) == 0 ){ MEM_PROF = 1 ; nopt++ ; continue ; } /* check for 1d argument */ if ( strcmp(argv[nopt],"-out1D") == 0 ){ if (!(fout1D = fopen(argv[++nopt], "w"))) { ERROR_message("Failed to open %s for writing", argv[nopt]); exit(1); } nopt++ ; continue ; } ERROR_exit("Illegal option: %s",argv[nopt]) ; } /*-- open dataset, check for legality --*/ if( nopt >= argc ) ERROR_exit("Need a dataset on command line!?") ; xset = THD_open_dataset(argv[nopt]); CHECK_OPEN_ERROR(xset,argv[nopt]); if( DSET_NVALS(xset) < 3 ) ERROR_exit("Input dataset %s does not have 3 or more sub-bricks!",argv[nopt]) ; DSET_load(xset) ; CHECK_LOAD_ERROR(xset) ; /*-- compute mask array, if desired --*/ nvox = DSET_NVOX(xset) ; nvals = DSET_NVALS(xset) ; INC_MEM_STATS((nvox * nvals * sizeof(double)), "input dset"); PRINT_MEM_STATS("inset"); /* if a mask was specified make sure it is appropriate */ if( mset ){ if( DSET_NVOX(mset) != nvox ) ERROR_exit("Input and mask dataset differ in number of voxels!") ; mask = THD_makemask(mset, 0, 1.0, 0.0) ; /* update running memory statistics to reflect loading the image */ INC_MEM_STATS( mset->dblk->total_bytes, "mask dset" ); PRINT_MEM_STATS( "mset load" ); nmask = THD_countmask( nvox , mask ) ; INC_MEM_STATS( nmask * sizeof(byte), "mask array" ); PRINT_MEM_STATS( "mask" ); INFO_message("%d voxels in -mask dataset",nmask) ; if( nmask < 2 ) ERROR_exit("Only %d voxels in -mask, exiting...",nmask); /* update running memory statistics to reflect loading the image */ DEC_MEM_STATS( mset->dblk->total_bytes, "mask dset" ); DSET_unload(mset) ; PRINT_MEM_STATS( "mset unload" ); } /* if automasking is requested, handle that now */ else if( do_autoclip ){ mask = THD_automask( xset ) ; nmask = THD_countmask( nvox , mask ) ; INFO_message("%d voxels survive -autoclip",nmask) ; if( nmask < 2 ) ERROR_exit("Only %d voxels in -automask!",nmask); } /* otherwise we use all of the voxels in the image */ else { nmask = nvox ; INFO_message("computing for all %d voxels",nmask) ; } if( method == ETA2 && polort >= 0 ) WARNING_message("Polort for -eta2 should probably be -1..."); /* djc - 1d file out init */ if (fout1D != NULL) { /* define affine matrix */ mat44 affine_mat = xset->daxes->ijk_to_dicom; /* print command line statement */ fprintf(fout1D,"#Similarity matrix from command:\n#"); for(ii=0; ii<argc; ++ii) fprintf(fout1D,"%s ", argv[ii]); /* Print affine matrix */ fprintf(fout1D,"\n"); fprintf(fout1D,"#[ "); int mi, mj; for(mi = 0; mi < 4; mi++) { for(mj = 0; mj < 4; mj++) { fprintf(fout1D, "%.6f ", affine_mat.m[mi][mj]); } } fprintf(fout1D, "]\n"); /* Print image extents*/ THD_dataxes *xset_daxes = xset->daxes; fprintf(fout1D, "#Image dimensions:\n"); fprintf(fout1D, "#[%d, %d, %d]\n", xset_daxes->nxx, xset_daxes->nyy, xset_daxes->nzz); /* Similarity matrix headers */ fprintf(fout1D,"#Voxel1 Voxel2 i1 j1 k1 i2 j2 k2 Corr\n"); } /* CC calculate the total number of possible correlations, will be usefule down the road */ totPosCor = (.5*((float)nmask))*((float)(nmask-1)); /** For the case of Pearson correlation, we make sure the **/ /** data time series have their mean removed (polort >= 0) **/ /** and are normalized, so that correlation = dot product, **/ /** and we can use function zm_THD_pearson_corr for speed. **/ switch( method ){ default: case PEARSON: corfun = zm_THD_pearson_corr ; break ; case ETA2: corfun = my_THD_eta_squared ; break ; } /*-- create vectim from input dataset --*/ INFO_message("vectim-izing input dataset") ; /*-- CC added in mask to reduce the size of xvectim -- */ xvectim = THD_dset_to_vectim( xset , mask , 0 ) ; if( xvectim == NULL ) ERROR_exit("Can't create vectim?!") ; /*-- CC update our memory stats to reflect vectim -- */ INC_MEM_STATS((xvectim->nvec*sizeof(int)) + ((xvectim->nvec)*(xvectim->nvals))*sizeof(float) + sizeof(MRI_vectim), "vectim"); PRINT_MEM_STATS( "vectim" ); /*--- CC the vectim contains a mapping between voxel index and mask index, tap into that here to avoid duplicating memory usage ---*/ if( mask != NULL ) { imap = xvectim->ivec; /* --- CC free the mask */ DEC_MEM_STATS( nmask*sizeof(byte), "mask array" ); free(mask); mask=NULL; PRINT_MEM_STATS( "mask unload" ); } /* -- CC unloading the dataset to reduce memory usage ?? -- */ DEC_MEM_STATS((DSET_NVOX(xset) * DSET_NVALS(xset) * sizeof(double)), "input dset"); DSET_unload(xset) ; PRINT_MEM_STATS("inset unload"); /* -- CC configure detrending --*/ if( polort < 0 && method == PEARSON ){ polort = 0; WARNING_message("Pearson correlation always uses polort >= 0"); } if( polort >= 0 ){ for( ii=0 ; ii < xvectim->nvec ; ii++ ){ /* remove polynomial trend */ DETREND_polort(polort,nvals,VECTIM_PTR(xvectim,ii)) ; } } /* -- this procedure does not change time series that have zero variance -- */ if( method == PEARSON ) THD_vectim_normalize(xvectim) ; /* L2 norm = 1 */ /* -- CC create arrays to hold degree and weighted centrality while they are being calculated -- */ if( dosparsity == 0 ) { if( ( binaryDC = (long*)calloc( nmask, sizeof(long) )) == NULL ) { ERROR_message( "Could not allocate %d byte array for binary DC calculation\n", nmask*sizeof(long)); } /* -- update running memory estimate to reflect memory allocation */ INC_MEM_STATS( nmask*sizeof(long), "binary DC array" ); PRINT_MEM_STATS( "binaryDC" ); if( ( weightedDC = (double*)calloc( nmask, sizeof(double) )) == NULL ) { if (binaryDC){ free(binaryDC); binaryDC = NULL; } ERROR_message( "Could not allocate %d byte array for weighted DC calculation\n", nmask*sizeof(double)); } /* -- update running memory estimate to reflect memory allocation */ INC_MEM_STATS( nmask*sizeof(double), "weighted DC array" ); PRINT_MEM_STATS( "weightedDC" ); } /* -- CC if we are using a sparsity threshold, build a histogram to calculate the threshold */ if (dosparsity == 1) { /* make sure that there is a bin for correlation values that == 1.0 */ binwidth = (1.005-thresh)/nhistnodes; /* calculate the number of correlations we wish to retain */ ngoal = nretain = (int)(((double)totPosCor)*((double)sparsity) / 100.0); /* allocate memory for the histogram bins */ if(( histogram = (hist_node_head*)malloc(nhistnodes*sizeof(hist_node_head))) == NULL ) { /* if the allocation fails, free all memory and exit */ if (binaryDC){ free(binaryDC); binaryDC = NULL; } if (weightedDC){ free(weightedDC); weightedDC = NULL; } ERROR_message( "Could not allocate %d byte array for histogram\n", nhistnodes*sizeof(hist_node_head)); } else { /* -- update running memory estimate to reflect memory allocation */ INC_MEM_STATS( nhistnodes*sizeof(hist_node_head), "hist bins" ); PRINT_MEM_STATS( "hist1" ); } /* initialize history bins */ for( kout = 0; kout < nhistnodes; kout++ ) { histogram[ kout ].bin_low = thresh+kout*binwidth; histogram[ kout ].bin_high = histogram[ kout ].bin_low+binwidth; histogram[ kout ].nbin = 0; histogram[ kout ].nodes = NULL; /*INFO_message("Hist bin %d [%3.3f, %3.3f) [%d, %p]\n", kout, histogram[ kout ].bin_low, histogram[ kout ].bin_high, histogram[ kout ].nbin, histogram[ kout ].nodes );*/ } } /*-- tell the user what we are about to do --*/ if (dosparsity == 0 ) { INFO_message( "Calculating degree centrality with threshold = %f.\n", thresh); } else { INFO_message( "Calculating degree centrality with threshold = %f and sparsity = %3.2f%% (%d)\n", thresh, sparsity, nretain); } /*---------- loop over mask voxels, correlate ----------*/ AFNI_OMP_START ; #pragma omp parallel if( nmask > 999 ) { int lii,ljj,lin,lout,ithr,nthr,vstep,vii ; float *xsar , *ysar ; hist_node* new_node = NULL ; hist_node* tptr = NULL ; hist_node* rptr = NULL ; int new_node_idx = 0; double car = 0.0 ; /*-- get information about who we are --*/ #ifdef USE_OMP ithr = omp_get_thread_num() ; nthr = omp_get_num_threads() ; if( ithr == 0 ) INFO_message("%d OpenMP threads started",nthr) ; #else ithr = 0 ; nthr = 1 ; #endif /*-- For the progress tracker, we want to print out 50 numbers, figure out a number of loop iterations that will make this easy */ vstep = (int)( nmask / (nthr*50.0f) + 0.901f ) ; vii = 0 ; if((MEM_STAT==0) && (ithr == 0 )) fprintf(stderr,"Looping:") ; #pragma omp for schedule(static, 1) for( lout=0 ; lout < xvectim->nvec ; lout++ ){ /*----- outer voxel loop -----*/ if( ithr == 0 && vstep > 2 ) /* allow small dsets 16 Jun 2011 [rickr] */ { vii++ ; if( vii%vstep == vstep/2 && MEM_STAT == 0 ) vstep_print(); } /* get ref time series from this voxel */ xsar = VECTIM_PTR(xvectim,lout) ; /* try to make calculation more efficient by only calculating the unique correlations */ for( lin=(lout+1) ; lin < xvectim->nvec ; lin++ ){ /*----- inner loop over voxels -----*/ /* extract the voxel time series */ ysar = VECTIM_PTR(xvectim,lin) ; /* now correlate the time series */ car = (double)(corfun(nvals,xsar,ysar)) ; if ( car <= thresh ) { continue ; } /* update degree centrality values, hopefully the pragma will handle mutual exclusion */ #pragma omp critical(dataupdate) { /* if the correlation is less than threshold, ignore it */ if ( car > thresh ) { totNumCor += 1; if ( dosparsity == 0 ) { binaryDC[lout] += 1; binaryDC[lin] += 1; weightedDC[lout] += car; weightedDC[lin] += car; /* print correlation out to the 1D file */ if ( fout1D != NULL ) { /* determine the i,j,k coords */ ix1 = DSET_index_to_ix(xset,lii) ; jy1 = DSET_index_to_jy(xset,lii) ; kz1 = DSET_index_to_kz(xset,lii) ; ix2 = DSET_index_to_ix(xset,ljj) ; jy2 = DSET_index_to_jy(xset,ljj) ; kz2 = DSET_index_to_kz(xset,ljj) ; /* add source, dest, correlation to 1D file */ fprintf(fout1D, "%d %d %d %d %d %d %d %d %.6f\n", lii, ljj, ix1, jy1, kz1, ix2, jy2, kz2, car); } } else { /* determine the index in the histogram to add the node */ new_node_idx = (int)floor((double)(car-othresh)/(double)binwidth); if ((new_node_idx > nhistnodes) || (new_node_idx < bottom_node_idx)) { /* this error should indicate a programming error and should not happen */ WARNING_message("Node index %d is out of range [%d,%d)!",new_node_idx, bottom_node_idx, nhistnodes); } else { /* create a node to add to the histogram */ new_node = (hist_node*)calloc(1,sizeof(hist_node)); if( new_node == NULL ) { /* allocate memory for this node, rather than fiddling with error handling here, lets just move on */ WARNING_message("Could not allocate a new node!"); } else { /* populate histogram node */ new_node->i = lout; new_node->j = lin; new_node->corr = car; new_node->next = NULL; /* -- update running memory estimate to reflect memory allocation */ INC_MEM_STATS( sizeof(hist_node), "hist nodes" ); if ((totNumCor % (1024*1024)) == 0) PRINT_MEM_STATS( "hist nodes" ); /* populate histogram */ new_node->next = histogram[new_node_idx].nodes; histogram[new_node_idx].nodes = new_node; histogram[new_node_idx].nbin++; /* see if there are enough correlations in the histogram for the sparsity */ if ((totNumCor - histogram[bottom_node_idx].nbin) > nretain) { /* delete the list of nodes */ rptr = histogram[bottom_node_idx].nodes; while(rptr != NULL) { tptr = rptr; rptr = rptr->next; /* check that the ptr is not null before freeing it*/ if(tptr!= NULL) { DEC_MEM_STATS( sizeof(hist_node), "hist nodes" ); free(tptr); } } PRINT_MEM_STATS( "unloaded hist nodes - thresh increase" ); histogram[bottom_node_idx].nodes = NULL; totNumCor -= histogram[bottom_node_idx].nbin; histogram[bottom_node_idx].nbin=0; /* get the new threshold */ thresh = (double)histogram[++bottom_node_idx].bin_low; if(MEM_STAT == 1) INFO_message("Increasing threshold to %3.2f (%d)\n", thresh,bottom_node_idx); } } /* else, newptr != NULL */ } /* else, new_node_idx in range */ } /* else, do_sparsity == 1 */ } /* car > thresh */ } /* this is the end of the critical section */ } /* end of inner loop over voxels */ } /* end of outer loop over ref voxels */ if( ithr == 0 ) fprintf(stderr,".\n") ; } /* end OpenMP */ AFNI_OMP_END ; /* update the user so that they know what we are up to */ INFO_message ("AFNI_OMP finished\n"); INFO_message ("Found %d (%3.2f%%) correlations above threshold (%f)\n", totNumCor, 100.0*((float)totNumCor)/((float)totPosCor), thresh); /*---------- Finish up ---------*/ /*if( dosparsity == 1 ) { for( kout = 0; kout < nhistnodes; kout++ ) { INFO_message("Hist bin %d [%3.3f, %3.3f) [%d, %p]\n", kout, histogram[ kout ].bin_low, histogram[ kout ].bin_high, histogram[ kout ].nbin, histogram[ kout ].nodes ); } }*/ /*-- create output dataset --*/ cset = EDIT_empty_copy( xset ) ; /*-- configure the output dataset */ if( abuc ){ EDIT_dset_items( cset , ADN_prefix , prefix , ADN_nvals , nsubbriks , /* 2 subbricks, degree and weighted centrality */ ADN_ntt , 0 , /* no time axis */ ADN_type , HEAD_ANAT_TYPE , ADN_func_type , ANAT_BUCK_TYPE , ADN_datum_all , MRI_float , ADN_none ) ; } else { EDIT_dset_items( cset , ADN_prefix , prefix , ADN_nvals , nsubbriks , /* 2 subbricks, degree and weighted centrality */ ADN_ntt , nsubbriks , /* num times */ ADN_ttdel , 1.0 , /* fake TR */ ADN_nsl , 0 , /* no slice offsets */ ADN_type , HEAD_ANAT_TYPE , ADN_func_type , ANAT_EPI_TYPE , ADN_datum_all , MRI_float , ADN_none ) ; } /* add history information to the hearder */ tross_Make_History( "3dDegreeCentrality" , argc,argv , cset ) ; ININFO_message("creating output dataset in memory") ; /* -- Configure the subbriks: Binary Degree Centrality */ subbrik = 0; EDIT_BRICK_TO_NOSTAT(cset,subbrik) ; /* stat params */ /* CC this sets the subbrik scaling factor, which we will probably want to do again after we calculate the voxel values */ EDIT_BRICK_FACTOR(cset,subbrik,1.0) ; /* scale factor */ sprintf(str,"Binary Degree Centrality") ; EDIT_BRICK_LABEL(cset,subbrik,str) ; EDIT_substitute_brick(cset,subbrik,MRI_float,NULL) ; /* make array */ /* copy measure data into the subbrik */ bodset = DSET_ARRAY(cset,subbrik); /* -- Configure the subbriks: Weighted Degree Centrality */ subbrik = 1; EDIT_BRICK_TO_NOSTAT(cset,subbrik) ; /* stat params */ /* CC this sets the subbrik scaling factor, which we will probably want to do again after we calculate the voxel values */ EDIT_BRICK_FACTOR(cset,subbrik,1.0) ; /* scale factor */ sprintf(str,"Weighted Degree Centrality") ; EDIT_BRICK_LABEL(cset,subbrik,str) ; EDIT_substitute_brick(cset,subbrik,MRI_float,NULL) ; /* make array */ /* copy measure data into the subbrik */ wodset = DSET_ARRAY(cset,subbrik); /* increment memory stats */ INC_MEM_STATS( (DSET_NVOX(cset)*DSET_NVALS(cset)*sizeof(float)), "output dset"); PRINT_MEM_STATS( "outset" ); /* pull the values out of the histogram */ if( dosparsity == 0 ) { for( kout = 0; kout < nmask; kout++ ) { if ( imap != NULL ) { ii = imap[kout] ; /* ii= source voxel (we know that ii is in the mask) */ } else { ii = kout ; } if( ii >= DSET_NVOX(cset) ) { WARNING_message("Avoiding bodset, wodset overflow %d > %d (%s,%d)\n", ii,DSET_NVOX(cset),__FILE__,__LINE__ ); } else { bodset[ ii ] = (float)(binaryDC[kout]); wodset[ ii ] = (float)(weightedDC[kout]); } } /* we are done with this memory, and can kill it now*/ if(binaryDC) { free(binaryDC); binaryDC=NULL; /* -- update running memory estimate to reflect memory allocation */ DEC_MEM_STATS( nmask*sizeof(long), "binary DC array" ); PRINT_MEM_STATS( "binaryDC" ); } if(weightedDC) { free(weightedDC); weightedDC=NULL; /* -- update running memory estimate to reflect memory allocation */ DEC_MEM_STATS( nmask*sizeof(double), "weighted DC array" ); PRINT_MEM_STATS( "weightedDC" ); } } else { /* add in the values from the histogram, this is a two stage procedure: at first we add in values a whole bin at the time until we get to a point where we need to add in a partial bin, then we create a new histogram to sort the values in the bin and then add those bins at a time */ kout = nhistnodes - 1; while (( histogram[kout].nbin < nretain ) && ( kout >= 0 )) { hptr = pptr = histogram[kout].nodes; while( hptr != NULL ) { /* determine the indices corresponding to this node */ if ( imap != NULL ) { ii = imap[hptr->i] ; /* ii= source voxel (we know that ii is in the mask) */ } else { ii = hptr->i ; } if ( imap != NULL ) { jj = imap[hptr->j] ; /* ii= source voxel (we know that ii is in the mask) */ } else { jj = hptr->j ; } /* add in the values */ if(( ii >= DSET_NVOX(cset) ) || ( jj >= DSET_NVOX(cset))) { if( ii >= DSET_NVOX(cset)) { WARNING_message("Avoiding bodset, wodset overflow (ii) %d > %d\n (%s,%d)\n", ii,DSET_NVOX(cset),__FILE__,__LINE__ ); } if( jj >= DSET_NVOX(cset)) { WARNING_message("Avoiding bodset, wodset overflow (jj) %d > %d\n (%s,%d)\n", jj,DSET_NVOX(cset),__FILE__,__LINE__ ); } } else { bodset[ ii ] += 1.0 ; wodset[ ii ] += (float)(hptr->corr); bodset[ jj ] += 1.0 ; wodset[ jj ] += (float)(hptr->corr); } if( fout1D != NULL ) { /* add source, dest, correlation to 1D file */ ix1 = DSET_index_to_ix(cset,ii) ; jy1 = DSET_index_to_jy(cset,ii) ; kz1 = DSET_index_to_kz(cset,ii) ; ix2 = DSET_index_to_ix(cset,jj) ; jy2 = DSET_index_to_jy(cset,jj) ; kz2 = DSET_index_to_kz(cset,jj) ; fprintf(fout1D, "%d %d %d %d %d %d %d %d %.6f\n", ii, jj, ix1, jy1, kz1, ix2, jy2, kz2, (float)(hptr->corr)); } /* increment node pointers */ pptr = hptr; hptr = hptr->next; /* delete the node */ if(pptr) { /* -- update running memory estimate to reflect memory allocation */ DEC_MEM_STATS(sizeof( hist_node ), "hist nodes" ); /* free the mem */ free(pptr); pptr=NULL; } } /* decrement the number of correlations we wish to retain */ nretain -= histogram[kout].nbin; histogram[kout].nodes = NULL; /* go on to the next bin */ kout--; } PRINT_MEM_STATS( "hist1 bins free - inc into output" ); /* if we haven't used all of the correlations that are available, go through and add a subset of the voxels from the remaining bin */ if(( nretain > 0 ) && (kout >= 0)) { hist_node_head* histogram2 = NULL; hist_node_head* histogram2_save = NULL; int h2nbins = 100; float h2binwidth = 0.0; int h2ndx=0; h2binwidth = (((1.0+binwidth/((float)h2nbins))*histogram[kout].bin_high) - histogram[kout].bin_low) / ((float)h2nbins); /* allocate the bins */ if(( histogram2 = (hist_node_head*)malloc(h2nbins*sizeof(hist_node_head))) == NULL ) { if (binaryDC){ free(binaryDC); binaryDC = NULL; } if (weightedDC){ free(weightedDC); weightedDC = NULL; } if (histogram){ histogram = free_histogram(histogram, nhistnodes); } ERROR_message( "Could not allocate %d byte array for histogram2\n", h2nbins*sizeof(hist_node_head)); } else { /* -- update running memory estimate to reflect memory allocation */ histogram2_save = histogram2; INC_MEM_STATS(( h2nbins*sizeof(hist_node_head )), "hist bins"); PRINT_MEM_STATS( "hist2" ); } /* initiatize the bins */ for( kin = 0; kin < h2nbins; kin++ ) { histogram2[ kin ].bin_low = histogram[kout].bin_low + kin*h2binwidth; histogram2[ kin ].bin_high = histogram2[ kin ].bin_low + h2binwidth; histogram2[ kin ].nbin = 0; histogram2[ kin ].nodes = NULL; /*INFO_message("Hist2 bin %d [%3.3f, %3.3f) [%d, %p]\n", kin, histogram2[ kin ].bin_low, histogram2[ kin ].bin_high, histogram2[ kin ].nbin, histogram2[ kin ].nodes );*/ } /* move correlations from histogram to histgram2 */ INFO_message ("Adding %d nodes from histogram to histogram2",histogram[kout].nbin); while ( histogram[kout].nodes != NULL ) { hptr = histogram[kout].nodes; h2ndx = (int)floor((double)(hptr->corr - histogram[kout].bin_low)/(double)h2binwidth); if(( h2ndx < h2nbins ) && ( h2ndx >= 0 )) { histogram[kout].nodes = hptr->next; hptr->next = histogram2[h2ndx].nodes; histogram2[h2ndx].nodes = hptr; histogram2[h2ndx].nbin++; histogram[kout].nbin--; } else { WARNING_message("h2ndx %d is not in range [0,%d) :: %.10f,%.10f\n",h2ndx,h2nbins,hptr->corr, histogram[kout].bin_low); } } /* free the remainder of histogram */ { int nbins_rem = 0; for(ii = 0; ii < nhistnodes; ii++) nbins_rem+=histogram[ii].nbin; histogram = free_histogram(histogram, nhistnodes); PRINT_MEM_STATS( "free remainder of histogram1" ); } kin = h2nbins - 1; while (( nretain > 0 ) && ( kin >= 0 )) { hptr = pptr = histogram2[kin].nodes; while( hptr != NULL ) { /* determine the indices corresponding to this node */ if ( imap != NULL ) { ii = imap[hptr->i] ; } else { ii = hptr->i ; } if ( imap != NULL ) { jj = imap[hptr->j] ; } else { jj = hptr->j ; } /* add in the values */ if(( ii >= DSET_NVOX(cset) ) || ( jj >= DSET_NVOX(cset))) { if( ii >= DSET_NVOX(cset)) { WARNING_message("Avoiding bodset, wodset overflow (ii) %d > %d\n (%s,%d)\n", ii,DSET_NVOX(cset),__FILE__,__LINE__ ); } if( jj >= DSET_NVOX(cset)) { WARNING_message("Avoiding bodset, wodset overflow (jj) %d > %d\n (%s,%d)\n", jj,DSET_NVOX(cset),__FILE__,__LINE__ ); } } else { bodset[ ii ] += 1.0 ; wodset[ ii ] += (float)(hptr->corr); bodset[ jj ] += 1.0 ; wodset[ jj ] += (float)(hptr->corr); } if( fout1D != NULL ) { /* add source, dest, correlation to 1D file */ ix1 = DSET_index_to_ix(cset,ii) ; jy1 = DSET_index_to_jy(cset,ii) ; kz1 = DSET_index_to_kz(cset,ii) ; ix2 = DSET_index_to_ix(cset,jj) ; jy2 = DSET_index_to_jy(cset,jj) ; kz2 = DSET_index_to_kz(cset,jj) ; fprintf(fout1D, "%d %d %d %d %d %d %d %d %.6f\n", ii, jj, ix1, jy1, kz1, ix2, jy2, kz2, (float)(hptr->corr)); } /* increment node pointers */ pptr = hptr; hptr = hptr->next; /* delete the node */ if(pptr) { free(pptr); DEC_MEM_STATS(( sizeof(hist_node) ), "hist nodes"); pptr=NULL; } } /* decrement the number of correlations we wish to retain */ nretain -= histogram2[kin].nbin; histogram2[kin].nodes = NULL; /* go on to the next bin */ kin--; } PRINT_MEM_STATS("hist2 nodes free - incorporated into output"); /* we are finished with histogram2 */ { histogram2 = free_histogram(histogram2, h2nbins); /* -- update running memory estimate to reflect memory allocation */ PRINT_MEM_STATS( "free hist2" ); } if (nretain < 0 ) { WARNING_message( "Went over sparsity goal %d by %d, with a resolution of %f", ngoal, -1*nretain, h2binwidth); } } if (nretain > 0 ) { WARNING_message( "Was not able to meet goal of %d (%3.2f%%) correlations, %d (%3.2f%%) correlations passed the threshold of %3.2f, maybe you need to change the threshold or the desired sparsity?", ngoal, 100.0*((float)ngoal)/((float)totPosCor), totNumCor, 100.0*((float)totNumCor)/((float)totPosCor), thresh); } } INFO_message("Done..\n") ; /* update running memory statistics to reflect freeing the vectim */ DEC_MEM_STATS(((xvectim->nvec*sizeof(int)) + ((xvectim->nvec)*(xvectim->nvals))*sizeof(float) + sizeof(MRI_vectim)), "vectim"); /* toss some trash */ VECTIM_destroy(xvectim) ; DSET_delete(xset) ; if(fout1D!=NULL)fclose(fout1D); PRINT_MEM_STATS( "vectim unload" ); if (weightedDC) free(weightedDC) ; weightedDC = NULL; if (binaryDC) free(binaryDC) ; binaryDC = NULL; /* finito */ INFO_message("Writing output dataset to disk [%s bytes]", commaized_integer_string(cset->dblk->total_bytes)) ; /* write the dataset */ DSET_write(cset) ; WROTE_DSET(cset) ; /* increment our memory stats, since we are relying on the header for this information, we update the stats before actually freeing the memory */ DEC_MEM_STATS( (DSET_NVOX(cset)*DSET_NVALS(cset)*sizeof(float)), "output dset"); /* free up the output dataset memory */ DSET_unload(cset) ; DSET_delete(cset) ; /* force a print */ MEM_STAT = 1; PRINT_MEM_STATS( "Fin" ); exit(0) ; }
int main( int argc , char *argv[] ) { int nx,ny,nz , nxyz , ii,kk , num1,num2 , num_tt=0 , iv , piece , fim_offset; float dx,dy,dz , dxyz , num1_inv=0.0 , num2_inv , num1m1_inv=0.0 , num2m1_inv , dof , dd,tt,q1,q2 , f1,f2 , tt_max=0.0 ; THD_3dim_dataset *dset=NULL , *new_dset=NULL ; THD_3dim_dataset * base_dset; float *av1 , *av2 , *sd1 , *sd2 , *ffim , *gfim ; float *base_ary=NULL; void *vsp ; void *vdif ; /* output mean difference */ char cbuf[THD_MAX_NAME] ; float fbuf[MAX_STAT_AUX] , fimfac ; int output_datum ; float npiece , memuse ; float *dofbrik=NULL , *dofar=NULL ; THD_3dim_dataset *dof_dset=NULL ; /*-- read command line arguments --*/ if( argc < 2 || strncmp(argv[1],"-help",5) == 0 ) TT_syntax(NULL) ; /*-- 20 Apr 2001: addto the arglist, if user wants to [RWCox] --*/ mainENTRY("3dttest main"); machdep() ; PRINT_VERSION("3dttest") ; INFO_message("For most purposes, 3dttest++ should be used instead of 3dttest!") ; { int new_argc ; char ** new_argv ; addto_args( argc , argv , &new_argc , &new_argv ) ; if( new_argv != NULL ){ argc = new_argc ; argv = new_argv ; } } AFNI_logger("3dttest",argc,argv) ; TT_read_opts( argc , argv ) ; if( ! TT_be_quiet ) printf("3dttest: t-tests of 3D datasets, by RW Cox\n") ; /*-- read first dataset in set2 to get dimensions, etc. --*/ dset = THD_open_dataset( TT_set2->ar[0] ) ; /* 20 Dec 1999 BDW */ if( ! ISVALID_3DIM_DATASET(dset) ) ERROR_exit("Unable to open dataset file %s",TT_set2->ar[0]); nx = dset->daxes->nxx ; ny = dset->daxes->nyy ; nz = dset->daxes->nzz ; nxyz = nx * ny * nz ; dx = fabs(dset->daxes->xxdel) ; dy = fabs(dset->daxes->yydel) ; dz = fabs(dset->daxes->zzdel) ; dxyz = dx * dy * dz ; #ifdef TTDEBUG printf("*** nx=%d ny=%d nz=%d\n",nx,ny,nz) ; #endif /*-- make an empty copy of this dataset, for eventual output --*/ #ifdef TTDEBUG printf("*** making empty dataset\n") ; #endif new_dset = EDIT_empty_copy( dset ) ; tross_Make_History( "3dttest" , argc,argv , new_dset ) ; strcpy( cbuf , dset->self_name ) ; strcat( cbuf , "+TT" ) ; iv = DSET_PRINCIPAL_VALUE(dset) ; if( TT_datum >= 0 ){ output_datum = TT_datum ; } else { output_datum = DSET_BRICK_TYPE(dset,iv) ; if( output_datum == MRI_byte ) output_datum = MRI_short ; } #ifdef TTDEBUG printf(" ** datum = %s\n",MRI_TYPE_name[output_datum]) ; #endif iv = EDIT_dset_items( new_dset , ADN_prefix , TT_prefix , ADN_label1 , TT_prefix , ADN_directory_name , TT_session , ADN_self_name , cbuf , ADN_type , ISHEAD(dset) ? HEAD_FUNC_TYPE : GEN_FUNC_TYPE , ADN_func_type , FUNC_TT_TYPE , ADN_nvals , FUNC_nvals[FUNC_TT_TYPE] , ADN_ntt , 0 , /* 07 Jun 2007 */ ADN_datum_all , output_datum , ADN_none ) ; if( iv > 0 ) ERROR_exit("%d errors in attempting to create output dataset!",iv ) ; if( THD_deathcon() && THD_is_file(new_dset->dblk->diskptr->header_name) ) ERROR_exit( "Output dataset file %s already exists--cannot continue!\a", new_dset->dblk->diskptr->header_name ) ; #ifdef TTDEBUG printf("*** deleting exemplar dataset\n") ; #endif THD_delete_3dim_dataset( dset , False ) ; dset = NULL ; /** macro to test a malloc-ed pointer for validity **/ #define MTEST(ptr) \ if((ptr)==NULL) \ ( fprintf(stderr,"*** Cannot allocate memory for statistics!\n"), exit(0) ) /*-- make space for the t-test computations --*/ /* (allocate entire volumes) 13 Dec 2005 [rickr] */ npiece = 3.0 ; /* need at least this many */ if( TT_paired ) npiece += 1.0 ; else if( TT_set1 != NULL ) npiece += 2.0 ; npiece += mri_datum_size(output_datum) / (float) sizeof(float) ; npiece += mri_datum_size(output_datum) / (float) sizeof(float) ; #if 0 piece_size = TT_workmem * MEGA / ( npiece * sizeof(float) ) ; if( piece_size > nxyz ) piece_size = nxyz ; #ifdef TTDEBUG printf("*** malloc-ing space for statistics: %g float arrays of length %d\n", npiece,piece_size) ; #endif #endif av2 = (float *) malloc( sizeof(float) * nxyz ) ; MTEST(av2) ; sd2 = (float *) malloc( sizeof(float) * nxyz ) ; MTEST(sd2) ; ffim = (float *) malloc( sizeof(float) * nxyz ) ; MTEST(ffim) ; num2 = TT_set2->num ; if( TT_paired ){ av1 = sd1 = NULL ; gfim = (float *) malloc( sizeof(float) * nxyz ) ; MTEST(gfim) ; num1 = num2 ; } else if( TT_set1 != NULL ){ av1 = (float *) malloc( sizeof(float) * nxyz ) ; MTEST(av1) ; sd1 = (float *) malloc( sizeof(float) * nxyz ) ; MTEST(sd1) ; gfim = NULL ; num1 = TT_set1->num ; } else { av1 = sd1 = NULL ; gfim = NULL ; num1 = 0 ; } vdif = (void *) malloc( mri_datum_size(output_datum) * nxyz ) ; MTEST(vdif) ; vsp = (void *) malloc( mri_datum_size(output_datum) * nxyz ) ; MTEST(vsp) ; /* 27 Dec 2002: make DOF dataset (if prefix is given, and unpooled is on) */ if( TT_pooled == 0 && TT_dof_prefix[0] != '\0' ){ dofbrik = (float *) malloc( sizeof(float) * nxyz ) ; MTEST(dofbrik) ; dof_dset = EDIT_empty_copy( new_dset ) ; tross_Make_History( "3dttest" , argc,argv , dof_dset ) ; EDIT_dset_items( dof_dset , ADN_prefix , TT_dof_prefix , ADN_directory_name , TT_session , ADN_type , ISHEAD(dset) ? HEAD_FUNC_TYPE : GEN_FUNC_TYPE, ADN_func_type , FUNC_BUCK_TYPE , ADN_nvals , 1 , ADN_datum_all , MRI_float , ADN_none ) ; if( THD_is_file(dof_dset->dblk->diskptr->header_name) ) ERROR_exit( "-dof_prefix dataset file %s already exists--cannot continue!\a", dof_dset->dblk->diskptr->header_name ) ; EDIT_substitute_brick( dof_dset , 0 , MRI_float , dofbrik ) ; } /* print out memory usage to edify the user */ if( ! TT_be_quiet ){ memuse = sizeof(float) * nxyz * npiece + ( mri_datum_size(output_datum) + sizeof(short) ) * nxyz ; if( dofbrik != NULL ) memuse += sizeof(float) * nxyz ; /* 27 Dec 2002 */ printf("--- allocated %d Megabytes memory for internal use (%d volumes)\n", (int)(memuse/MEGA), (int)npiece) ; } mri_fix_data_pointer( vdif , DSET_BRICK(new_dset,0) ) ; /* attach bricks */ mri_fix_data_pointer( vsp , DSET_BRICK(new_dset,1) ) ; /* to new dataset */ /** only short and float are allowed for output **/ if( output_datum != MRI_short && output_datum != MRI_float ) ERROR_exit("Illegal output data type %d = %s", output_datum , MRI_TYPE_name[output_datum] ) ; num2_inv = 1.0 / num2 ; num2m1_inv = 1.0 / (num2-1) ; if( num1 > 0 ){ num1_inv = 1.0 / num1 ; num1m1_inv = 1.0 / (num1-1) ; } /*----- loop over pieces to process the input datasets with -----*/ /** macro to open a dataset and make it ready for processing **/ #define DOPEN(ds,name) \ do{ int pv ; (ds) = THD_open_dataset((name)) ; /* 16 Sep 1999 */ \ if( !ISVALID_3DIM_DATASET((ds)) ) \ ERROR_exit("Can't open dataset: %s",(name)) ; \ if( (ds)->daxes->nxx!=nx || (ds)->daxes->nyy!=ny || (ds)->daxes->nzz!=nz ) \ ERROR_exit("Axes size mismatch: %s",(name)) ; \ if( !EQUIV_GRIDS((ds),new_dset) ) \ WARNING_message("Grid mismatch: %s",(name)) ; \ if( DSET_NUM_TIMES((ds)) > 1 ) \ ERROR_exit("Can't use time-dependent data: %s",(name)) ; \ if( TT_use_editor ) EDIT_one_dataset( (ds), &TT_edopt ) ; \ else DSET_load((ds)) ; \ pv = DSET_PRINCIPAL_VALUE((ds)) ; \ if( DSET_ARRAY((ds),pv) == NULL ) \ ERROR_exit("Can't access data: %s",(name)) ; \ if( DSET_BRICK_TYPE((ds),pv) == MRI_complex ) \ ERROR_exit("Can't use complex data: %s",(name)) ; \ break ; } while (0) #if 0 /* can do it directly now (without offsets) 13 Dec 2005 [rickr] */ /** macro to return pointer to correct location in brick for current processing **/ #define SUB_POINTER(ds,vv,ind,ptr) \ do{ switch( DSET_BRICK_TYPE((ds),(vv)) ){ \ default: ERROR_exit("Illegal datum! ***"); \ case MRI_short:{ short * fim = (short *) DSET_ARRAY((ds),(vv)) ; \ (ptr) = (void *)( fim + (ind) ) ; \ } break ; \ case MRI_byte:{ byte * fim = (byte *) DSET_ARRAY((ds),(vv)) ; \ (ptr) = (void *)( fim + (ind) ) ; \ } break ; \ case MRI_float:{ float * fim = (float *) DSET_ARRAY((ds),(vv)) ; \ (ptr) = (void *)( fim + (ind) ) ; \ } break ; } break ; } while(0) #endif /** number of pieces to process **/ /* num_piece = (nxyz + piece_size - 1) / nxyz ; */ #if 0 nice(2) ; /** lower priority a little **/ #endif /* possibly open TT_base_dset now, and convert to floats */ if( TT_base_dname ) { DOPEN(base_dset, TT_base_dname) ; base_ary = (float *) malloc( sizeof(float) * nxyz ) ; MTEST(base_ary) ; EDIT_coerce_scale_type(nxyz , DSET_BRICK_FACTOR(base_dset,0) , DSET_BRICK_TYPE(base_dset,0),DSET_ARRAY(base_dset,0), /* input */ MRI_float ,base_ary ) ; /* output */ THD_delete_3dim_dataset( base_dset , False ) ; base_dset = NULL ; } /* only 1 'piece' now 13 Dec 2005 [rickr] */ for( piece=0 ; piece < 1 ; piece++ ){ fim_offset = 0 ; #ifdef TTDEBUG printf("*** start of piece %d: length=%d offset=%d\n",piece,nxyz,fim_offset) ; #else if( ! TT_be_quiet ){ printf("--- starting piece %d/%d (%d voxels) ",piece+1,1,nxyz) ; fflush(stdout) ; } #endif /** process set2 (and set1, if paired) **/ for( ii=0 ; ii < nxyz ; ii++ ) av2[ii] = 0.0 ; for( ii=0 ; ii < nxyz ; ii++ ) sd2[ii] = 0.0 ; for( kk=0 ; kk < num2 ; kk++ ){ /** read in the data **/ DOPEN(dset,TT_set2->ar[kk]) ; iv = DSET_PRINCIPAL_VALUE(dset) ; #ifndef TTDEBUG if( ! TT_be_quiet ){ printf(".") ; fflush(stdout) ; } /* progress */ #else printf(" ** opened dataset file %s\n",TT_set2->ar[kk]); #endif #if 0 /* fimfac will be compute when the results are ready */ if( piece == 0 && kk == 0 ){ fimfac = DSET_BRICK_FACTOR(dset,iv) ; if( fimfac == 0.0 ) fimfac = 1.0 ; fimfacinv = 1.0 / fimfac ; #ifdef TTDEBUG printf(" ** set fimfac = %g\n",fimfac) ; #endif } #endif /** convert it to floats (in ffim) **/ EDIT_coerce_scale_type(nxyz , DSET_BRICK_FACTOR(dset,iv) , DSET_BRICK_TYPE(dset,iv),DSET_ARRAY(dset,iv), /* input */ MRI_float ,ffim ) ; /* output */ THD_delete_3dim_dataset( dset , False ) ; dset = NULL ; /** get the paired dataset, if present **/ if( TT_paired ){ DOPEN(dset,TT_set1->ar[kk]) ; iv = DSET_PRINCIPAL_VALUE(dset) ; #ifndef TTDEBUG if( ! TT_be_quiet ){ printf(".") ; fflush(stdout) ; } /* progress */ #else printf(" ** opened dataset file %s\n",TT_set1->ar[kk]); #endif EDIT_coerce_scale_type( nxyz , DSET_BRICK_FACTOR(dset,iv) , DSET_BRICK_TYPE(dset,iv),DSET_ARRAY(dset,iv), /* input */ MRI_float ,gfim ) ; /* output */ THD_delete_3dim_dataset( dset , False ) ; dset = NULL ; if( TT_voxel >= 0 ) fprintf(stderr,"-- paired values #%02d: %f, %f\n", kk,ffim[TT_voxel],gfim[TT_voxel]) ; for( ii=0 ; ii < nxyz ; ii++ ) ffim[ii] -= gfim[ii] ; } else if( TT_voxel >= 0 ) fprintf(stderr,"-- set2 value #%02d: %f\n",kk,ffim[TT_voxel]); #ifdef TTDEBUG printf(" * adding into av2 and sd2\n") ; #endif /* accumulate into av2 and sd2 */ for( ii=0 ; ii < nxyz ; ii++ ){ dd = ffim[ii] ; av2[ii] += dd ; sd2[ii] += dd * dd ; } } /* end of loop over set2 datasets */ /** form the mean and stdev of set2 **/ #ifdef TTDEBUG printf(" ** forming mean and sigma of set2\n") ; #endif for( ii=0 ; ii < nxyz ; ii++ ){ av2[ii] *= num2_inv ; dd = (sd2[ii] - num2*av2[ii]*av2[ii]) ; sd2[ii] = (dd > 0.0) ? sqrt( num2m1_inv * dd ) : 0.0 ; } if( TT_voxel >= 0 ) fprintf(stderr,"-- s2 mean = %g, sd = %g\n", av2[TT_voxel],sd2[TT_voxel]) ; /** if set1 exists but is not paired with set2, process it now **/ if( ! TT_paired && TT_set1 != NULL ){ for( ii=0 ; ii < nxyz ; ii++ ) av1[ii] = 0.0 ; for( ii=0 ; ii < nxyz ; ii++ ) sd1[ii] = 0.0 ; for( kk=0 ; kk < num1 ; kk++ ){ DOPEN(dset,TT_set1->ar[kk]) ; iv = DSET_PRINCIPAL_VALUE(dset) ; #ifndef TTDEBUG if( ! TT_be_quiet ){ printf(".") ; fflush(stdout) ; } /* progress */ #else printf(" ** opened dataset file %s\n",TT_set1->ar[kk]); #endif EDIT_coerce_scale_type( nxyz , DSET_BRICK_FACTOR(dset,iv) , DSET_BRICK_TYPE(dset,iv),DSET_ARRAY(dset,iv), /* input */ MRI_float ,ffim ) ; /* output */ THD_delete_3dim_dataset( dset , False ) ; dset = NULL ; #ifdef TTDEBUG printf(" * adding into av1 and sd1\n") ; #endif for( ii=0 ; ii < nxyz ; ii++ ){ dd = ffim[ii] ; av1[ii] += dd ; sd1[ii] += dd * dd ; } if( TT_voxel >= 0 ) fprintf(stderr,"-- set1 value #%02d: %g\n",kk,ffim[TT_voxel]) ; } /* end of loop over set1 datasets */ /** form the mean and stdev of set1 **/ #ifdef TTDEBUG printf(" ** forming mean and sigma of set1\n") ; #endif for( ii=0 ; ii < nxyz ; ii++ ){ av1[ii] *= num1_inv ; dd = (sd1[ii] - num1*av1[ii]*av1[ii]) ; sd1[ii] = (dd > 0.0) ? sqrt( num1m1_inv * dd ) : 0.0 ; } if( TT_voxel >= 0 ) fprintf(stderr,"-- s1 mean = %g, sd = %g\n", av1[TT_voxel], sd1[TT_voxel]) ; } /* end of processing set1 by itself */ /***** now form difference and t-statistic *****/ #ifndef TTDEBUG if( ! TT_be_quiet ){ printf("+") ; fflush(stdout) ; } /* progress */ #else printf(" ** computing t-tests next\n") ; #endif #if 0 /* will do at end using EDIT_convert_dtype 13 Dec 2005 [rickr] */ /** macro to assign difference value to correct type of array **/ #define DIFASS switch( output_datum ){ \ case MRI_short: sdar[ii] = (short) (fimfacinv*dd) ; break ; \ case MRI_float: fdar[ii] = (float) dd ; break ; } #define TOP_SS 32700 #define TOP_TT (32700.0/FUNC_TT_SCALE_SHORT) #endif if( TT_paired || TT_use_bval == 1 ){ /** case 1: paired estimate or 1-sample **/ if( TT_paired || TT_n1 == 0 ){ /* the olde waye: 1 sample test */ f2 = 1.0 / sqrt( (double) num2 ) ; for( ii=0 ; ii < nxyz ; ii++ ){ av2[ii] -= (base_ary ? base_ary[ii] : TT_bval) ; /* final mean */ if( sd2[ii] > 0.0 ){ num_tt++ ; tt = av2[ii] / (f2 * sd2[ii]) ; sd2[ii] = tt; /* final t-stat */ tt = fabs(tt) ; if( tt > tt_max ) tt_max = tt ; } else { sd2[ii] = 0.0; } } if( TT_voxel >= 0 ) fprintf(stderr,"-- paired/bval mean = %g, t = %g\n", av2[TT_voxel], sd2[TT_voxel]) ; } else { /* 10 Oct 2007: -sdn1 was used with -base1: 'two' sample test */ f1 = (TT_n1-1.0) * (1.0/TT_n1 + 1.0/num2) / (TT_n1+num2-2.0) ; f2 = (num2 -1.0) * (1.0/TT_n1 + 1.0/num2) / (TT_n1+num2-2.0) ; for( ii=0 ; ii < nxyz ; ii++ ){ av2[ii] -= (base_ary ? base_ary[ii] : TT_bval) ; /* final mean */ q1 = f1 * TT_sd1*TT_sd1 + f2 * sd2[ii]*sd2[ii] ; if( q1 > 0.0 ){ num_tt++ ; tt = av2[ii] / sqrt(q1) ; sd2[ii] = tt ; /* final t-stat */ tt = fabs(tt) ; if( tt > tt_max ) tt_max = tt ; } else { sd2[ii] = 0.0 ; } } } /* end of -sdn1 special case */ #ifdef TTDEBUG printf(" ** paired or bval test: num_tt = %d\n",num_tt) ; #endif } else if( TT_pooled ){ /** case 2: unpaired 2-sample, pooled variance **/ f1 = (num1-1.0) * (1.0/num1 + 1.0/num2) / (num1+num2-2.0) ; f2 = (num2-1.0) * (1.0/num1 + 1.0/num2) / (num1+num2-2.0) ; for( ii=0 ; ii < nxyz ; ii++ ){ av2[ii] -= av1[ii] ; /* final mean */ q1 = f1 * sd1[ii]*sd1[ii] + f2 * sd2[ii]*sd2[ii] ; if( q1 > 0.0 ){ num_tt++ ; tt = av2[ii] / sqrt(q1) ; sd2[ii] = tt ; /* final t-stat */ tt = fabs(tt) ; if( tt > tt_max ) tt_max = tt ; } else { sd2[ii] = 0.0 ; } } if( TT_voxel >= 0 ) fprintf(stderr,"-- unpaired, pooled mean = %g, t = %g\n", av2[TT_voxel], sd2[TT_voxel]) ; #ifdef TTDEBUG printf(" ** pooled test: num_tt = %d\n",num_tt) ; #endif } else { /** case 3: unpaired 2-sample, unpooled variance **/ /** 27 Dec 2002: modified to save DOF into dofar **/ if( dofbrik != NULL ) dofar = dofbrik + fim_offset ; /* 27 Dec 2002 */ for( ii=0 ; ii < nxyz ; ii++ ){ av2[ii] -= av1[ii] ; q1 = num1_inv * sd1[ii]*sd1[ii] ; q2 = num2_inv * sd2[ii]*sd2[ii] ; if( q1>0.0 && q2>0.0 ){ /* have positive variances? */ num_tt++ ; tt = av2[ii] / sqrt(q1+q2) ; sd2[ii] = tt ; /* final t-stat */ tt = fabs(tt) ; if( tt > tt_max ) tt_max = tt ; if( dofar != NULL ) /* 27 Dec 2002 */ dofar[ii] = (q1+q2)*(q1+q2) / (num1m1_inv*q1*q1 + num2m1_inv*q2*q2) ; } else { sd2[ii] = 0.0 ; if( dofar != NULL ) dofar[ii] = 1.0 ; /* 27 Dec 2002 */ } } if( TT_voxel >= 0 ) fprintf(stderr,"-- unpaired, unpooled mean = %g, t = %g\n", av2[TT_voxel], sd2[TT_voxel]) ; #ifdef TTDEBUG printf(" ** unpooled test: num_tt = %d\n",num_tt) ; #endif } #ifndef TTDEBUG if( ! TT_be_quiet ){ printf("\n") ; fflush(stdout) ; } #endif } /* end of loop over pieces of the input */ if( TT_paired ){ printf("--- Number of degrees of freedom = %d (paired test)\n",num2-1) ; dof = num2 - 1 ; } else if( TT_use_bval == 1 ){ if( TT_n1 == 0 ){ printf("--- Number of degrees of freedom = %d (1-sample test)\n",num2-1) ; dof = num2 - 1 ; } else { dof = TT_n1+num2-2 ; printf("--- Number of degrees of freedom = %d (-sdn1 2-sample test)\n",(int)dof) ; } } else { printf("--- Number of degrees of freedom = %d (2-sample test)\n",num1+num2-2) ; dof = num1+num2-2 ; if( ! TT_pooled ) printf(" (For unpooled variance estimate, this is only approximate!)\n") ; } printf("--- Number of t-tests performed = %d out of %d voxels\n",num_tt,nxyz) ; printf("--- Largest |t| value found = %g\n",tt_max) ; kk = sizeof(ptable) / sizeof(float) ; for( ii=0 ; ii < kk ; ii++ ){ tt = student_p2t( ptable[ii] , dof ) ; printf("--- Double sided tail p = %8f at t = %8f\n" , ptable[ii] , tt ) ; } /**----------------------------------------------------------------------**/ /** now convert data to output format 13 Dec 2005 [rickr] **/ /* first set mean */ fimfac = EDIT_convert_dtype(nxyz , MRI_float,av2 , output_datum,vdif , 0.0) ; DSET_BRICK_FACTOR(new_dset, 0) = (fimfac != 0.0) ? 1.0/fimfac : 0.0 ; dd = fimfac; /* save for debug output */ /* if output is of type short, limit t-stat magnitude to 32.7 */ if( output_datum == MRI_short ){ for( ii=0 ; ii < nxyz ; ii++ ){ if ( sd2[ii] > 32.7 ) sd2[ii] = 32.7 ; else if( sd2[ii] < -32.7 ) sd2[ii] = -32.7 ; } } fimfac = EDIT_convert_dtype(nxyz , MRI_float,sd2 , output_datum,vsp , 0.0) ; DSET_BRICK_FACTOR(new_dset, 1) = (fimfac != 0.0) ? 1.0/fimfac : 0.0 ; #ifdef TTDEBUG printf(" ** fimfac for mean, t-stat = %g, %g\n",dd, fimfac) ; #endif /**----------------------------------------------------------------------**/ INFO_message("Writing combined dataset into %s\n", DSET_BRIKNAME(new_dset) ) ; fbuf[0] = dof ; for( ii=1 ; ii < MAX_STAT_AUX ; ii++ ) fbuf[ii] = 0.0 ; (void) EDIT_dset_items( new_dset , ADN_stat_aux , fbuf , ADN_none ) ; #if 0 /* factors already set */ fbuf[0] = (output_datum == MRI_short && fimfac != 1.0 ) ? fimfac : 0.0 ; fbuf[1] = (output_datum == MRI_short ) ? 1.0 / FUNC_TT_SCALE_SHORT : 0.0 ; (void) EDIT_dset_items( new_dset , ADN_brick_fac , fbuf , ADN_none ) ; #endif if( !AFNI_noenv("AFNI_AUTOMATIC_FDR") ) ii = THD_create_all_fdrcurves(new_dset) ; else ii = 0 ; THD_load_statistics( new_dset ) ; THD_write_3dim_dataset( NULL,NULL , new_dset , True ) ; if( ii > 0 ) ININFO_message("created %d FDR curves in header",ii) ; if( dof_dset != NULL ){ /* 27 Dec 2002 */ DSET_write( dof_dset ) ; WROTE_DSET( dof_dset ) ; } exit(0) ; }
int main( int argc , char *argv[] ) { int iarg=1 , ii , do_iwarp=0 ; char *prefix = "NwarpCat" ; mat44 wmat , smat , qmat ; THD_3dim_dataset *oset=NULL ; char *cwarp_all=NULL ; int ntot=0 ; AFNI_SETUP_OMP(0) ; /* 24 Jun 2013 */ if( argc < 2 || strcasecmp(argv[1],"-help") == 0 ) NWC_help() ; /*-- bureaucracy --*/ mainENTRY("3dNwarpCat"); machdep(); AFNI_logger("3dNwarpCat",argc,argv); PRINT_VERSION("3dNwarpCat"); AUTHOR("Zhark the Warper"); (void)COX_clock_time() ; putenv("AFNI_WSINC5_SILENT=YES") ; /*-- initialization --*/ CW_no_expad = 1 ; /* don't allow automatic padding of input warp */ Hverb = 0 ; /* don't be verbose inside mri_nwarp.c */ for( ii=0 ; ii < NWMAX ; ii++ ) cwarp[ii] = NULL ; /*-- scan args --*/ while( iarg < argc && argv[iarg][0] == '-' ){ /*---------------*/ if( strcasecmp(argv[iarg],"-iwarp") == 0 ){ do_iwarp = 1 ; iarg++ ; continue ; } /*---------------*/ if( strcasecmp(argv[iarg],"-space") == 0 ){ sname = strdup(argv[++iarg]) ; iarg++ ; continue ; } /*---------------*/ if( strcasecmp(argv[iarg],"-NN") == 0 || strncasecmp(argv[iarg],"-nearest",6) == 0 ){ WARNING_message("NN interpolation not legal here -- switched to linear") ; interp_code = MRI_LINEAR ; iarg++ ; continue ; } if( strncasecmp(argv[iarg],"-linear",4)==0 || strncasecmp(argv[iarg],"-trilinear",6)==0 ){ interp_code = MRI_LINEAR ; iarg++ ; continue ; } if( strncasecmp(argv[iarg],"-cubic",4)==0 || strncasecmp(argv[iarg],"-tricubic",6)==0 ){ WARNING_message("cubic interplation not legal here -- switched to quintic") ; interp_code = MRI_QUINTIC ; iarg++ ; continue ; } if( strncasecmp(argv[iarg],"-quintic",4)==0 || strncasecmp(argv[iarg],"-triquintic",6)==0 ){ interp_code = MRI_QUINTIC ; iarg++ ; continue ; } if( strncasecmp(argv[iarg],"-wsinc",5) == 0 ){ interp_code = MRI_WSINC5 ; iarg++ ; continue ; } /*---------------*/ if( strcasecmp(argv[iarg],"-expad") == 0 ){ int expad ; if( ++iarg >= argc ) ERROR_exit("no argument after '%s' :-(",argv[iarg-1]) ; expad = (int)strtod(argv[iarg],NULL) ; if( expad < 0 ){ WARNING_message("-expad %d is illegal and is set to zero",expad) ; expad = 0 ; } CW_extra_pad = expad ; /* this is how we force extra padding */ iarg++ ; continue ; } /*---------------*/ if( strncasecmp(argv[iarg],"-interp",5)==0 ){ char *inam ; if( ++iarg >= argc ) ERROR_exit("no argument after '%s' :-(",argv[iarg-1]) ; inam = argv[iarg] ; if( *inam == '-' ) inam++ ; if( strcasecmp(inam,"NN")==0 || strncasecmp(inam,"nearest",5)==0 ){ WARNING_message("NN interpolation not legal here -- changed to linear") ; interp_code = MRI_LINEAR ; } else if( strncasecmp(inam,"linear",3)==0 || strncasecmp(inam,"trilinear",5)==0 ){ interp_code = MRI_LINEAR ; } else if( strncasecmp(inam,"cubic",3)==0 || strncasecmp(inam,"tricubic",5)==0 ){ WARNING_message("cubic interplation not legal here -- changed to quintic") ; interp_code = MRI_QUINTIC ; } else if( strncasecmp(inam,"quintic",3)==0 || strncasecmp(inam,"triquintic",5)==0 ){ interp_code = MRI_QUINTIC ; } else if( strncasecmp(inam,"wsinc",4)==0 ){ interp_code = MRI_WSINC5 ; } else { ERROR_exit("Unknown code '%s' after '%s' :-(",argv[iarg],argv[iarg-1]) ; } iarg++ ; continue ; } /*---------------*/ if( strcasecmp(argv[iarg],"-verb") == 0 ){ verb++ ; NwarpCalcRPN_verb(verb) ; iarg++ ; continue ; } /*---------------*/ if( strcasecmp(argv[iarg],"-prefix") == 0 ){ if( ++iarg >= argc ) ERROR_exit("no argument after '%s' :-(",argv[iarg-1]) ; prefix = argv[iarg] ; if( !THD_filename_ok(prefix) ) ERROR_exit("Illegal name after '%s'",argv[iarg-1]) ; iarg++ ; continue ; } /*---------------*/ if( strncasecmp(argv[iarg],"-warp",5) == 0 ){ int nn ; if( iarg >= argc-1 ) ERROR_exit("no argument after '%s' :-(",argv[iarg]) ; if( !isdigit(argv[iarg][5]) ) ERROR_exit("illegal format for '%s' :-(",argv[iarg]) ; nn = (int)strtod(argv[iarg]+5,NULL) ; if( nn <= 0 || nn > NWMAX ) ERROR_exit("illegal warp index in '%s' :-(",argv[iarg]) ; if( cwarp[nn-1] != NULL ) ERROR_exit("'%s': you can't specify warp #%d more than once :-(",argv[iarg],nn) ; cwarp[nn-1] = strdup(argv[++iarg]) ; if( nn > nwtop ) nwtop = nn ; iarg++ ; continue ; } /*---------------*/ ERROR_message("Confusingly Unknown option '%s' :-(",argv[iarg]) ; suggest_best_prog_option(argv[0],argv[iarg]) ; exit(1) ; } /*-- load any warps left on the command line, after options --*/ for( ; iarg < argc && nwtop < NWMAX-1 ; iarg++ ) cwarp[nwtop++] = strdup(argv[iarg]) ; /*-- check if all warp strings are affine matrices --*/ #undef AFFINE_WARP_STRING #define AFFINE_WARP_STRING(ss) \ ( strstr((ss)," ") == NULL && \ ( strcasestr((ss),".1D") != NULL || strcasestr((ss),".txt") != NULL ) ) for( ntot=ii=0 ; ii < nwtop ; ii++ ){ if( cwarp[ii] == NULL ) continue ; ntot += strlen(cwarp[ii]) ; if( ! AFFINE_WARP_STRING(cwarp[ii]) ) break ; /* not affine */ } if( ntot == 0 ) ERROR_exit("No warps on command line?!") ; if( ii == nwtop ){ /* all are affine (this is for Ziad) */ char *fname = malloc(sizeof(char)*(strlen(prefix)+16)) ; FILE *fp ; float a11,a12,a13,a14,a21,a22,a23,a24,a31,a32,a33,a34 ; LOAD_IDENT_MAT44(wmat) ; for( ii=0 ; ii < nwtop ; ii++ ){ if( cwarp[ii] == NULL ) continue ; smat = CW_read_affine_warp_OLD(cwarp[ii]) ; qmat = MAT44_MUL(smat,wmat) ; wmat = qmat ; } if( strcmp(prefix,"-") == 0 || strncmp(prefix,"stdout",6) == 0 ){ fp = stdout ; strcpy(fname,"stdout") ; } else { strcpy(fname,prefix) ; if( strstr(fname,".1D") == NULL ) strcat(fname,".aff12.1D") ; fp = fopen(fname,"w") ; if( fp == NULL ) ERROR_exit("Can't open output matrix file %s",fname) ; } if( do_iwarp ){ qmat = MAT44_INV(wmat) ; wmat = qmat ; } UNLOAD_MAT44(wmat,a11,a12,a13,a14,a21,a22,a23,a24,a31,a32,a33,a34) ; fprintf(fp, " %13.6g %13.6g %13.6g %13.6g %13.6g %13.6g %13.6g %13.6g %13.6g %13.6g %13.6g %13.6g\n", a11,a12,a13,a14,a21,a22,a23,a24,a31,a32,a33,a34 ) ; if( verb && fp != stdout ) INFO_message("Wrote matrix to %s",fname) ; if( fp != stdout ) fclose(fp) ; exit(0) ; } /*** at least one nonlinear warp ==> cat all strings, use library function to read ***/ cwarp_all = (char *)calloc(sizeof(char),(ntot+NWMAX)*2) ; for( ii=0 ; ii < nwtop ; ii++ ){ if( cwarp[ii] != NULL ){ strcat(cwarp_all,cwarp[ii]) ; strcat(cwarp_all," ") ; } } oset = IW3D_read_catenated_warp( cwarp_all ) ; /* process all of them at once */ if( do_iwarp ){ /* 18 Jul 2014 */ THD_3dim_dataset *qwarp ; if( verb ) fprintf(stderr,"Applying -iwarp option") ; qwarp = THD_nwarp_invert(oset) ; DSET_delete(oset) ; oset = qwarp ; if( verb ) fprintf(stderr,"\n") ; } tross_Make_History( "3dNwarpCat" , argc,argv , oset ) ; if( sname != NULL ) MCW_strncpy( oset->atlas_space , sname , THD_MAX_NAME ) ; EDIT_dset_items( oset , ADN_prefix,prefix , ADN_none ) ; DSET_write(oset) ; WROTE_DSET(oset) ; /*--- run away screaming into the night, never to be seen again ---*/ INFO_message("total CPU time = %.1f sec Elapsed = %.1f\n", COX_cpu_time() , COX_clock_time() ) ; exit(0) ; }
int main( int argc , char *argv[] ) { THD_3dim_dataset *yset=NULL , *aset=NULL , *mset=NULL , *wset=NULL ; MRI_IMAGE *fim=NULL, *qim,*tim, *pfim=NULL , *vim , *wim=NULL ; float *flar , *qar,*tar, *par=NULL , *var , *war=NULL ; MRI_IMARR *fimar=NULL ; MRI_IMAGE *aim , *yim ; float *aar , *yar ; int nt=0 , nxyz=0 , nvox=0 , nparam=0 , nqbase , polort=0 , ii,jj,kk,bb ; byte *mask=NULL ; int nmask=0 , iarg ; char *fname_out="-" ; /** equiv to stdout **/ float alpha=0.0f ; int nfir =0 ; float firwt[5]={0.09f,0.25f,0.32f,0.25f,0.09f} ; int nmed =0 ; int nwt =0 ; #define METHOD_C 3 #define METHOD_K 11 int method = METHOD_C ; /**--- help the pitiful user? ---**/ if( argc < 2 || strcmp(argv[1],"-help") == 0 ){ printf( "Usage: 3dInvFMRI [options]\n" "Program to compute stimulus time series, given a 3D+time dataset\n" "and an activation map (the inverse of the usual FMRI analysis problem).\n" "-------------------------------------------------------------------\n" "OPTIONS:\n" "\n" " -data yyy =\n" " *OR* = Defines input 3D+time dataset [a non-optional option].\n" " -input yyy =\n" "\n" " -map aaa = Defines activation map; 'aaa' should be a bucket dataset,\n" " each sub-brick of which defines the beta weight map for\n" " an unknown stimulus time series [also non-optional].\n" "\n" " -mapwt www = Defines a weighting factor to use for each element of\n" " the map. The dataset 'www' can have either 1 sub-brick,\n" " or the same number as in the -map dataset. In the\n" " first case, in each voxel, each sub-brick of the map\n" " gets the same weight in the least squares equations.\n" " [default: all weights are 1]\n" "\n" " -mask mmm = Defines a mask dataset, to restrict input voxels from\n" " -data and -map. [default: all voxels are used]\n" "\n" " -base fff = Each column of the 1D file 'fff' defines a baseline time\n" " series; these columns should be the same length as\n" " number of time points in 'yyy'. Multiple -base options\n" " can be given.\n" " -polort pp = Adds polynomials of order 'pp' to the baseline collection.\n" " The default baseline model is '-polort 0' (constant).\n" " To specify no baseline model at all, use '-polort -1'.\n" "\n" " -out vvv = Name of 1D output file will be 'vvv'.\n" " [default = '-', which is stdout; probably not good]\n" "\n" " -method M = Determines the method to use. 'M' is a single letter:\n" " -method C = least squares fit to data matrix Y [default]\n" " -method K = least squares fit to activation matrix A\n" "\n" " -alpha aa = Set the 'alpha' factor to 'aa'; alpha is used to penalize\n" " large values of the output vectors. Default is 0.\n" " A large-ish value for alpha would be 0.1.\n" "\n" " -fir5 = Smooth the results with a 5 point lowpass FIR filter.\n" " -median5 = Smooth the results with a 5 point median filter.\n" " [default: no smoothing; only 1 of these can be used]\n" "-------------------------------------------------------------------\n" "METHODS:\n" " Formulate the problem as\n" " Y = V A' + F C' + errors\n" " where Y = data matrix (N x M) [from -data]\n" " V = stimulus (N x p) [to -out]\n" " A = map matrix (M x p) [from -map]\n" " F = baseline matrix (N x q) [from -base and -polort]\n" " C = baseline weights (M x q) [not computed]\n" " N = time series length = length of -data file\n" " M = number of voxels in mask\n" " p = number of stimulus time series to estimate\n" " = number of parameters in -map file\n" " q = number of baseline parameters\n" " and ' = matrix transpose operator\n" " Next, define matrix Z (Y detrended relative to columns of F) by\n" " -1\n" " Z = [I - F(F'F) F'] Y\n" "-------------------------------------------------------------------\n" " The method C solution is given by\n" " -1\n" " V0 = Z A [A'A]\n" "\n" " This solution minimizes the sum of squares over the N*M elements\n" " of the matrix Y - V A' + F C' (N.B.: A' means A-transpose).\n" "-------------------------------------------------------------------\n" " The method K solution is given by\n" " -1 -1\n" " W = [Z Z'] Z A and then V = W [W'W]\n" "\n" " This solution minimizes the sum of squares of the difference between\n" " the A(V) predicted from V and the input A, where A(V) is given by\n" " -1\n" " A(V) = Z' V [V'V] = Z'W\n" "-------------------------------------------------------------------\n" " Technically, the solution is unidentfiable up to an arbitrary\n" " multiple of the columns of F (i.e., V = V0 + F G, where G is\n" " an arbitrary q x p matrix); the solution above is the solution\n" " that is orthogonal to the columns of F.\n" "\n" "-- RWCox - March 2006 - purely for experimental purposes!\n" ) ; printf("\n" "===================== EXAMPLE USAGE =====================================\n" "** Step 1: From a training dataset, generate activation map.\n" " The input dataset has 4 runs, each 108 time points long. 3dDeconvolve\n" " is used on the first 3 runs (time points 0..323) to generate the\n" " activation map. There are two visual stimuli (Complex and Simple).\n" "\n" " 3dDeconvolve -x1D xout_short_two.1D -input rall_vr+orig'[0..323]' \\\n" " -num_stimts 2 \\\n" " -stim_file 1 hrf_complex.1D -stim_label 1 Complex \\\n" " -stim_file 2 hrf_simple.1D -stim_label 2 Simple \\\n" " -concat '1D:0,108,216' \\\n" " -full_first -fout -tout \\\n" " -bucket func_ht2_short_two -cbucket cbuc_ht2_short_two\n" "\n" " N.B.: You may want to de-spike, smooth, and register the 3D+time\n" " dataset prior to the analysis (as usual). These steps are not\n" " shown here -- I'm presuming you know how to use AFNI already.\n" "\n" "** Step 2: Create a mask of highly activated voxels.\n" " The F statistic threshold is set to 30, corresponding to a voxel-wise\n" " p = 1e-12 = very significant. The mask is also lightly clustered, and\n" " restricted to brain voxels.\n" "\n" " 3dAutomask -prefix Amask rall_vr+orig\n" " 3dcalc -a 'func_ht2_short+orig[0]' -b Amask+orig -datum byte \\\n" " -nscale -expr 'step(a-30)*b' -prefix STmask300\n" " 3dmerge -dxyz=1 -1clust 1.1 5 -prefix STmask300c STmask300+orig\n" "\n" "** Step 3: Run 3dInvFMRI to estimate the stimulus functions in run #4.\n" " Run #4 is time points 324..431 of the 3D+time dataset (the -data\n" " input below). The -map input is the beta weights extracted from\n" " the -cbucket output of 3dDeconvolve.\n" "\n" " 3dInvFMRI -mask STmask300c+orig \\\n" " -data rall_vr+orig'[324..431]' \\\n" " -map cbuc_ht2_short_two+orig'[6..7]' \\\n" " -polort 1 -alpha 0.01 -median5 -method K \\\n" " -out ii300K_short_two.1D\n" "\n" " 3dInvFMRI -mask STmask300c+orig \\\n" " -data rall_vr+orig'[324..431]' \\\n" " -map cbuc_ht2_short_two+orig'[6..7]' \\\n" " -polort 1 -alpha 0.01 -median5 -method C \\\n" " -out ii300C_short_two.1D\n" "\n" "** Step 4: Plot the results, and get confused.\n" "\n" " 1dplot -ynames VV KK CC -xlabel Run#4 -ylabel ComplexStim \\\n" " hrf_complex.1D'{324..432}' \\\n" " ii300K_short_two.1D'[0]' \\\n" " ii300C_short_two.1D'[0]'\n" "\n" " 1dplot -ynames VV KK CC -xlabel Run#4 -ylabel SimpleStim \\\n" " hrf_simple.1D'{324..432}' \\\n" " ii300K_short_two.1D'[1]' \\\n" " ii300C_short_two.1D'[1]'\n" "\n" " N.B.: I've found that method K works better if MORE voxels are\n" " included in the mask (lower threshold) and method C if\n" " FEWER voxels are included. The above threshold gave 945\n" " voxels being used to determine the 2 output time series.\n" "=========================================================================\n" ) ; PRINT_COMPILE_DATE ; exit(0) ; } /**--- bureaucracy ---**/ mainENTRY("3dInvFMRI main"); machdep(); PRINT_VERSION("3dInvFMRI"); AUTHOR("Zhark"); AFNI_logger("3dInvFMRI",argc,argv) ; /**--- scan command line ---**/ iarg = 1 ; while( iarg < argc ){ if( strcmp(argv[iarg],"-method") == 0 ){ switch( argv[++iarg][0] ){ default: WARNING_message("Ignoring illegal -method '%s'",argv[iarg]) ; break ; case 'C': method = METHOD_C ; break ; case 'K': method = METHOD_K ; break ; } iarg++ ; continue ; } if( strcmp(argv[iarg],"-fir5") == 0 ){ if( nmed > 0 ) WARNING_message("Ignoring -fir5 in favor of -median5") ; else nfir = 5 ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-median5") == 0 ){ if( nfir > 0 ) WARNING_message("Ignoring -median5 in favor of -fir5") ; else nmed = 5 ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-alpha") == 0 ){ alpha = (float)strtod(argv[++iarg],NULL) ; if( alpha <= 0.0f ){ alpha = 0.0f ; WARNING_message("-alpha '%s' ignored!",argv[iarg]) ; } iarg++ ; continue ; } if( strcmp(argv[iarg],"-data") == 0 || strcmp(argv[iarg],"-input") == 0 ){ if( yset != NULL ) ERROR_exit("Can't input 2 3D+time datasets") ; yset = THD_open_dataset(argv[++iarg]) ; CHECK_OPEN_ERROR(yset,argv[iarg]) ; nt = DSET_NVALS(yset) ; if( nt < 2 ) ERROR_exit("Only 1 sub-brick in dataset %s",argv[iarg]) ; nxyz = DSET_NVOX(yset) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-map") == 0 ){ if( aset != NULL ) ERROR_exit("Can't input 2 -map datasets") ; aset = THD_open_dataset(argv[++iarg]) ; CHECK_OPEN_ERROR(aset,argv[iarg]) ; nparam = DSET_NVALS(aset) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-mapwt") == 0 ){ if( wset != NULL ) ERROR_exit("Can't input 2 -mapwt datasets") ; wset = THD_open_dataset(argv[++iarg]) ; CHECK_OPEN_ERROR(wset,argv[iarg]) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-mask") == 0 ){ if( mset != NULL ) ERROR_exit("Can't input 2 -mask datasets") ; mset = THD_open_dataset(argv[++iarg]) ; CHECK_OPEN_ERROR(mset,argv[iarg]) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-polort") == 0 ){ char *cpt ; polort = (int)strtod(argv[++iarg],&cpt) ; if( *cpt != '\0' ) WARNING_message("Illegal non-numeric value after -polort") ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-out") == 0 ){ fname_out = strdup(argv[++iarg]) ; if( !THD_filename_ok(fname_out) ) ERROR_exit("Bad -out filename '%s'",fname_out) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-base") == 0 ){ if( fimar == NULL ) INIT_IMARR(fimar) ; qim = mri_read_1D( argv[++iarg] ) ; if( qim == NULL ) ERROR_exit("Can't read 1D file %s",argv[iarg]) ; ADDTO_IMARR(fimar,qim) ; iarg++ ; continue ; } ERROR_exit("Unrecognized option '%s'",argv[iarg]) ; } /**--- finish up processing options ---**/ if( yset == NULL ) ERROR_exit("No input 3D+time dataset?!") ; if( aset == NULL ) ERROR_exit("No input FMRI -map dataset?!") ; if( DSET_NVOX(aset) != nxyz ) ERROR_exit("Grid mismatch between -data and -map") ; INFO_message("Loading dataset for Y") ; DSET_load(yset); CHECK_LOAD_ERROR(yset) ; INFO_message("Loading dataset for A") ; DSET_load(aset); CHECK_LOAD_ERROR(aset) ; if( wset != NULL ){ if( DSET_NVOX(wset) != nxyz ) ERROR_exit("Grid mismatch between -data and -mapwt") ; nwt = DSET_NVALS(wset) ; if( nwt > 1 && nwt != nparam ) ERROR_exit("Wrong number of values=%d in -mapwt; should be 1 or %d", nwt , nparam ) ; INFO_message("Loading dataset for mapwt") ; DSET_load(wset); CHECK_LOAD_ERROR(wset) ; } if( mset != NULL ){ if( DSET_NVOX(mset) != nxyz ) ERROR_exit("Grid mismatch between -data and -mask") ; INFO_message("Loading dataset for mask") ; DSET_load(mset); CHECK_LOAD_ERROR(mset) ; mask = THD_makemask( mset , 0 , 1.0f,-1.0f ); DSET_delete(mset); nmask = THD_countmask( nxyz , mask ) ; if( nmask < 3 ){ WARNING_message("Mask has %d voxels -- ignoring!",nmask) ; free(mask) ; mask = NULL ; nmask = 0 ; } } nvox = (nmask > 0) ? nmask : nxyz ; INFO_message("N = time series length = %d",nt ) ; INFO_message("M = number of voxels = %d",nvox ) ; INFO_message("p = number of params = %d",nparam) ; /**--- set up baseline funcs in one array ---*/ nqbase = (polort >= 0 ) ? polort+1 : 0 ; if( fimar != NULL ){ for( kk=0 ; kk < IMARR_COUNT(fimar) ; kk++ ){ qim = IMARR_SUBIMAGE(fimar,kk) ; if( qim != NULL && qim->nx != nt ) WARNING_message("-base #%d length=%d; data length=%d",kk+1,qim->nx,nt) ; nqbase += qim->ny ; } } INFO_message("q = number of baselines = %d",nqbase) ; #undef F #define F(i,j) flar[(i)+(j)*nt] /* nt X nqbase */ if( nqbase > 0 ){ fim = mri_new( nt , nqbase , MRI_float ) ; /* F matrix */ flar = MRI_FLOAT_PTR(fim) ; bb = 0 ; if( polort >= 0 ){ /** load polynomial baseline **/ double a = 2.0/(nt-1.0) ; for( jj=0 ; jj <= polort ; jj++ ){ for( ii=0 ; ii < nt ; ii++ ) F(ii,jj) = (float)Plegendre( a*ii-1.0 , jj ) ; } bb = polort+1 ; } #undef Q #define Q(i,j) qar[(i)+(j)*qim->nx] /* qim->nx X qim->ny */ if( fimar != NULL ){ /** load -base baseline columns **/ for( kk=0 ; kk < IMARR_COUNT(fimar) ; kk++ ){ qim = IMARR_SUBIMAGE(fimar,kk) ; qar = MRI_FLOAT_PTR(qim) ; for( jj=0 ; jj < qim->ny ; jj++ ){ for( ii=0 ; ii < nt ; ii++ ) F(ii,bb+jj) = (ii < qim->nx) ? Q(ii,jj) : 0.0f ; } bb += qim->ny ; } DESTROY_IMARR(fimar) ; fimar=NULL ; } /* remove mean from each column after first? */ if( polort >= 0 && nqbase > 1 ){ float sum ; for( jj=1 ; jj < nqbase ; jj++ ){ sum = 0.0f ; for( ii=0 ; ii < nt ; ii++ ) sum += F(ii,jj) ; sum /= nt ; for( ii=0 ; ii < nt ; ii++ ) F(ii,jj) -= sum ; } } /* compute pseudo-inverse of baseline matrix, so we can project it out from the data time series */ /* -1 */ /* (F'F) F' matrix */ INFO_message("Computing pseudo-inverse of baseline matrix F") ; pfim = mri_matrix_psinv(fim,NULL,0.0f) ; par = MRI_FLOAT_PTR(pfim) ; #undef P #define P(i,j) par[(i)+(j)*nqbase] /* nqbase X nt */ #if 0 qim = mri_matrix_transpose(pfim) ; /** save to disk? **/ mri_write_1D( "Fpsinv.1D" , qim ) ; mri_free(qim) ; #endif } /**--- set up map image into aim/aar = A matrix ---**/ #undef GOOD #define GOOD(i) (mask==NULL || mask[i]) #undef A #define A(i,j) aar[(i)+(j)*nvox] /* nvox X nparam */ INFO_message("Loading map matrix A") ; aim = mri_new( nvox , nparam , MRI_float ); aar = MRI_FLOAT_PTR(aim); for( jj=0 ; jj < nparam ; jj++ ){ for( ii=kk=0 ; ii < nxyz ; ii++ ){ if( GOOD(ii) ){ A(kk,jj) = THD_get_voxel(aset,ii,jj); kk++; } }} DSET_unload(aset) ; /**--- set up map weight into wim/war ---**/ #undef WT #define WT(i,j) war[(i)+(j)*nvox] /* nvox X nparam */ if( wset != NULL ){ int numneg=0 , numpos=0 ; float fac ; INFO_message("Loading map weight matrix") ; wim = mri_new( nvox , nwt , MRI_float ) ; war = MRI_FLOAT_PTR(wim) ; for( jj=0 ; jj < nwt ; jj++ ){ for( ii=kk=0 ; ii < nxyz ; ii++ ){ if( GOOD(ii) ){ WT(kk,jj) = THD_get_voxel(wset,ii,jj); if( WT(kk,jj) > 0.0f ){ numpos++; WT(kk,jj) = sqrt(WT(kk,jj)); } else if( WT(kk,jj) < 0.0f ){ numneg++; WT(kk,jj) = 0.0f; } kk++; } }} DSET_unload(wset) ; if( numpos <= nparam ) WARNING_message("Only %d positive weights found in -wtmap!",numpos) ; if( numneg > 0 ) WARNING_message("%d negative weights found in -wtmap!",numneg) ; for( jj=0 ; jj < nwt ; jj++ ){ fac = 0.0f ; for( kk=0 ; kk < nvox ; kk++ ) if( WT(kk,jj) > fac ) fac = WT(kk,jj) ; if( fac > 0.0f ){ fac = 1.0f / fac ; for( kk=0 ; kk < nvox ; kk++ ) WT(kk,jj) *= fac ; } } } /**--- set up data image into yim/yar = Y matrix ---**/ #undef Y #define Y(i,j) yar[(i)+(j)*nt] /* nt X nvox */ INFO_message("Loading data matrix Y") ; yim = mri_new( nt , nvox , MRI_float ); yar = MRI_FLOAT_PTR(yim); for( ii=0 ; ii < nt ; ii++ ){ for( jj=kk=0 ; jj < nxyz ; jj++ ){ if( GOOD(jj) ){ Y(ii,kk) = THD_get_voxel(yset,jj,ii); kk++; } }} DSET_unload(yset) ; /**--- project baseline out of data image = Z matrix ---**/ if( pfim != NULL ){ #undef T #define T(i,j) tar[(i)+(j)*nt] /* nt X nvox */ INFO_message("Projecting baseline out of Y") ; qim = mri_matrix_mult( pfim , yim ) ; /* nqbase X nvox */ tim = mri_matrix_mult( fim , qim ) ; /* nt X nvox */ tar = MRI_FLOAT_PTR(tim) ; /* Y projected onto baseline */ for( jj=0 ; jj < nvox ; jj++ ) for( ii=0 ; ii < nt ; ii++ ) Y(ii,jj) -= T(ii,jj) ; mri_free(tim); mri_free(qim); mri_free(pfim); mri_free(fim); } /***** At this point: matrix A is in aim, matrix Z is in yim. Solve for V into vim, using the chosen method *****/ switch( method ){ default: ERROR_exit("Illegal method code! WTF?") ; /* Huh? */ /*.....................................................................*/ case METHOD_C: /**--- compute pseudo-inverse of A map ---**/ INFO_message("Method C: Computing pseudo-inverse of A") ; if( wim != NULL ) WARNING_message("Ignoring -mapwt dataset") ; pfim = mri_matrix_psinv(aim,NULL,alpha) ; /* nparam X nvox */ if( pfim == NULL ) ERROR_exit("mri_matrix_psinv() fails") ; mri_free(aim) ; /**--- and apply to data to get results ---*/ INFO_message("Computing result V") ; vim = mri_matrix_multranB( yim , pfim ) ; /* nt x nparam */ mri_free(pfim) ; mri_free(yim) ; break ; /*.....................................................................*/ case METHOD_K: /**--- compute pseudo-inverse of transposed Z ---*/ INFO_message("Method K: Computing pseudo-inverse of Z'") ; if( nwt > 1 ){ WARNING_message("Ignoring -mapwt dataset: more than 1 sub-brick") ; nwt = 0 ; mri_free(wim) ; wim = NULL ; war = NULL ; } if( nwt == 1 ){ float fac ; for( kk=0 ; kk < nvox ; kk++ ){ fac = war[kk] ; for( ii=0 ; ii < nt ; ii++ ) Y(ii,kk) *= fac ; for( ii=0 ; ii < nparam ; ii++ ) A(kk,ii) *= fac ; } } tim = mri_matrix_transpose(yim) ; mri_free(yim) ; pfim = mri_matrix_psinv(tim,NULL,alpha) ; mri_free(tim) ; if( pfim == NULL ) ERROR_exit("mri_matrix_psinv() fails") ; INFO_message("Computing W") ; tim = mri_matrix_mult( pfim , aim ) ; mri_free(aim) ; mri_free(pfim) ; INFO_message("Computing result V") ; pfim = mri_matrix_psinv(tim,NULL,0.0f) ; mri_free(tim) ; vim = mri_matrix_transpose(pfim) ; mri_free(pfim); break ; } /* end of switch on method */ if( wim != NULL ) mri_free(wim) ; /**--- smooth? ---**/ if( nfir > 0 && vim->nx > nfir ){ INFO_message("FIR-5-ing result") ; var = MRI_FLOAT_PTR(vim) ; for( jj=0 ; jj < vim->ny ; jj++ ) linear_filter_reflect( nfir,firwt , vim->nx , var + (jj*vim->nx) ) ; } if( nmed > 0 && vim->nx > nmed ){ INFO_message("Median-5-ing result") ; var = MRI_FLOAT_PTR(vim) ; for( jj=0 ; jj < vim->ny ; jj++ ) median5_filter_reflect( vim->nx , var + (jj*vim->nx) ) ; } /**--- write results ---**/ INFO_message("Writing result to '%s'",fname_out) ; mri_write_1D( fname_out , vim ) ; exit(0) ; }
int main( int argc , char * argv[] ) { Widget rc , lab ; int ww , uu ; if( argc < 2 || strcmp(argv[1],"-help") == 0 ){ printf("Usage: Xphace im1 [im2]\n" "Interactive image mergerizing via FFTs.\n" "Image files are in PGM or JPEG format.\n") ; exit(0) ; } mainENTRY("Xphace main") ; machdep() ; ww = PH_loadim( argv[1] ) ; if( ww < 0 ) exit(1) ; if( argc > 2 ){ ww = PH_loadim( argv[2] ) ; if( ww < 0 ) exit(1) ; } else { PH_loadim( "noise=1" ) ; } MAIN_shell = XtVaAppInitialize( &MAIN_app , "AFNI" , NULL , 0 , &argc , argv , FALLback , NULL ) ; if( MAIN_shell == NULL ){ fprintf(stderr,"\n*** Cannot initialize X11 ***\n") ; exit(1) ; } MAIN_dc = MCW_new_DC( MAIN_shell , 32 , 0 , NULL,NULL , 1.0 , 0 ) ; XtVaSetValues( XmGetXmDisplay(XtDisplay(MAIN_shell)) , XmNdragInitiatorProtocolStyle , XmDRAG_NONE , XmNdragReceiverProtocolStyle , XmDRAG_NONE , NULL ) ; MAIN_rc = XtVaCreateWidget( "AFNI" , xmRowColumnWidgetClass , MAIN_shell , XmNpacking , XmPACK_TIGHT , XmNorientation , XmVERTICAL , XmNtraversalOn , True , NULL ) ; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ rc = XtVaCreateWidget( "AFNI" , xmRowColumnWidgetClass , MAIN_rc , XmNpacking , XmPACK_TIGHT , XmNorientation , XmHORIZONTAL , XmNtraversalOn , True , NULL ) ; lab = XtVaCreateManagedWidget( "AFNI" , xmLabelWidgetClass , rc , LABEL_ARG( "Magn. " ) , XmNmarginHeight, 0 , XmNmarginWidth , 0 , NULL ) ; MAGN_scale = XtVaCreateManagedWidget( "AFNI" , xmScaleWidgetClass , rc , XmNminimum , 0 , XmNmaximum , 100 , XmNvalue , 0 , XmNwidth , P_swide , XmNshowValue , True , XmNscaleMultiple , 10 , XmNorientation , XmHORIZONTAL , XmNtraversalOn , True , NULL ) ; XtAddCallback( MAGN_scale , XmNvalueChangedCallback , PH_scale_CB , NULL ) ; XtManageChild( rc ) ; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ rc = XtVaCreateWidget( "AFNI" , xmRowColumnWidgetClass , MAIN_rc , XmNpacking , XmPACK_TIGHT , XmNorientation , XmHORIZONTAL , XmNtraversalOn , True , NULL ) ; lab = XtVaCreateManagedWidget( "AFNI" , xmLabelWidgetClass , rc , LABEL_ARG( "Phase " ) , XmNmarginHeight, 0 , XmNmarginWidth , 0 , NULL ) ; PHASE_scale = XtVaCreateManagedWidget( "AFNI" , xmScaleWidgetClass , rc , XmNminimum , 0 , XmNmaximum , 100 , XmNvalue , 0 , XmNwidth , P_swide , XmNshowValue , True , XmNscaleMultiple , 10 , XmNorientation , XmHORIZONTAL , XmNtraversalOn , True , NULL ) ; XtAddCallback( PHASE_scale , XmNvalueChangedCallback , PH_scale_CB , NULL ) ; XtManageChild( rc ) ; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ XtManageChild( MAIN_rc ) ; XtRealizeWidget( MAIN_shell ) ; NI_sleep(1) ; #if 0 XtVaSetValues( MAIN_rc , XmNwidth , P_swide , NULL ) ; XtVaSetValues( MAGN_scale , XmNwidth , P_swide , NULL ) ; XtVaSetValues( PHASE_scale , XmNwidth , P_swide , NULL ) ; #endif XtVaSetValues( MAIN_shell , XmNmwmDecorations, MWM_DECOR_BORDER | MWM_DECOR_TITLE | MWM_DECOR_MENU , XmNmwmFunctions , MWM_FUNC_MOVE | MWM_FUNC_CLOSE , XmNtitle , "Xphace Controls" , NULL ) ; (void) XtAppAddTimeOut( MAIN_app , 1234 , PH_startup_timeout_CB , NULL ) ; XtAppMainLoop( MAIN_app ) ; exit(0) ; }
int main( int argc , char *argv[] ) { THD_3dim_dataset *inset=NULL , *outset ; THD_3dim_dataset **insar=NULL ; int nsar=0 ; int iarg=1 , ii,kk , ids ; MCW_cluster *nbhd=NULL ; char *prefix="./localhistog" ; int ntype=0 ; float na=0.0f,nb=0.0f,nc=0.0f ; int verb=1 , do_prob=0 ; int nx=0,ny=0,nz=0,nvox=0, rbot,rtop ; char *labfile=NULL ; NI_element *labnel=NULL ; int nlab=0 , *labval=NULL ; char **lablab=NULL ; char buf[THD_MAX_SBLABEL] ; UINT32 *ohist , *mhist=NULL ; char *ohist_name=NULL ; int ohzadd=0 ; int *rlist , numval ; float mincount=0.0f ; int mcc ; int *exlist=NULL, numex=0 ; int do_excNONLAB=0 ; /*---- for the clueless who wish to become clued-in ----*/ if( argc == 1 ){ usage_3dLocalHistog(1); exit(0); } /* Bob's help shortcut */ /*---- official startup ---*/ #if defined(USING_MCW_MALLOC) && !defined(USE_OMP) enable_mcw_malloc() ; #endif PRINT_VERSION("3dLocalHistog"); mainENTRY("3dLocalHistog main"); machdep(); AFNI_logger("3dLocalHistog",argc,argv); if( getpid()%2 ) AUTHOR("Bilbo Baggins"); else AUTHOR("Thorin Oakenshield"); AFNI_SETUP_OMP(0) ; /* 24 Jun 2013 */ /*---- loop over options ----*/ while( iarg < argc && argv[iarg][0] == '-' ){ if( strcmp(argv[iarg],"-help") == 0 || strcmp(argv[iarg],"-h") == 0){ usage_3dLocalHistog(strlen(argv[iarg])>3 ? 2:1); exit(0); } if( strncmp(argv[iarg],"-qu",3) == 0 ){ verb = 0 ; iarg++ ; continue ; } if( strncmp(argv[iarg],"-verb",5) == 0 ){ verb++ ; iarg++ ; continue ; } #ifdef ALLOW_PROB if( strncmp(argv[iarg],"-prob",5) == 0 ){ do_prob = 1 ; iarg++ ; continue ; } #endif if( strcmp(argv[iarg],"-exclude") == 0 ){ int ebot=-6666666,etop=-6666666 , ee ; if( ++iarg >= argc ) ERROR_exit("Need argument after '-exclude'") ; sscanf(argv[iarg],"%d..%d",&ebot,&etop) ; if( ebot >= -TWO15 && ebot <= TWO15 ){ if( etop < -TWO15 || etop > TWO15 || etop < ebot ) etop = ebot ; exlist = (int *)realloc(exlist,sizeof(int)*(etop-ebot+1+numex+1)) ; for( ee=ebot ; ee <= etop ; ee++ ){ if( ee != 0 ) exlist[numex++] = ee ; } } iarg++ ; continue ; } if( strcmp(argv[iarg],"-excNONLAB") == 0 ){ do_excNONLAB = 1 ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-prefix") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '-prefix'") ; prefix = strdup(argv[iarg]) ; if( !THD_filename_ok(prefix) ) ERROR_exit("Bad -prefix!") ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-hsave") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '-hsave'") ; ohist_name = strdup(argv[iarg]) ; if( !THD_filename_ok(ohist_name) ) ERROR_exit("Bad -hsave!") ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-mincount") == 0 ){ char *cpt ; if( ++iarg >= argc ) ERROR_exit("Need argument after '-mincount'") ; mincount = (float)strtod(argv[iarg],&cpt) ; #if 0 if( mincount > 0.0f && mincount < 50.0f && *cpt == '%' ) /* percentage */ mincount = -0.01f*mincount ; #endif iarg++ ; continue ; } if( strcmp(argv[iarg],"-nbhd") == 0 ){ char *cpt ; if( ntype > 0 ) ERROR_exit("Can't have 2 '-nbhd' options") ; if( ++iarg >= argc ) ERROR_exit("Need argument after '-nbhd'") ; cpt = argv[iarg] ; if( strncasecmp(cpt,"SPHERE",6) == 0 ){ sscanf( cpt+7 , "%f" , &na ) ; ntype = NTYPE_SPHERE ; } else if( strncasecmp(cpt,"RECT",4) == 0 ){ sscanf( cpt+5 , "%f,%f,%f" , &na,&nb,&nc ) ; if( na == 0.0f && nb == 0.0f && nc == 0.0f ) ERROR_exit("'RECT(0,0,0)' is not a legal neighborhood") ; ntype = NTYPE_RECT ; } else if( strncasecmp(cpt,"RHDD",4) == 0 ){ sscanf( cpt+5 , "%f" , &na ) ; if( na == 0.0f ) ERROR_exit("Can't have a RHDD of radius 0") ; ntype = NTYPE_RHDD ; } else if( strncasecmp(cpt,"TOHD",4) == 0 ){ sscanf( cpt+5 , "%f" , &na ) ; if( na == 0.0f ) ERROR_exit("Can't have a TOHD of radius 0") ; ntype = NTYPE_TOHD ; } else { ERROR_exit("Unknown -nbhd shape: '%s'",cpt) ; } iarg++ ; continue ; } if( strcmp(argv[iarg],"-lab_file") == 0 || strcmp(argv[iarg],"-labfile") == 0 ){ char **labnum ; int nbad=0 ; if( ++iarg >= argc ) ERROR_exit("Need argument after '%s'",argv[iarg-1]) ; if( labfile != NULL ) ERROR_exit("Can't use '%s' twice!",argv[iarg-1]) ; labfile = strdup(argv[iarg]) ; labnel = THD_string_table_read(labfile,0) ; if( labnel == NULL || labnel->vec_num < 2 ) ERROR_exit("Can't read label file '%s'",labfile) ; nlab = labnel->vec_len ; labnum = (char **)labnel->vec[0] ; lablab = (char **)labnel->vec[1] ; labval = (int *)calloc(sizeof(int),nlab) ; for( ii=0 ; ii < nlab ; ii++ ){ if( labnum[ii] != NULL ){ labval[ii] = (int)strtod(labnum[ii],NULL) ; if( labval[ii] < -TWO15 || labval[ii] > TWO15 ){ labval[ii] = 0; nbad++; } } } if( nbad > 0 ) ERROR_message("%d label values are outside the range %d..%d :-(" , nbad , -TWO15 , TWO15 ) ; iarg++ ; continue ; } ERROR_message("** 3dLocalHistog: Illegal option: '%s'",argv[iarg]) ; suggest_best_prog_option(argv[0], argv[iarg]); exit(1) ; } /*--- end of loop over options ---*/ /*---- check for stupid user inputs ----*/ if( iarg >= argc ) ERROR_exit("No datasets on command line?") ; if( ohist_name == NULL && strcmp(prefix,"NULL") == 0 ) ERROR_exit("-prefix NULL is only meaningful if you also use -hsave :-(") ; /*------------ scan input datasets, built overall histogram ------------*/ nsar = argc - iarg ; insar = (THD_3dim_dataset **)malloc(sizeof(THD_3dim_dataset *)*nsar) ; if( verb ) fprintf(stderr,"Scanning %d datasets ",nsar) ; ohist = (UINT32 *)calloc(sizeof(UINT32),TWO16) ; for( ids=iarg ; ids < argc ; ids++ ){ /* dataset loop */ insar[ids-iarg] = inset = THD_open_dataset(argv[ids]) ; CHECK_OPEN_ERROR(inset,argv[ids]) ; if( ids == iarg ){ nx = DSET_NX(inset); ny = DSET_NY(inset); nz = DSET_NZ(inset); nvox = nx*ny*nz; } else if( nx != DSET_NX(inset) || ny != DSET_NY(inset) || nz != DSET_NZ(inset) ){ ERROR_exit("Dataset %s grid doesn't match!",argv[ids]) ; } if( !THD_datum_constant(inset->dblk) ) ERROR_exit("Dataset %s doesn't have a fixed data type! :-(",argv[ids]) ; if( THD_need_brick_factor(inset) ) ERROR_exit("Dataset %s has scale factors! :-(",argv[ids]) ; if( DSET_BRICK_TYPE(inset,0) != MRI_byte && DSET_BRICK_TYPE(inset,0) != MRI_short && DSET_BRICK_TYPE(inset,0) != MRI_float ) ERROR_exit("Dataset %s is not byte- or short-valued! :-(",argv[ids]) ; DSET_load(inset) ; CHECK_LOAD_ERROR(inset) ; for( ii=0 ; ii < DSET_NVALS(inset) ; ii++ ){ /* add to overall histogram */ if( verb ) fprintf(stderr,".") ; switch( DSET_BRICK_TYPE(inset,ii) ){ case MRI_short:{ short *sar = (short *)DSET_BRICK_ARRAY(inset,ii) ; for( kk=0 ; kk < nvox ; kk++ ) ohist[ sar[kk]+TWO15 ]++ ; } break ; case MRI_byte:{ byte *bar = (byte *)DSET_BRICK_ARRAY(inset,ii) ; for( kk=0 ; kk < nvox ; kk++ ) ohist[ bar[kk]+TWO15 ]++ ; } break ; case MRI_float:{ float *far = (float *)DSET_BRICK_ARRAY(inset,ii) ; short ss ; for( kk=0 ; kk < nvox ; kk++ ){ ss = SHORTIZE(far[kk]); ohist[ss+TWO15]++; } } break ; } } /* end of sub-brick loop */ DSET_unload(inset) ; /* will re-load later, as needed */ } /* end of dataset loop */ if( verb ) fprintf(stderr,"\n") ; /*-------------- process overall histogram for fun and profit -------------*/ /* if we didn't actually find 0, put it in the histogram now */ if( ohist[0+TWO15] == 0 ){ ohist[0+TWO15] = 1 ; ohzadd = 1 ; } /* excNONLAB? */ if( nlab > 0 && do_excNONLAB ){ byte *klist = (byte *)calloc(sizeof(byte),TWO16) ; int nee ; for( ii=0 ; ii < nlab ; ii++ ){ if( labval[ii] != 0 ) klist[labval[ii]+TWO15] = 1 ; } for( nee=ii=0 ; ii < TWO16 ; ii++ ){ if( !klist[ii] ) nee++ ; } exlist = (int *)realloc(exlist,sizeof(int)*(numex+nee+1)) ; for( ii=0 ; ii < TWO16 ; ii++ ){ if( ii != TWO15 && !klist[ii] ) exlist[numex++] = ii-TWO15 ; } free(klist) ; } /* make a copy of ohist and edit it for mincount, etc */ mhist = (UINT32 *)malloc(sizeof(UINT32)*TWO16) ; memcpy(mhist,ohist,sizeof(UINT32)*TWO16) ; mcc = (mincount < 0.0f) ? (int)(-mincount*nvox) : (int)mincount ; if( mcc > 1 ){ for( ids=ii=0 ; ii < TWO16 ; ii++ ){ if( ii != TWO15 && mhist[ii] > 0 && mhist[ii] < mcc ){ mhist[ii] = 0; ids++; } } if( ids > 0 && verb ) INFO_message("Edited out %d values with overall histogram counts less than %d",ids,mcc) ; } if( numex > 0 ){ int ee ; for( ids=0,ii=0 ; ii < numex ; ii++ ){ ee = exlist[ii] ; if( mhist[ee+TWO15] > 0 ){ mhist[ee+TWO15] = 0; ids++; } } free(exlist) ; if( ids > 0 && verb ) INFO_message("Edited out %d values from the exclude list",ids) ; } /* count number of values with nonzero (edited) counts */ numval = 0 ; for( ii=0 ; ii < TWO16 ; ii++ ) if( mhist[ii] != 0 ) numval++ ; if( numval == 0 ) ERROR_exit("Nothing found! WTF?") ; /* should not happen */ /* make list of all values with nonzero (edited) count */ rlist = (int *)malloc(sizeof(int)*numval) ; if( verb > 1 ) fprintf(stderr,"++ Include list:") ; for( ii=kk=0 ; ii < TWO16 ; ii++ ){ if( mhist[ii] != 0 ){ rlist[kk++] = ii-TWO15 ; if( verb > 1 ) fprintf(stderr," %d[%u]",ii-TWO15,mhist[ii]) ; } } if( verb > 1 ) fprintf(stderr,"\n") ; rbot = rlist[0] ; rtop = rlist[numval-1] ; /* smallest and largest values found */ if( rbot == rtop ) ERROR_exit("Only one value (%d) found in all inputs!",rbot) ; /* if 0 isn't first in rlist, then put it in first place and move negative values up by one spot */ if( rbot < 0 ){ for( kk=0 ; kk < numval && rlist[kk] != 0 ; kk++ ) ; /*nada*/ if( kk < numval ){ /* should always be true */ for( ii=kk-1 ; ii >= 0 ; ii-- ) rlist[ii+1] = rlist[ii] ; rlist[0] = 0 ; } } if( verb ) INFO_message("Value range = %d..%d (%d distinct values)",rbot,rtop,numval ); /* save overall histogram? */ if( ohist_name != NULL ){ FILE *fp = fopen(ohist_name,"w") ; int nl=0 ; if( fp == NULL ) ERROR_exit("Can't open -hsave '%s' for output!",ohist_name) ; if( ohzadd ) ohist[0+TWO15] = 0 ; for( ii=0 ; ii < TWO16 ; ii++ ){ if( ohist[ii] != 0 ){ fprintf(fp,"%6d %u\n",ii-TWO15,ohist[ii]); nl++; } } fclose(fp) ; if( verb ) INFO_message("Wrote %d lines to -hsave file %s",nl,ohist_name) ; } free(ohist) ; free(mhist) ; mhist = ohist = NULL ; /* done with this */ if( strcmp(prefix,"NULL") == 0 ) exit(0) ; /* special case */ /*----------- build the neighborhood mask -----------*/ if( ntype <= 0 ){ /* default neighborhood */ ntype = NTYPE_SPHERE ; na = 0.0f ; if( verb ) INFO_message("Using default neighborhood = self") ; } switch( ntype ){ default: ERROR_exit("WTF? ntype=%d",ntype) ; /* should not happen */ case NTYPE_SPHERE:{ float dx , dy , dz ; if( na < 0.0f ){ dx = dy = dz = 1.0f ; na = -na ; } else { dx = fabsf(DSET_DX(insar[0])) ; dy = fabsf(DSET_DY(insar[0])) ; dz = fabsf(DSET_DZ(insar[0])) ; } nbhd = MCW_spheremask( dx,dy,dz , na ) ; } break ; case NTYPE_RECT:{ float dx , dy , dz ; if( na < 0.0f ){ dx = 1.0f; na = -na; } else dx = fabsf(DSET_DX(insar[0])); if( nb < 0.0f ){ dy = 1.0f; nb = -nb; } else dy = fabsf(DSET_DY(insar[0])); if( nc < 0.0f ){ dz = 1.0f; nc = -nc; } else dz = fabsf(DSET_DZ(insar[0])); nbhd = MCW_rectmask( dx,dy,dz , na,nb,nc ) ; } break ; case NTYPE_RHDD:{ float dx , dy , dz ; if( na < 0.0f ){ dx = dy = dz = 1.0f ; na = -na ; } else { dx = fabsf(DSET_DX(insar[0])) ; dy = fabsf(DSET_DY(insar[0])) ; dz = fabsf(DSET_DZ(insar[0])) ; } nbhd = MCW_rhddmask( dx,dy,dz , na ) ; } break ; case NTYPE_TOHD:{ float dx , dy , dz ; if( na < 0.0f ){ dx = dy = dz = 1.0f ; na = -na ; } else { dx = fabsf(DSET_DX(insar[0])) ; dy = fabsf(DSET_DY(insar[0])) ; dz = fabsf(DSET_DZ(insar[0])) ; } nbhd = MCW_tohdmask( dx,dy,dz , na ) ; } break ; } if( verb ) INFO_message("Neighborhood comprises %d voxels",nbhd->num_pt) ; /*------- actually do some work for a change (is it lunchtime yet?) -------*/ if( verb ) fprintf(stderr,"Voxel-wise histograms ") ; outset = THD_localhistog( nsar,insar , numval,rlist , nbhd , do_prob,verb ) ; if( outset == NULL ) ERROR_exit("Function THD_localhistog() fails?!") ; /*---- save resulting dataset ----*/ EDIT_dset_items( outset , ADN_prefix,prefix , ADN_none ) ; tross_Copy_History( insar[0] , outset ) ; tross_Make_History( "3dLocalHistog" , argc,argv , outset ) ; /* but first attach labels to sub-bricks */ EDIT_BRICK_LABEL(outset,0,"0:Other") ; for( kk=1 ; kk < numval ; kk++ ){ sprintf(buf,"%d:",rlist[kk]) ; for( ii=0 ; ii < nlab ; ii++ ){ if( labval[ii] == rlist[kk] && lablab[ii] != NULL ){ ids = strlen(buf) ; MCW_strncpy(buf+ids,lablab[ii],THD_MAX_SBLABEL-ids) ; break ; } } EDIT_BRICK_LABEL(outset,kk,buf) ; } DSET_write( outset ) ; if( verb ) WROTE_DSET( outset ) ; exit(0) ; }
int main( int argc , char *argv[] ) { MRI_shindss *shd ; int ids , nopt , kk ; char *prefix = "EIC" ; char *fname=NULL , *buf ; MRI_vectim *mv ; THD_3dim_dataset *dset ; /*--- official AFNI startup stuff ---*/ mainENTRY("3dExtractGroupInCorr"); machdep(); AFNI_logger("3dExtractGroupInCorr",argc,argv); PRINT_VERSION("3dExtractGroupInCorr"); AUTHOR("RW Cox"); /*-- process options --*/ nopt = 1 ; while( nopt < argc && argv[nopt][0] == '-' ){ if( strcasecmp(argv[nopt],"-prefix") == 0 ){ nopt++ ; if( strcasecmp(argv[nopt],"NULL") == 0 ) prefix = NULL ; else prefix = strdup(argv[nopt]) ; nopt++ ; continue ; } ERROR_message("Unknown option: '%s'",argv[nopt]) ; suggest_best_prog_option(argv[0], argv[nopt]); exit(1); } if( argc < 2 ){ usage_3dExtractGroupInCorr(2) ; exit(0) ; } /* check for errors */ if( nopt >= argc ) ERROR_exit("No input filename on command line?!") ; /*-- read input file --*/ fname = strdup(argv[nopt]) ; if( STRING_HAS_SUFFIX(fname,".data") ){ strcpy(fname+strlen(fname)-5,".niml") ; WARNING_message("EIC: Replaced '.data' with '.niml' in filename") ; } else if( STRING_HAS_SUFFIX(fname,".grpincorr") ){ fname = (char *)realloc(fname,strlen(fname)+16) ; strcat(fname,".niml") ; INFO_message("EIC: Added '.niml' to end of filename") ; } else if( STRING_HAS_SUFFIX(fname,".grpincorr.") ){ fname = (char *)realloc(fname,strlen(fname)+16) ; strcat(fname,"niml") ; INFO_message("EIC: Added 'niml' to end of filename") ; } shd = GRINCOR_read_input( fname ) ; if( shd == NULL ) ERROR_exit("EIC: Cannot continue after input error") ; INFO_message("EIC: file opened, contains %d datasets, %d time series, %s bytes", shd->ndset , shd->nvec , commaized_integer_string(shd->nbytes) ) ; /*-- process input file --*/ fprintf(stderr,"++ %d datasets: ",shd->ndset) ; for( ids=0 ; ids < shd->ndset ; ids++ ){ fprintf(stderr,"%d",ids+1) ; dset = GRINCOR_extract_dataset( shd, ids, prefix ) ; fprintf(stderr,".") ; DSET_write(dset) ; DSET_delete(dset) ; } fprintf(stderr,"\n") ; exit(0) ; }
int main( int argc , char * argv[] ) { int do_norm=0 , qdet=2 , have_freq=0 , do_automask=0 ; float dt=0.0f , fbot=0.0f,ftop=999999.9f , blur=0.0f ; MRI_IMARR *ortar=NULL ; MRI_IMAGE *ortim=NULL ; THD_3dim_dataset **ortset=NULL ; int nortset=0 ; THD_3dim_dataset *inset=NULL , *outset ; char *prefix="bandpass" ; byte *mask=NULL ; int mask_nx=0,mask_ny=0,mask_nz=0,nmask , verb=1 , nx,ny,nz,nvox , nfft=0 , kk ; float **vec , **ort=NULL ; int nort=0 , vv , nopt , ntime ; MRI_vectim *mrv ; float pvrad=0.0f ; int nosat=0 ; int do_despike=0 ; /*-- help? --*/ AFNI_SETUP_OMP(0) ; /* 24 Jun 2013 */ if( argc < 2 || strcmp(argv[1],"-help") == 0 ){ printf( "\n" "** NOTA BENE: For the purpose of preparing resting-state FMRI datasets **\n" "** for analysis (e.g., with 3dGroupInCorr), this program is now mostly **\n" "** superseded by the afni_proc.py script. See the 'afni_proc.py -help' **\n" "** section 'Resting state analysis (modern)' to get our current rs-FMRI **\n" "** pre-processing recommended sequence of steps. -- RW Cox, et alii. **\n" "\n" "Usage: 3dBandpass [options] fbot ftop dataset\n" "\n" "* One function of this program is to prepare datasets for input\n" " to 3dSetupGroupInCorr. Other uses are left to your imagination.\n" "\n" "* 'dataset' is a 3D+time sequence of volumes\n" " ++ This must be a single imaging run -- that is, no discontinuities\n" " in time from 3dTcat-ing multiple datasets together.\n" "\n" "* fbot = lowest frequency in the passband, in Hz\n" " ++ fbot can be 0 if you want to do a lowpass filter only;\n" " HOWEVER, the mean and Nyquist freq are always removed.\n" "\n" "* ftop = highest frequency in the passband (must be > fbot)\n" " ++ if ftop > Nyquist freq, then it's a highpass filter only.\n" "\n" "* Set fbot=0 and ftop=99999 to do an 'allpass' filter.\n" " ++ Except for removal of the 0 and Nyquist frequencies, that is.\n" "\n" "* You cannot construct a 'notch' filter with this program!\n" " ++ You could use 3dBandpass followed by 3dcalc to get the same effect.\n" " ++ If you are understand what you are doing, that is.\n" " ++ Of course, that is the AFNI way -- if you don't want to\n" " understand what you are doing, use Some other PrograM, and\n" " you can still get Fine StatisticaL maps.\n" "\n" "* 3dBandpass will fail if fbot and ftop are too close for comfort.\n" " ++ Which means closer than one frequency grid step df,\n" " where df = 1 / (nfft * dt) [of course]\n" "\n" "* The actual FFT length used will be printed, and may be larger\n" " than the input time series length for the sake of efficiency.\n" " ++ The program will use a power-of-2, possibly multiplied by\n" " a power of 3 and/or 5 (up to and including the 3rd power of\n" " each of these: 3, 9, 27, and 5, 25, 125).\n" "\n" "* Note that the results of combining 3dDetrend and 3dBandpass will\n" " depend on the order in which you run these programs. That's why\n" " 3dBandpass has the '-ort' and '-dsort' options, so that the\n" " time series filtering can be done properly, in one place.\n" "\n" "* The output dataset is stored in float format.\n" "\n" "* The order of processing steps is the following (most are optional):\n" " (0) Check time series for initial transients [does not alter data]\n" " (1) Despiking of each time series\n" " (2) Removal of a constant+linear+quadratic trend in each time series\n" " (3) Bandpass of data time series\n" " (4) Bandpass of -ort time series, then detrending of data\n" " with respect to the -ort time series\n" " (5) Bandpass and de-orting of the -dsort dataset,\n" " then detrending of the data with respect to -dsort\n" " (6) Blurring inside the mask [might be slow]\n" " (7) Local PV calculation [WILL be slow!]\n" " (8) L2 normalization [will be fast.]\n" "\n" "--------\n" "OPTIONS:\n" "--------\n" " -despike = Despike each time series before other processing.\n" " ++ Hopefully, you don't actually need to do this,\n" " which is why it is optional.\n" " -ort f.1D = Also orthogonalize input to columns in f.1D\n" " ++ Multiple '-ort' options are allowed.\n" " -dsort fset = Orthogonalize each voxel to the corresponding\n" " voxel time series in dataset 'fset', which must\n" " have the same spatial and temporal grid structure\n" " as the main input dataset.\n" " ++ At present, only one '-dsort' option is allowed.\n" " -nodetrend = Skip the quadratic detrending of the input that\n" " occurs before the FFT-based bandpassing.\n" " ++ You would only want to do this if the dataset\n" " had been detrended already in some other program.\n" " -dt dd = set time step to 'dd' sec [default=from dataset header]\n" " -nfft N = set the FFT length to 'N' [must be a legal value]\n" " -norm = Make all output time series have L2 norm = 1\n" " ++ i.e., sum of squares = 1\n" " -mask mset = Mask dataset\n" " -automask = Create a mask from the input dataset\n" " -blur fff = Blur (inside the mask only) with a filter\n" " width (FWHM) of 'fff' millimeters.\n" " -localPV rrr = Replace each vector by the local Principal Vector\n" " (AKA first singular vector) from a neighborhood\n" " of radius 'rrr' millimiters.\n" " ++ Note that the PV time series is L2 normalized.\n" " ++ This option is mostly for Bob Cox to have fun with.\n" "\n" " -input dataset = Alternative way to specify input dataset.\n" " -band fbot ftop = Alternative way to specify passband frequencies.\n" "\n" " -prefix ppp = Set prefix name of output dataset.\n" " -quiet = Turn off the fun and informative messages. (Why?)\n" "\n" " -notrans = Don't check for initial positive transients in the data:\n" " *OR* ++ The test is a little slow, so skipping it is OK,\n" " -nosat if you KNOW the data time series are transient-free.\n" " ++ Or set AFNI_SKIP_SATCHECK to YES.\n" " ++ Initial transients won't be handled well by the\n" " bandpassing algorithm, and in addition may seriously\n" " contaminate any further processing, such as inter-voxel\n" " correlations via InstaCorr.\n" " ++ No other tests are made [yet] for non-stationary behavior\n" " in the time series data.\n" ) ; PRINT_AFNI_OMP_USAGE( "3dBandpass" , "* At present, the only part of 3dBandpass that is parallelized is the\n" " '-blur' option, which processes each sub-brick independently.\n" ) ; PRINT_COMPILE_DATE ; exit(0) ; } /*-- startup --*/ mainENTRY("3dBandpass"); machdep(); AFNI_logger("3dBandpass",argc,argv); PRINT_VERSION("3dBandpass"); AUTHOR("RW Cox"); nosat = AFNI_yesenv("AFNI_SKIP_SATCHECK") ; nopt = 1 ; while( nopt < argc && argv[nopt][0] == '-' ){ if( strcmp(argv[nopt],"-despike") == 0 ){ /* 08 Oct 2010 */ do_despike++ ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-nfft") == 0 ){ int nnup ; if( ++nopt >= argc ) ERROR_exit("need an argument after -nfft!") ; nfft = (int)strtod(argv[nopt],NULL) ; nnup = csfft_nextup_even(nfft) ; if( nfft < 16 || nfft != nnup ) ERROR_exit("value %d after -nfft is illegal! Next legal value = %d",nfft,nnup) ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-blur") == 0 ){ if( ++nopt >= argc ) ERROR_exit("need an argument after -blur!") ; blur = strtod(argv[nopt],NULL) ; if( blur <= 0.0f ) WARNING_message("non-positive blur?!") ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-localPV") == 0 ){ if( ++nopt >= argc ) ERROR_exit("need an argument after -localpv!") ; pvrad = strtod(argv[nopt],NULL) ; if( pvrad <= 0.0f ) WARNING_message("non-positive -localpv?!") ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-prefix") == 0 ){ if( ++nopt >= argc ) ERROR_exit("need an argument after -prefix!") ; prefix = strdup(argv[nopt]) ; if( !THD_filename_ok(prefix) ) ERROR_exit("bad -prefix option!") ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-automask") == 0 ){ if( mask != NULL ) ERROR_exit("Can't use -mask AND -automask!") ; do_automask = 1 ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-mask") == 0 ){ THD_3dim_dataset *mset ; if( ++nopt >= argc ) ERROR_exit("Need argument after '-mask'") ; if( mask != NULL || do_automask ) ERROR_exit("Can't have two mask inputs") ; mset = THD_open_dataset( argv[nopt] ) ; CHECK_OPEN_ERROR(mset,argv[nopt]) ; DSET_load(mset) ; CHECK_LOAD_ERROR(mset) ; mask_nx = DSET_NX(mset); mask_ny = DSET_NY(mset); mask_nz = DSET_NZ(mset); mask = THD_makemask( mset , 0 , 0.5f, 0.0f ) ; DSET_delete(mset) ; if( mask == NULL ) ERROR_exit("Can't make mask from dataset '%s'",argv[nopt]) ; nmask = THD_countmask( mask_nx*mask_ny*mask_nz , mask ) ; if( verb ) INFO_message("Number of voxels in mask = %d",nmask) ; if( nmask < 1 ) ERROR_exit("Mask is too small to process") ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-norm") == 0 ){ do_norm = 1 ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-quiet") == 0 ){ verb = 0 ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-notrans") == 0 || strcmp(argv[nopt],"-nosat") == 0 ){ nosat = 1 ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-ort") == 0 ){ if( ++nopt >= argc ) ERROR_exit("need an argument after -ort!") ; if( ortar == NULL ) INIT_IMARR(ortar) ; ortim = mri_read_1D( argv[nopt] ) ; if( ortim == NULL ) ERROR_exit("can't read from -ort '%s'",argv[nopt]) ; mri_add_name(argv[nopt],ortim) ; ADDTO_IMARR(ortar,ortim) ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-dsort") == 0 ){ THD_3dim_dataset *qset ; if( ++nopt >= argc ) ERROR_exit("need an argument after -dsort!") ; if( nortset > 0 ) ERROR_exit("only 1 -dsort option is allowed!") ; qset = THD_open_dataset(argv[nopt]) ; CHECK_OPEN_ERROR(qset,argv[nopt]) ; ortset = (THD_3dim_dataset **)realloc(ortset, sizeof(THD_3dim_dataset *)*(nortset+1)) ; ortset[nortset++] = qset ; nopt++ ; continue ; } if( strncmp(argv[nopt],"-nodetrend",6) == 0 ){ qdet = 0 ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-dt") == 0 ){ if( ++nopt >= argc ) ERROR_exit("need an argument after -dt!") ; dt = (float)strtod(argv[nopt],NULL) ; if( dt <= 0.0f ) WARNING_message("value after -dt illegal!") ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-input") == 0 ){ if( inset != NULL ) ERROR_exit("Can't have 2 -input options!") ; if( ++nopt >= argc ) ERROR_exit("need an argument after -input!") ; inset = THD_open_dataset(argv[nopt]) ; CHECK_OPEN_ERROR(inset,argv[nopt]) ; nopt++ ; continue ; } if( strncmp(argv[nopt],"-band",5) == 0 ){ if( ++nopt >= argc-1 ) ERROR_exit("need 2 arguments after -band!") ; if( have_freq ) WARNING_message("second -band option replaces first one!") ; fbot = strtod(argv[nopt++],NULL) ; ftop = strtod(argv[nopt++],NULL) ; have_freq = 1 ; continue ; } ERROR_exit("Unknown option: '%s'",argv[nopt]) ; } /** check inputs for reasonablositiness **/ if( !have_freq ){ if( nopt+1 >= argc ) ERROR_exit("Need frequencies on command line after options!") ; fbot = (float)strtod(argv[nopt++],NULL) ; ftop = (float)strtod(argv[nopt++],NULL) ; } if( inset == NULL ){ if( nopt >= argc ) ERROR_exit("Need input dataset name on command line after options!") ; inset = THD_open_dataset(argv[nopt]) ; CHECK_OPEN_ERROR(inset,argv[nopt]) ; nopt++ ; } DSET_UNMSEC(inset) ; if( fbot < 0.0f ) ERROR_exit("fbot value can't be negative!") ; if( ftop <= fbot ) ERROR_exit("ftop value %g must be greater than fbot value %g!",ftop,fbot) ; ntime = DSET_NVALS(inset) ; if( ntime < 9 ) ERROR_exit("Input dataset is too short!") ; if( nfft <= 0 ){ nfft = csfft_nextup_even(ntime) ; if( verb ) INFO_message("Data length = %d FFT length = %d",ntime,nfft) ; (void)THD_bandpass_set_nfft(nfft) ; } else if( nfft < ntime ){ ERROR_exit("-nfft %d is less than data length = %d",nfft,ntime) ; } else { kk = THD_bandpass_set_nfft(nfft) ; if( kk != nfft && verb ) INFO_message("Data length = %d FFT length = %d",ntime,kk) ; } if( dt <= 0.0f ){ dt = DSET_TR(inset) ; if( dt <= 0.0f ){ WARNING_message("Setting dt=1.0 since input dataset lacks a time axis!") ; dt = 1.0f ; } } if( !THD_bandpass_OK(ntime,dt,fbot,ftop,1) ) ERROR_exit("Can't continue!") ; nx = DSET_NX(inset); ny = DSET_NY(inset); nz = DSET_NZ(inset); nvox = nx*ny*nz; /* check mask, or create it */ if( verb ) INFO_message("Loading input dataset time series" ) ; DSET_load(inset) ; if( mask != NULL ){ if( mask_nx != nx || mask_ny != ny || mask_nz != nz ) ERROR_exit("-mask dataset grid doesn't match input dataset") ; } else if( do_automask ){ mask = THD_automask( inset ) ; if( mask == NULL ) ERROR_message("Can't create -automask from input dataset?") ; nmask = THD_countmask( DSET_NVOX(inset) , mask ) ; if( verb ) INFO_message("Number of voxels in automask = %d",nmask); if( nmask < 1 ) ERROR_exit("Automask is too small to process") ; } else { mask = (byte *)malloc(sizeof(byte)*nvox) ; nmask = nvox ; memset(mask,1,sizeof(byte)*nvox) ; if( verb ) INFO_message("No mask ==> processing all %d voxels",nvox); } /* A simple check of dataset quality [08 Feb 2010] */ if( !nosat ){ float val ; INFO_message( "Checking dataset for initial transients [use '-notrans' to skip this test]") ; val = THD_saturation_check(inset,mask,0,0) ; kk = (int)(val+0.54321f) ; if( kk > 0 ) ININFO_message( "Looks like there %s %d non-steady-state initial time point%s :-(" , ((kk==1) ? "is" : "are") , kk , ((kk==1) ? " " : "s") ) ; else if( val > 0.3210f ) /* don't ask where this threshold comes from! */ ININFO_message( "MAYBE there's an initial positive transient of 1 point, but it's hard to tell\n") ; else ININFO_message("No widespread initial positive transient detected :-)") ; } /* check -dsort inputs for match to inset */ for( kk=0 ; kk < nortset ; kk++ ){ if( DSET_NX(ortset[kk]) != nx || DSET_NY(ortset[kk]) != ny || DSET_NZ(ortset[kk]) != nz || DSET_NVALS(ortset[kk]) != ntime ) ERROR_exit("-dsort %s doesn't match input dataset grid" , DSET_BRIKNAME(ortset[kk]) ) ; } /* convert input dataset to a vectim, which is more fun */ mrv = THD_dset_to_vectim( inset , mask , 0 ) ; if( mrv == NULL ) ERROR_exit("Can't load time series data!?") ; DSET_unload(inset) ; /* similarly for the ort vectors */ if( ortar != NULL ){ for( kk=0 ; kk < IMARR_COUNT(ortar) ; kk++ ){ ortim = IMARR_SUBIM(ortar,kk) ; if( ortim->nx < ntime ) ERROR_exit("-ort file %s is shorter than input dataset time series", ortim->name ) ; ort = (float **)realloc( ort , sizeof(float *)*(nort+ortim->ny) ) ; for( vv=0 ; vv < ortim->ny ; vv++ ) ort[nort++] = MRI_FLOAT_PTR(ortim) + ortim->nx * vv ; } } /* check whether processing leaves any DoF remaining 18 Mar 2015 [rickr] */ { int nbprem = THD_bandpass_remain_dim(ntime, dt, fbot, ftop, 1); int bpused, nremain; int wlimit; /* warning limit */ bpused = ntime - nbprem; /* #dim lost in bandpass step */ nremain = nbprem - nort; /* #dim left in output */ if( nortset == 1 ) nremain--; nremain -= (qdet+1); if( verb ) INFO_message("%d dimensional data reduced to %d by:\n" " %d (bandpass), %d (-ort), %d (-dsort), %d (detrend)", ntime, nremain, bpused, nort, nortset?1:0, qdet+1); /* possibly warn (if 95% lost) user or fail */ wlimit = ntime/20; if( wlimit < 3 ) wlimit = 3; if( nremain < wlimit && nremain > 0 ) WARNING_message("dimensionality reduced from %d to %d, be careful!", ntime, nremain); if( nremain <= 0 ) /* FAILURE */ ERROR_exit("dimensionality reduced from %d to %d, failing!", ntime, nremain); } /* all the real work now */ if( do_despike ){ int_pair nsp ; if( verb ) INFO_message("Testing data time series for spikes") ; nsp = THD_vectim_despike9( mrv ) ; if( verb ) ININFO_message(" -- Squashed %d spikes from %d voxels",nsp.j,nsp.i) ; } if( verb ) INFO_message("Bandpassing data time series") ; (void)THD_bandpass_vectim( mrv , dt,fbot,ftop , qdet , nort,ort ) ; /* OK, maybe a little more work */ if( nortset == 1 ){ MRI_vectim *orv ; orv = THD_dset_to_vectim( ortset[0] , mask , 0 ) ; if( orv == NULL ){ ERROR_message("Can't load -dsort %s",DSET_BRIKNAME(ortset[0])) ; } else { float *dp , *mvv , *ovv , ff ; if( verb ) INFO_message("Orthogonalizing to bandpassed -dsort") ; (void)THD_bandpass_vectim( orv , dt,fbot,ftop , qdet , nort,ort ) ; THD_vectim_normalize( orv ) ; dp = malloc(sizeof(float)*mrv->nvec) ; THD_vectim_vectim_dot( mrv , orv , dp ) ; for( vv=0 ; vv < mrv->nvec ; vv++ ){ ff = dp[vv] ; if( ff != 0.0f ){ mvv = VECTIM_PTR(mrv,vv) ; ovv = VECTIM_PTR(orv,vv) ; for( kk=0 ; kk < ntime ; kk++ ) mvv[kk] -= ff*ovv[kk] ; } } VECTIM_destroy(orv) ; free(dp) ; } } if( blur > 0.0f ){ if( verb ) INFO_message("Blurring time series data spatially; FWHM=%.2f",blur) ; mri_blur3D_vectim( mrv , blur ) ; } if( pvrad > 0.0f ){ if( verb ) INFO_message("Local PV-ing time series data spatially; radius=%.2f",pvrad) ; THD_vectim_normalize( mrv ) ; THD_vectim_localpv( mrv , pvrad ) ; } if( do_norm && pvrad <= 0.0f ){ if( verb ) INFO_message("L2 normalizing time series data") ; THD_vectim_normalize( mrv ) ; } /* create output dataset, populate it, write it, then quit */ if( verb ) INFO_message("Creating output dataset in memory, then writing it") ; outset = EDIT_empty_copy(inset) ; /* do not copy scalars 11 Sep 2015 [rickr] */ EDIT_dset_items( outset , ADN_prefix,prefix , ADN_brick_fac,NULL , ADN_none ) ; tross_Copy_History( inset , outset ) ; tross_Make_History( "3dBandpass" , argc,argv , outset ) ; for( vv=0 ; vv < ntime ; vv++ ) EDIT_substitute_brick( outset , vv , MRI_float , NULL ) ; #if 1 THD_vectim_to_dset( mrv , outset ) ; #else AFNI_OMP_START ; #pragma omp parallel { float *far , *var ; int *ivec=mrv->ivec ; int vv,kk ; #pragma omp for for( vv=0 ; vv < ntime ; vv++ ){ far = DSET_BRICK_ARRAY(outset,vv) ; var = mrv->fvec + vv ; for( kk=0 ; kk < nmask ; kk++ ) far[ivec[kk]] = var[kk*ntime] ; } } AFNI_OMP_END ; #endif VECTIM_destroy(mrv) ; DSET_write(outset) ; if( verb ) WROTE_DSET(outset) ; exit(0) ; }
int main(int argc, char *argv[]) { int i,j,k,m,n,aa,ii,jj,kk,mm,rr; int iarg; int nmask1=0; int nmask2=0; THD_3dim_dataset *insetFA = NULL, *insetV1 = NULL, *insetMD = NULL, *insetL1 = NULL; THD_3dim_dataset *insetEXTRA=NULL; THD_3dim_dataset *mset2=NULL; THD_3dim_dataset *mset1=NULL; THD_3dim_dataset *outsetMAP=NULL, *outsetMASK=NULL; char *prefix="tracky"; int LOG_TYPE=0; char in_FA[300]; char in_V1[300]; char in_MD[300]; char in_L1[300]; int EXTRAFILE=0; // switch for whether other file is input as WM map char OUT_bin[300]; char OUT_tracstat[300]; char prefix_mask[300]; char prefix_map[300]; // FACT algopts FILE *fout0; float MinFA=0.2,MaxAngDeg=45,MinL=20.0; float MaxAng; int SeedPerV[3]={2,2,2}; int ArrMax=0; float tempvmagn; int Nvox=-1; // tot number vox int Dim[3]={0,0,0}; // dim in each dir int Nseed=0,M=30,bval=1000; int DimSeed[3]; // number of seeds there will be float Ledge[3]; // voxel edge lengths int *ROI1, *ROI2; short int *temp_arr; char *temp_byte; int **Tforw, **Tback; int **Ttot; float **flTforw, **flTback; float ****coorded; int ****INDEX; int len_forw, len_back; // int count of num of squares through float phys_forw[1], phys_back[1]; int idx; float ave_tract_len, ave_tract_len_phys; int inroi1, inroi2, KEEPIT; // switches for detecting int in[3]; // to pass to trackit float physin[3]; // also for trackit, physical loc, int totlen; float totlen_phys; int Numtract; int READS_in; float READS_fl; int end[2][3]; int test_ind[2][3]; int roi3_ct=0, id=0; float roi3_mu_MD = 0.,roi3_mu_RD = 0.,roi3_mu_L1 = 0.,roi3_mu_FA = 0.; float roi3_sd_MD = 0.,roi3_sd_RD = 0.,roi3_sd_L1 = 0.,roi3_sd_FA = 0.; float tempMD,tempFA,tempRD,tempL1; char dset_or[4] = "RAI"; THD_3dim_dataset *dsetn; int TV_switch[3] = {0,0,0}; TAYLOR_BUNDLE *tb=NULL; TAYLOR_TRACT *tt=NULL; char *mode = "NI_fast_binary"; NI_element *nel=NULL; int dump_opts=0; tv_io_header header1 = {.id_string = "TRACK\0", .origin = {0,0,0}, .n_scalars = 3, .scal_n[0] = "FA", .scal_n[1] = "MD", .scal_n[2] = "L1", .n_properties = 0, .vox_to_ras = {{0.,0.,0.,0.},{0.,0.,0.,0.}, {0.,0.,0.,0.},{0.,0.,0.,0.}}, // reset this later based on actual data set .voxel_order = "RAI\0", .invert_x = 0, .invert_y = 0, .invert_z = 0, .swap_xy = 0, .swap_yz = 0, .swap_zx = 0, .n_count = 0, .version = 2, .hdr_size = 1000}; // for testing names... char *postfix[4]={"+orig.HEAD\0",".nii.gz\0",".nii\0","+tlrc.HEAD\0"}; int FOUND =-1; int RECORD_ORIG = 0; float Orig[3] = {0.0,0.0,0.0}; mainENTRY("3dTrackID"); machdep(); // **************************************************************** // **************************************************************** // load AFNI stuff // **************************************************************** // **************************************************************** INFO_message("version: MU"); /** scan args **/ if (argc == 1) { usage_TrackID(1); exit(0); } iarg = 1; while( iarg < argc && argv[iarg][0] == '-' ){ if( strcmp(argv[iarg],"-help") == 0 || strcmp(argv[iarg],"-h") == 0 ) { usage_TrackID(strlen(argv[iarg])>3 ? 2:1); exit(0); } if( strcmp(argv[iarg],"-verb") == 0) { if( ++iarg >= argc ) ERROR_exit("Need argument after '-verb'") ; set_tract_verb(atoi(argv[iarg])); iarg++ ; continue ; } if( strcmp(argv[iarg],"-write_opts") == 0) { dump_opts=1; iarg++ ; continue ; } if( strcmp(argv[iarg],"-rec_orig") == 0) { RECORD_ORIG=1; iarg++ ; continue ; } if( strcmp(argv[iarg],"-tract_out_mode") == 0) { if( ++iarg >= argc ) ERROR_exit("Need argument after '-tract_out_mode'") ; if (strcmp(argv[iarg], "NI_fast_binary") && strcmp(argv[iarg], "NI_fast_text") && strcmp(argv[iarg], "NI_slow_binary") && strcmp(argv[iarg], "NI_slow_text") ) { ERROR_message("Bad value (%s) for -tract_out_mode",argv[iarg]); exit(1); } mode = argv[iarg]; iarg++ ; continue ; } if( strcmp(argv[iarg],"-mask1") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '-mask1'") ; mset1 = THD_open_dataset( argv[iarg] ) ; if( mset1 == NULL ) ERROR_exit("Can't open mask1 dataset '%s'", argv[iarg]) ; DSET_load(mset1) ; CHECK_LOAD_ERROR(mset1) ; nmask1 = DSET_NVOX(mset1) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-mask2") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '-mask2'") ; mset2 = THD_open_dataset( argv[iarg] ) ; if( mset2 == NULL ) ERROR_exit("Can't open mask2 dataset '%s'", argv[iarg]) ; DSET_load(mset2) ; CHECK_LOAD_ERROR(mset2) ; nmask2 = DSET_NVOX(mset2) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-prefix") == 0 ){ iarg++ ; if( iarg >= argc ) ERROR_exit("Need argument after '-prefix'"); prefix = strdup(argv[iarg]) ; if( !THD_filename_ok(prefix) ) ERROR_exit("Illegal name after '-prefix'"); iarg++ ; continue ; } if( strcmp(argv[iarg],"-input") == 0 ){ iarg++ ; if( iarg >= argc ) ERROR_exit("Need argument after '-input'"); for( i=0 ; i<4 ; i++) { sprintf(in_FA,"%s_FA%s", argv[iarg],postfix[i]); if(THD_is_ondisk(in_FA)) { FOUND = i; break; } } insetFA = THD_open_dataset(in_FA) ; if( (insetFA == NULL ) || (FOUND==-1)) ERROR_exit("Can't open dataset '%s': for FA.",in_FA); DSET_load(insetFA) ; CHECK_LOAD_ERROR(insetFA) ; Nvox = DSET_NVOX(insetFA) ; Dim[0] = DSET_NX(insetFA); Dim[1] = DSET_NY(insetFA); Dim[2] = DSET_NZ(insetFA); Ledge[0] = fabs(DSET_DX(insetFA)); Ledge[1] = fabs(DSET_DY(insetFA)); Ledge[2] = fabs(DSET_DZ(insetFA)); Orig[0] = DSET_XORG(insetFA); Orig[1] = DSET_YORG(insetFA); Orig[2] = DSET_ZORG(insetFA); // check tot num vox match (as proxy for dims...) if( (Nvox != nmask1) || (Nvox != nmask2) ) ERROR_exit("Input dataset does not match both mask volumes!"); // this stores the original data file orientation for later use, // as well since we convert everything to RAI temporarily, as // described below header1.voxel_order[0]=ORIENT_typestr[insetFA->daxes->xxorient][0]; header1.voxel_order[1]=ORIENT_typestr[insetFA->daxes->yyorient][0]; header1.voxel_order[2]=ORIENT_typestr[insetFA->daxes->zzorient][0]; for( i=0 ; i<3 ; i++) { header1.dim[i] = Dim[i]; header1.voxel_size[i] = Ledge[i]; // will want this when outputting file later for TrackVis. TV_switch[i] = !(dset_or[i]==header1.voxel_order[i]); } dset_or[3]='\0'; FOUND = -1; for( i=0 ; i<4 ; i++) { sprintf(in_V1,"%s_V1%s", argv[iarg],postfix[i]); if(THD_is_ondisk(in_V1)) { FOUND = i; break; } } insetV1 = THD_open_dataset(in_V1); if( insetV1 == NULL ) ERROR_exit("Can't open dataset '%s':V1",in_V1); DSET_load(insetV1) ; CHECK_LOAD_ERROR(insetV1) ; FOUND = -1; for( i=0 ; i<4 ; i++) { sprintf(in_L1,"%s_L1%s", argv[iarg],postfix[i]); if(THD_is_ondisk(in_L1)) { FOUND = i; break; } } insetL1 = THD_open_dataset(in_L1); if( insetL1 == NULL ) ERROR_exit("Can't open dataset '%s':L1",in_L1); DSET_load(insetL1) ; CHECK_LOAD_ERROR(insetL1) ; FOUND = -1; for( i=0 ; i<4 ; i++) { sprintf(in_MD,"%s_MD%s", argv[iarg],postfix[i]); if(THD_is_ondisk(in_MD)) { FOUND = i; break; } } insetMD = THD_open_dataset(in_MD); if( insetMD == NULL ) ERROR_exit("Can't open dataset '%s':MD",in_MD); DSET_load(insetMD) ; CHECK_LOAD_ERROR(insetMD) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-algopt") == 0 ){ iarg++ ; if( iarg >= argc ) ERROR_exit("Need argument after '-algopt'"); if (!(nel = ReadTractAlgOpts(argv[iarg]))) { ERROR_message("Failed to read options in %s\n", argv[iarg]); exit(19); } if (NI_getTractAlgOpts(nel, &MinFA, &MaxAngDeg, &MinL, SeedPerV, &M, &bval)) { ERROR_message("Failed to get options"); exit(1); } NI_free_element(nel); nel=NULL; iarg++ ; continue ; } if( strcmp(argv[iarg],"-logic") == 0 ){ iarg++ ; if( iarg >= argc ) ERROR_exit("Need argument after '-logic'"); INFO_message("ROI logic type is: %s",argv[iarg]); if( strcmp(argv[iarg],"AND") == 0 ) LOG_TYPE = 1; else if( strcmp(argv[iarg],"OR") == 0 ) LOG_TYPE = 0; else if( strcmp(argv[iarg],"ALL") == 0 ) LOG_TYPE = -1; else ERROR_exit("Illegal after '-logic': need 'OR' or 'AND'"); iarg++ ; continue ; } //@@ if( strcmp(argv[iarg],"-extra_set") == 0) { if( ++iarg >= argc ) ERROR_exit("Need argument after '-extra_set'"); EXTRAFILE = 1; // switch on insetEXTRA = THD_open_dataset(argv[iarg]); if( (insetEXTRA == NULL ) ) ERROR_exit("Can't open dataset '%s': for extra set.",argv[iarg]); DSET_load(insetEXTRA) ; CHECK_LOAD_ERROR(insetEXTRA) ; if( !((Dim[0] == DSET_NX(insetEXTRA)) && (Dim[1] == DSET_NY(insetEXTRA)) && (Dim[2] == DSET_NZ(insetEXTRA)))) ERROR_exit("Dimensions of extra set '%s' don't match those of the DTI prop ones ('%s', etc.).",argv[iarg], in_FA); iarg++ ; continue ; } ERROR_message("Bad option '%s'\n",argv[iarg]) ; suggest_best_prog_option(argv[0], argv[iarg]); exit(1); } if (iarg < 4) { ERROR_message("Too few options. Try -help for details.\n"); exit(1); } if (dump_opts) { nel = NI_setTractAlgOpts(NULL, &MinFA, &MaxAngDeg, &MinL, SeedPerV, &M, &bval); WriteTractAlgOpts(prefix, nel); NI_free_element(nel); nel=NULL; } // Process the options a little for( i=0 ; i<3 ; i++) DimSeed[i] = Dim[i]*SeedPerV[i]; Nseed = Nvox*SeedPerV[0]*SeedPerV[1]*SeedPerV[2]; // convert to cos of rad value for comparisons, instead of using acos() MaxAng = cos(CONV*MaxAngDeg); // switch to add header-- option for now, added Sept. 2012 // for use with map_TrackID to map tracks to different space if(RECORD_ORIG) { for( i=0 ; i<3 ; i++) header1.origin[i] = Orig[i]; } // at some point, we will have to convert indices into // pseudo-locations; being forced into this choice means that // different data set orientations would be represented differently // and incorrectly in some instances... so, for now, we'll resample // everything to RAI, and then resample back later. guess this will // just slow things down slightly. // have all be RAI for processing here if(TV_switch[0] || TV_switch[1] || TV_switch[2]) { dsetn = r_new_resam_dset(insetFA, NULL, 0.0, 0.0, 0.0, dset_or, RESAM_NN_TYPE, NULL, 1, 0); DSET_delete(insetFA); insetFA=dsetn; dsetn=NULL; dsetn = r_new_resam_dset(insetMD, NULL, 0.0, 0.0, 0.0, dset_or, RESAM_NN_TYPE, NULL, 1, 0); DSET_delete(insetMD); insetMD=dsetn; dsetn=NULL; dsetn = r_new_resam_dset(insetV1, NULL, 0.0, 0.0, 0.0, dset_or, RESAM_NN_TYPE, NULL, 1, 0); DSET_delete(insetV1); insetV1=dsetn; dsetn=NULL; dsetn = r_new_resam_dset(insetL1, NULL, 0.0, 0.0, 0.0, dset_or, RESAM_NN_TYPE, NULL, 1, 0); DSET_delete(insetL1); insetL1=dsetn; dsetn=NULL; dsetn = r_new_resam_dset(mset1, NULL, 0.0, 0.0, 0.0, dset_or, RESAM_NN_TYPE, NULL, 1, 0); DSET_delete(mset1); mset1=dsetn; dsetn=NULL; dsetn = r_new_resam_dset(mset2, NULL, 0.0, 0.0, 0.0, dset_or, RESAM_NN_TYPE, NULL, 1, 0); DSET_delete(mset2); mset2=dsetn; dsetn=NULL; if(EXTRAFILE) { dsetn = r_new_resam_dset(insetEXTRA, NULL, 0.0, 0.0, 0.0, dset_or, RESAM_NN_TYPE, NULL, 1, 0); DSET_delete(insetEXTRA); insetEXTRA=dsetn; dsetn=NULL; } } // **************************************************************** // **************************************************************** // make arrays for tracking // **************************************************************** // **************************************************************** // for temp storage array, just a multiple of longest dimension! if(Dim[0] > Dim[1]) ArrMax = Dim[0] * 4; else ArrMax = Dim[1] * 4; if(4*Dim[2] > ArrMax) ArrMax = Dim[2] * 4; ROI1 = (int *)calloc(Nvox, sizeof(int)); ROI2 = (int *)calloc(Nvox, sizeof(int)); temp_arr = (short int *)calloc(Nvox, sizeof(short int)); temp_byte = (char *)calloc(Nvox, sizeof(char)); // temp storage whilst tracking Tforw = calloc(ArrMax, sizeof(Tforw)); for(i=0 ; i<ArrMax ; i++) Tforw[i] = calloc(3, sizeof(int)); Ttot = calloc(2*ArrMax , sizeof(Ttot)); for(i=0 ; i<2*ArrMax ; i++) Ttot[i] = calloc(3, sizeof(int)); Tback = calloc(ArrMax, sizeof(Tback)); for(i=0 ; i<ArrMax ; i++) Tback[i] = calloc(3, sizeof(int)); // temp storage whilst tracking, physical loc flTforw = calloc(ArrMax, sizeof(flTforw)); for(i=0 ; i<ArrMax ; i++) flTforw[i] = calloc(3, sizeof(int)); flTback = calloc(ArrMax,sizeof(flTback)); for(i=0 ; i<ArrMax ; i++) flTback[i] = calloc(3, sizeof(int)); if( (ROI1 == NULL) || (ROI2 == NULL) || (temp_arr == NULL) || (Tforw == NULL) || (Tback == NULL) || (flTforw == NULL) || (flTback == NULL) || (Ttot == NULL)) { fprintf(stderr, "\n\n MemAlloc failure.\n\n"); exit(12); } coorded = (float ****) calloc( Dim[0], sizeof(float ***) ); for ( i = 0 ; i < Dim[0] ; i++ ) coorded[i] = (float ***) calloc( Dim[1], sizeof(float **) ); for ( i = 0 ; i < Dim[0] ; i++ ) for ( j = 0 ; j < Dim[1] ; j++ ) coorded[i][j] = (float **) calloc( Dim[2], sizeof(float *) ); for ( i=0 ; i<Dim[0] ; i++ ) for ( j=0 ; j<Dim[1] ; j++ ) for ( k= 0 ; k<Dim[2] ; k++ ) //3 comp of V1 and FA coorded[i][j][k] = (float *) calloc( 4, sizeof(float) ); INDEX = (int ****) calloc( Dim[0], sizeof(int ***) ); for ( i = 0 ; i < Dim[0] ; i++ ) INDEX[i] = (int ***) calloc( Dim[1], sizeof(int **) ); for ( i = 0 ; i < Dim[0] ; i++ ) for ( j = 0 ; j < Dim[1] ; j++ ) INDEX[i][j] = (int **) calloc( Dim[2], sizeof(int *) ); for ( i=0 ; i<Dim[0] ; i++ ) for ( j=0 ; j<Dim[1] ; j++ ) for ( k= 0 ; k<Dim[2] ; k++ ) INDEX[i][j][k] = (int *) calloc( 4, sizeof(int) ); // this statement will never be executed if allocation fails above if( (INDEX == NULL) || (coorded == NULL) ) { fprintf(stderr, "\n\n MemAlloc failure.\n\n"); exit(122); } for(i=0 ; i<Nvox ; i++) { if(THD_get_voxel( mset1, i, 0) >0.5){ ROI1[i] = 1; } if(THD_get_voxel( mset2, i, 0) >0.5) ROI2[i] = 1; } // set up eigvecs in 3D coord sys, // mark off where ROIs are and keep index handy idx=0; for( k=0 ; k<Dim[2] ; k++ ) for( j=0 ; j<Dim[1] ; j++ ) for( i=0 ; i<Dim[0] ; i++ ) { for( m=0 ; m<3 ; m++ ) coorded[i][j][k][m] = THD_get_voxel(insetV1, idx, m); if(EXTRAFILE) coorded[i][j][k][3] = THD_get_voxel(insetEXTRA, idx, 0); else coorded[i][j][k][3] = THD_get_voxel(insetFA, idx, 0); // make sure that |V1| == 1 for all eigenvects, otherwise it's /// a problem in the tractography; currently, some from // 3dDWItoDT do not have this property... tempvmagn = sqrt(coorded[i][j][k][0]*coorded[i][j][k][0]+ coorded[i][j][k][1]*coorded[i][j][k][1]+ coorded[i][j][k][2]*coorded[i][j][k][2]); if( tempvmagn<0.99 ) for( m=0 ; m<3 ; m++ ) coorded[i][j][k][m]/= tempvmagn; INDEX[i][j][k][0] =idx; // first value is the index itself if( ROI1[idx]==1 ) INDEX[i][j][k][1]=1; // second value identifies ROI1 mask else INDEX[i][j][k][1]=0; if( ROI2[idx]==1 ) INDEX[i][j][k][2]=1; // third value identifies ROI2 mask else INDEX[i][j][k][2]=0; // fourth value will be counter for number of kept tracks // passing through INDEX[i][j][k][3] = 0; idx+= 1; } // ************************************************************* // ************************************************************* // Beginning of main loop // ************************************************************* // ************************************************************* Numtract = 0; ave_tract_len = 0.; ave_tract_len_phys = 0.; sprintf(OUT_bin,"%s.trk",prefix); if( (fout0 = fopen(OUT_bin, "w")) == NULL) { fprintf(stderr, "Error opening file %s.",OUT_bin); exit(16); } fwrite(&header1,sizeof(tv_io_header),1,fout0); if (get_tract_verb()) { INFO_message("Begin tracking..."); } tb = AppCreateBundle(NULL, 0, NULL, insetFA); // start bundle id = 0; for( k=0 ; k<Dim[2] ; k++ ) for( j=0 ; j<Dim[1] ; j++ ) for( i=0 ; i<Dim[0] ; i++ ) if(coorded[i][j][k][3] >= MinFA) { for( ii=0 ; ii<SeedPerV[0] ; ii++ ) for( jj=0 ; jj<SeedPerV[1] ; jj++ ) for( kk=0 ; kk<SeedPerV[2] ; kk++ ) { in[0] = i; in[1] = j; in[2] = k; physin[0] = ((float) in[0] + (0.5 + (float) ii)/SeedPerV[0])*Ledge[0]; physin[1] = ((float) in[1] + (0.5 + (float) jj)/SeedPerV[1])*Ledge[1]; physin[2] = ((float) in[2] + (0.5 + (float) kk)/SeedPerV[2])*Ledge[2]; len_forw = TrackIt(coorded, in, physin, Ledge, Dim, MinFA, MaxAng, ArrMax, Tforw, flTforw, 1, phys_forw); // reset, because it's changed in TrackIt func in[0] = i; in[1] = j; in[2] = k; physin[0] = ((float) in[0] + (0.5 + (float) ii)/SeedPerV[0])*Ledge[0]; physin[1] = ((float) in[1] + (0.5 + (float) jj)/SeedPerV[1])*Ledge[1]; physin[2] = ((float) in[2] + (0.5 + (float) kk)/SeedPerV[2])*Ledge[2]; len_back = TrackIt(coorded, in, physin, Ledge, Dim, MinFA, MaxAng, ArrMax, Tback, flTback, -1, phys_back); KEEPIT = 0; // a simple switch totlen = len_forw+len_back-1; // NB: overlap of starts totlen_phys = phys_forw[0] + phys_back[0]; if( totlen_phys >= MinL ) { // glue together for simpler notation later for( n=0 ; n<len_back ; n++) { // all of this rr = len_back-n-1; // read in backward for(m=0;m<3;m++) Ttot[rr][m] = Tback[n][m]; } for( n=1 ; n<len_forw ; n++){// skip first->overlap rr = n+len_back-1; // put after for(m=0;m<3;m++) Ttot[rr][m] = Tforw[n][m]; } // <<So close and orthogonal condition>>: // test projecting ends, to see if they abut ROI. for(m=0;m<3;m++) { //actual projected ends end[1][m] = 2*Ttot[totlen-1][m]-Ttot[totlen-2][m]; end[0][m] = 2*Ttot[0][m]-Ttot[1][m]; // default choice, just retest known ends // as default test_ind[1][m] = test_ind[0][m] = Ttot[0][m]; } tt = Create_Tract(len_back, flTback, len_forw, flTforw, id, insetFA); ++id; if (LOG_TYPE == -1) { KEEPIT = 1; } else { inroi1 = 0; // check forw for( n=0 ; n<len_forw ; n++) { if(INDEX[Tforw[n][0]][Tforw[n][1]][Tforw[n][2]][1]==1){ inroi1 = 1; break; } else continue; } if( inroi1==0 ){// after 1st half, check 2nd half for( m=0 ; m<len_back ; m++) { if(INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][1]==1){ inroi1 = 1; break; } else continue; } } // after 1st&2nd halves, check bound/neigh if( inroi1==0 ) { if(INDEX[test_ind[1][0]][test_ind[1][1]][test_ind[1][2]][1]==1) inroi1 = 1; if(INDEX[test_ind[0][0]][test_ind[0][1]][test_ind[0][2]][1]==1) inroi1 = 1; } if( ((LOG_TYPE ==0) && (inroi1 ==0)) || ((LOG_TYPE ==1) && (inroi1 ==1))) { // have to check in ROI2 inroi2 = 0; // check forw for( n=0 ; n<len_forw ; n++) { if(INDEX[Tforw[n][0]][Tforw[n][1]][Tforw[n][2]][2]==1){ inroi2 = 1; break; } else continue; } //after 1st half, check 2nd half if( inroi2==0 ) { for( m=0 ; m<len_back ; m++) { if(INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][2]==1){ inroi2 = 1; break; } else continue; } } // after 1st&2nd halves, check bound/neigh if( inroi2==0 ) { if(INDEX[test_ind[1][0]][test_ind[1][1]][test_ind[1][2]][2]==1) inroi2 = 1; if(INDEX[test_ind[0][0]][test_ind[0][1]][test_ind[0][2]][2]==1) inroi2 = 1; } // for both cases, need to see it here to keep if( inroi2 ==1 ) KEEPIT = 1; // otherwise, it's gone } else if((LOG_TYPE ==0) && (inroi1 ==1)) KEEPIT = 1; } } // by now, we *know* if we're keeping this or not. if( KEEPIT == 1 ) { tb = AppCreateBundle(tb, 1, tt, NULL); tt = Free_Tracts(tt, 1); READS_in = totlen; fwrite(&READS_in,sizeof(READS_in),1,fout0); for( n=0 ; n<len_back ; n++) { //put this one in backwords, to make it connect m = len_back - 1 - n; for(aa=0 ; aa<3 ; aa++) { // recenter phys loc for trackvis, if nec... // just works this way (where they define // origin) READS_fl = flTback[m][aa]; if(!TV_switch[aa]) READS_fl = Ledge[aa]*Dim[aa]-READS_fl; fwrite(&READS_fl,sizeof(READS_fl),1,fout0); } mm = INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][0]; READS_fl =THD_get_voxel(insetFA, mm, 0); // FA fwrite(&READS_fl,sizeof(READS_fl),1,fout0); READS_fl =THD_get_voxel(insetMD, mm, 0); // MD fwrite(&READS_fl,sizeof(READS_fl),1,fout0); READS_fl =THD_get_voxel(insetL1, mm, 0); // L1 fwrite(&READS_fl,sizeof(READS_fl),1,fout0); // count this voxel for having a tract INDEX[Tback[m][0]][Tback[m][1]][Tback[m][2]][3]+= 1; } for( m=1 ; m<len_forw ; m++) { for(aa=0 ; aa<3 ; aa++) { // recenter phys loc for trackvis, if nec... READS_fl = flTforw[m][aa]; if(!TV_switch[aa]) READS_fl = Ledge[aa]*Dim[aa]-READS_fl; fwrite(&READS_fl,sizeof(READS_fl),1,fout0); } mm = INDEX[Tforw[m][0]][Tforw[m][1]][Tforw[m][2]][0]; READS_fl =THD_get_voxel(insetFA, mm, 0); // FA fwrite(&READS_fl,sizeof(READS_fl),1,fout0); READS_fl =THD_get_voxel(insetMD, mm, 0); // MD fwrite(&READS_fl,sizeof(READS_fl),1,fout0); READS_fl =THD_get_voxel(insetL1, mm, 0); // L1 fwrite(&READS_fl,sizeof(READS_fl),1,fout0); // count this voxel for having a tract INDEX[Tforw[m][0]][Tforw[m][1]][Tforw[m][2]][3]+= 1; } ave_tract_len+= totlen; ave_tract_len_phys+= totlen_phys; Numtract+=1; } } } fclose(fout0); if (get_tract_verb()) { INFO_message("Done tracking, have %d tracks.", tb->N_tracts); Show_Taylor_Bundle(tb, NULL, 3); } if (!Write_Bundle(tb,prefix,mode)) { ERROR_message("Failed to write the bundle"); } // ************************************************************** // ************************************************************** // Some simple stats on ROIs and outputs // ************************************************************** // ************************************************************** for( k=0 ; k<Dim[2] ; k++ ) for( j=0 ; j<Dim[1] ; j++ ) for( i=0 ; i<Dim[0] ; i++ ) { if( INDEX[i][j][k][3]>=1 ) { tempMD = THD_get_voxel(insetMD,INDEX[i][j][k][0],0); tempFA = THD_get_voxel(insetFA,INDEX[i][j][k][0],0); tempL1 = THD_get_voxel(insetL1,INDEX[i][j][k][0],0); tempRD = 0.5*(3*tempMD-tempL1); roi3_mu_MD+= tempMD; roi3_mu_FA+= tempFA; roi3_mu_L1+= tempL1; roi3_mu_RD+= tempRD; roi3_sd_MD+= tempMD*tempMD; roi3_sd_FA+= tempFA*tempFA; roi3_sd_L1+= tempL1*tempL1; roi3_sd_RD+= tempRD*tempRD; roi3_ct+= 1; } } if(roi3_ct > 0 ) { // !!!! make into afni file roi3_mu_MD/= (float) roi3_ct; roi3_mu_FA/= (float) roi3_ct; roi3_mu_L1/= (float) roi3_ct; roi3_mu_RD/= (float) roi3_ct; roi3_sd_MD-= roi3_ct*roi3_mu_MD*roi3_mu_MD; roi3_sd_FA-= roi3_ct*roi3_mu_FA*roi3_mu_FA; roi3_sd_L1-= roi3_ct*roi3_mu_L1*roi3_mu_L1; roi3_sd_RD-= roi3_ct*roi3_mu_RD*roi3_mu_RD; roi3_sd_MD/= (float) roi3_ct-1; roi3_sd_FA/= (float) roi3_ct-1; roi3_sd_L1/= (float) roi3_ct-1; roi3_sd_RD/= (float) roi3_ct-1; roi3_sd_MD = sqrt(roi3_sd_MD); roi3_sd_FA = sqrt(roi3_sd_FA); roi3_sd_L1 = sqrt(roi3_sd_L1); roi3_sd_RD = sqrt(roi3_sd_RD); sprintf(OUT_tracstat,"%s.stats",prefix); if( (fout0 = fopen(OUT_tracstat, "w")) == NULL) { fprintf(stderr, "Error opening file %s.",OUT_tracstat); exit(19); } fprintf(fout0,"%d\t%d\n",Numtract,roi3_ct); fprintf(fout0,"%.3f\t%.3f\n",ave_tract_len/Numtract, ave_tract_len_phys/Numtract); // as usual, these next values would have to be divided by the // bval to get their actual value in standard phys units fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_FA,roi3_sd_FA); fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_MD,roi3_sd_MD); fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_RD,roi3_sd_RD); fprintf(fout0,"%.4f\t%.4f\n",roi3_mu_L1,roi3_sd_L1); fclose(fout0); sprintf(prefix_map,"%s_MAP",prefix); sprintf(prefix_mask,"%s_MASK",prefix); outsetMAP = EDIT_empty_copy( mset1 ) ; EDIT_dset_items( outsetMAP , ADN_datum_all , MRI_short , ADN_prefix , prefix_map , ADN_none ) ; if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMAP)) ) ERROR_exit("Can't overwrite existing dataset '%s'", DSET_HEADNAME(outsetMAP)); outsetMASK = EDIT_empty_copy( mset1 ) ; EDIT_dset_items( outsetMASK , ADN_datum_all , MRI_byte , ADN_prefix , prefix_mask , ADN_none ) ; if(!THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMASK)) ) ERROR_exit("Can't overwrite existing dataset '%s'", DSET_HEADNAME(outsetMASK)); m=0; for( k=0 ; k<Dim[2] ; k++ ) for( j=0 ; j<Dim[1] ; j++ ) for( i=0 ; i<Dim[0] ; i++ ) { temp_arr[m]=INDEX[i][j][k][3]; if(temp_arr[m]>0.5) temp_byte[m]=1; else temp_byte[m]=0; m++; } // re-orient the data as original inputs // (this function copies the pointer) EDIT_substitute_brick(outsetMAP, 0, MRI_short, temp_arr); temp_arr=NULL; if(TV_switch[0] || TV_switch[1] || TV_switch[2]) { dsetn = r_new_resam_dset(outsetMAP, NULL, 0.0, 0.0, 0.0, header1.voxel_order, RESAM_NN_TYPE, NULL, 1, 0); DSET_delete(outsetMAP); outsetMAP=dsetn; dsetn=NULL; } EDIT_dset_items( outsetMAP , ADN_prefix , prefix_map , ADN_none ) ; THD_load_statistics(outsetMAP ); if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMAP)) ) ERROR_exit("Can't overwrite existing dataset '%s'", DSET_HEADNAME(outsetMAP)); tross_Make_History( "3dTrackID" , argc , argv , outsetMAP) ; THD_write_3dim_dataset(NULL, NULL, outsetMAP, True); // re-orient the data as original inputs EDIT_substitute_brick(outsetMASK, 0, MRI_byte, temp_byte); temp_byte=NULL; if(TV_switch[0] || TV_switch[1] || TV_switch[2]) { dsetn = r_new_resam_dset(outsetMASK, NULL, 0.0, 0.0, 0.0, header1.voxel_order, RESAM_NN_TYPE, NULL, 1, 0); DSET_delete(outsetMASK); outsetMASK=dsetn; dsetn=NULL; } EDIT_dset_items( outsetMASK , ADN_prefix , prefix_mask , ADN_none ) ; THD_load_statistics(outsetMASK); if(!THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetMASK)) ) ERROR_exit("Can't overwrite existing dataset '%s'", DSET_HEADNAME(outsetMASK)); tross_Make_History( "3dTrackID" , argc , argv , outsetMASK) ; THD_write_3dim_dataset(NULL, NULL, outsetMASK, True); INFO_message("Number of tracts found = %d",Numtract) ; } else INFO_message("\n No Tracts Found!!!\n"); // ************************************************************ // ************************************************************ // Freeing // ************************************************************ // ************************************************************ // !!! need to free afni-sets? DSET_delete(insetFA); DSET_delete(insetMD); DSET_delete(insetL1); DSET_delete(insetV1); DSET_delete(insetEXTRA); //DSET_delete(outsetMAP); //DSET_delete(outsetMASK); DSET_delete(mset2); DSET_delete(mset1); free(prefix); free(insetV1); free(insetFA); free(mset1); free(mset2); free(insetEXTRA); free(ROI1); free(ROI2); free(temp_byte); for( i=0 ; i<ArrMax ; i++) { free(Tforw[i]); free(Tback[i]); free(flTforw[i]); free(flTback[i]); } free(Tforw); free(Tback); free(flTforw); free(flTback); for( i=0 ; i<Dim[0] ; i++) for( j=0 ; j<Dim[1] ; j++) for( k=0 ; k<Dim[2] ; k++) free(coorded[i][j][k]); for( i=0 ; i<Dim[0] ; i++) for( j=0 ; j<Dim[1] ; j++) free(coorded[i][j]); for( i=0 ; i<Dim[0] ; i++) free(coorded[i]); free(coorded); for( i=0 ; i<Dim[0] ; i++) for( j=0 ; j<Dim[1] ; j++) for( k=0 ; k<Dim[2] ; k++) free(INDEX[i][j][k]); for( i=0 ; i<Dim[0] ; i++) for( j=0 ; j<Dim[1] ; j++) free(INDEX[i][j]); for( i=0 ; i<Dim[0] ; i++) free(INDEX[i]); free(INDEX); free(temp_arr); // need to free for( i=0 ; i<2*ArrMax ; i++) free(Ttot[i]); free(Ttot); //free(mode); return 0; }
int main( int argc , char *argv[] ) { THD_3dim_dataset *inset=NULL ; byte *mask=NULL ; int mask_nx=0,mask_ny=0,mask_nz=0 , automask=0 , masknum=0 ; int iarg=1 , verb=1 , ntype=0 , nev,kk,ii,nxyz,nt ; float na,nb,nc , dx,dy,dz ; MRI_IMARR *imar=NULL ; int *ivox ; MRI_IMAGE *pim ; int do_vmean=0 , do_vnorm=0 , sval_itop=0 ; int polort=-1 ; float *ev ; MRI_IMARR *ortar ; MRI_IMAGE *ortim ; int nyort=0 ; float bpass_L=0.0f , bpass_H=0.0f , dtime ; int do_bpass=0 ; if( argc < 2 || strcmp(argv[1],"-help") == 0 ){ printf( "Usage: 3dmaskSVD [options] inputdataset\n" "Author: Zhark the Gloriously Singular\n" "\n" "* Computes the principal singular vector of the time series\n" " vectors extracted from the input dataset over the input mask.\n" " ++ You can use the '-sval' option to change which singular\n" " vectors are output.\n" "* The sign of the output vector is chosen so that the average\n" " of arctanh(correlation coefficient) over all input data\n" " vectors (from the mask) is positive.\n" "* The output vector is normalized: the sum of its components\n" " squared is 1.\n" "* You probably want to use 3dDetrend (or something similar) first,\n" " to get rid of annoying artifacts, such as motion, breathing,\n" " dark matter interactions with the brain, etc.\n" " ++ If you are lazy scum like Zhark, you might be able to get\n" " away with using the '-polort' option.\n" " ++ In particular, if your data time series has a nonzero mean,\n" " then you probably want at least '-polort 0' to remove the\n" " mean, otherwise you'll pretty much just get a constant\n" " time series as the principal singular vector!\n" "* An alternative to this program would be 3dmaskdump followed\n" " by 1dsvd, which could give you all the singular vectors you\n" " could ever want, and much more -- enough to confuse you for days.\n" " ++ In particular, although you COULD input a 1D file into\n" " 3dmaskSVD, the 1dsvd program would make much more sense.\n" "* This program will be pretty slow if there are over about 2000\n" " voxels in the mask. It could be made more efficient for\n" " such cases, but you'll have to give Zhark some 'incentive'.\n" "* Result vector goes to stdout. Redirect per your pleasures and needs.\n" "* Also see program 3dLocalSVD if you want to compute the principal\n" " singular time series vector from a neighborhood of EACH voxel.\n" " ++ (Which is a pretty slow operation!)\n" "* http://en.wikipedia.org/wiki/Singular_value_decomposition\n" "\n" "-------\n" "Options:\n" "-------\n" " -vnorm = L2 normalize all time series before SVD [recommended!]\n" " -sval a = output singular vectors 0 .. a [default a=0 = first one only]\n" " -mask mset = define the mask [default is entire dataset == slow!]\n" " -automask = you'll have to guess what this option does\n" " -polort p = if you are lazy and didn't run 3dDetrend (like Zhark)\n" " -bpass L H = bandpass [mutually exclusive with -polort]\n" " -ort xx.1D = time series to remove from the data before SVD-ization\n" " ++ You can give more than 1 '-ort' option\n" " ++ 'xx.1D' can contain more than 1 column\n" " -input ddd = alternative way to give the input dataset name\n" "\n" "-------\n" "Example:\n" "-------\n" " You have a mask dataset with discrete values 1, 2, ... 77 indicating\n" " some ROIs; you want to get the SVD from each ROI's time series separately,\n" " and then put these into 1 big 77 column .1D file. You can do this using\n" " a csh shell script like the one below:\n" "\n" " # Compute the individual SVD vectors\n" " foreach mm ( `count 1 77` )\n" " 3dmaskSVD -vnorm -mask mymask+orig\"<${mm}..${mm}>\" epi+orig > qvec${mm}.1D\n" " end\n" " # Glue them together into 1 big file, then delete the individual files\n" " 1dcat qvec*.1D > allvec.1D\n" " /bin/rm -f qvec*.1D\n" " # Plot the results to a JPEG file, then compute their correlation matrix\n" " 1dplot -one -nopush -jpg allvec.jpg allvec.1D\n" " 1ddot -terse allvec.1D > allvec_COR.1D\n" "\n" " [[ If you use the bash shell, you'll have to figure out the syntax ]]\n" " [[ yourself. Zhark has no sympathy for you bash shell infidels, and ]]\n" " [[ considers you only slightly better than those lowly Emacs users. ]]\n" " [[ And do NOT ever even mention 'nedit' in Zhark's august presence! ]]\n" ) ; PRINT_COMPILE_DATE ; exit(0) ; } /*---- official startup ---*/ PRINT_VERSION("3dmaskSVD"); mainENTRY("3dmaskSVD main"); machdep(); AFNI_logger("3dmaskSVD",argc,argv); AUTHOR("Zhark the Singular"); /*---- loop over options ----*/ INIT_IMARR(ortar) ; mpv_sign_meth = AFNI_yesenv("AFNI_3dmaskSVD_meansign") ; while( iarg < argc && argv[iarg][0] == '-' ){ if( strcasecmp(argv[iarg],"-bpass") == 0 ){ if( iarg+2 >= argc ) ERROR_exit("need 2 args after -bpass") ; bpass_L = (float)strtod(argv[++iarg],NULL) ; bpass_H = (float)strtod(argv[++iarg],NULL) ; if( bpass_L < 0.0f || bpass_H <= bpass_L ) ERROR_exit("Illegal values after -bpass: %g %g",bpass_L,bpass_H) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-ort") == 0 ){ /* 01 Oct 2009 */ int nx,ny ; if( ++iarg >= argc ) ERROR_exit("Need argument after '-ort'") ; ortim = mri_read_1D( argv[iarg] ) ; if( ortim == NULL ) ERROR_exit("-ort '%s': Can't read 1D file",argv[iarg]) ; nx = ortim->nx ; ny = ortim->ny ; if( nx == 1 && ny > 1 ){ MRI_IMAGE *tim=mri_transpose(ortim); mri_free(ortim); ortim = tim; ny = 1; } mri_add_name(argv[iarg],ortim) ; ADDTO_IMARR(ortar,ortim) ; nyort += ny ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-polort") == 0 ){ char *qpt ; if( ++iarg >= argc ) ERROR_exit("Need argument after '-polort'") ; polort = (int)strtod(argv[iarg],&qpt) ; if( *qpt != '\0' ) WARNING_message("Illegal non-numeric value after -polort") ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-vnorm") == 0 ){ do_vnorm = 1 ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-input") == 0 ){ if( inset != NULL ) ERROR_exit("Can't have two -input options") ; if( ++iarg >= argc ) ERROR_exit("Need argument after '-input'") ; inset = THD_open_dataset( argv[iarg] ) ; CHECK_OPEN_ERROR(inset,argv[iarg]) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-sval") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '-sval'") ; sval_itop = (int)strtod(argv[iarg],NULL) ; if( sval_itop < 0 ){ sval_itop = 0 ; WARNING_message("'-sval' reset to 0") ; } iarg++ ; continue ; } if( strcmp(argv[iarg],"-mask") == 0 ){ THD_3dim_dataset *mset ; int mmm ; if( ++iarg >= argc ) ERROR_exit("Need argument after '-mask'") ; if( mask != NULL || automask ) ERROR_exit("Can't have two mask inputs") ; mset = THD_open_dataset( argv[iarg] ) ; CHECK_OPEN_ERROR(mset,argv[iarg]) ; DSET_load(mset) ; CHECK_LOAD_ERROR(mset) ; mask_nx = DSET_NX(mset); mask_ny = DSET_NY(mset); mask_nz = DSET_NZ(mset); mask = THD_makemask( mset , 0 , 0.5f, 0.0f ) ; DSET_delete(mset) ; if( mask == NULL ) ERROR_exit("Can't make mask from dataset '%s'",argv[iarg]) ; masknum = mmm = THD_countmask( mask_nx*mask_ny*mask_nz , mask ) ; INFO_message("Number of voxels in mask = %d",mmm) ; if( mmm < 2 ) ERROR_exit("Mask is too small to process") ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-automask") == 0 ){ if( mask != NULL ) ERROR_exit("Can't have two mask inputs!") ; automask = 1 ; iarg++ ; continue ; } ERROR_exit("Unknown option '%s'",argv[iarg]) ; } /*--- end of loop over options ---*/ /*---- deal with input dataset ----*/ if( inset == NULL ){ if( iarg >= argc ) ERROR_exit("No input dataset on command line?") ; inset = THD_open_dataset( argv[iarg] ) ; CHECK_OPEN_ERROR(inset,argv[iarg]) ; } nt = DSET_NVALS(inset) ; /* vector lengths */ if( nt < 9 ) ERROR_exit("Must have at least 9 values per voxel") ; if( polort+1 >= nt ) ERROR_exit("'-polort %d' too big for time series length = %d",polort,nt) ; DSET_load(inset) ; CHECK_LOAD_ERROR(inset) ; nxyz = DSET_NVOX(inset) ; DSET_UNMSEC(inset) ; dtime = DSET_TR(inset) ; if( dtime <= 0.0f ) dtime = 1.0f ; do_bpass = (bpass_L < bpass_H) ; if( do_bpass ){ kk = THD_bandpass_OK( nt , dtime , bpass_L , bpass_H , 1 ) ; if( kk <= 0 ) ERROR_exit("Can't continue since -bpass setup is illegal") ; polort = -1 ; } /*--- deal with the masking ---*/ if( mask != NULL ){ if( mask_nx != DSET_NX(inset) || mask_ny != DSET_NY(inset) || mask_nz != DSET_NZ(inset) ) ERROR_exit("-mask dataset grid doesn't match input dataset") ; } else if( automask ){ int mmm ; mask = THD_automask( inset ) ; if( mask == NULL ) ERROR_message("Can't create -automask from input dataset?") ; masknum = mmm = THD_countmask( DSET_NVOX(inset) , mask ) ; INFO_message("Number of voxels in automask = %d",mmm) ; if( mmm < 9 ) ERROR_exit("Automask is too small to process") ; } else { mask = (byte *)malloc(sizeof(byte)*nxyz) ; masknum = nxyz ; memset( mask , 1 , sizeof(byte)*nxyz ) ; INFO_message("Using all %d voxels in dataset",nxyz) ; } nev = MIN(nt,masknum) ; /* max possible number of eigenvalues */ if( sval_itop >= nev ){ sval_itop = nev-1 ; WARNING_message("'-sval' reset to '%d'",sval_itop) ; } mri_principal_vector_params( 0 , do_vnorm , sval_itop ) ; mri_principal_setev(nev) ; /*-- get data vectors --*/ ivox = (int *)malloc(sizeof(int)*masknum) ; for( kk=ii=0 ; ii < nxyz ; ii++ ) if( mask[ii] ) ivox[kk++] = ii ; INFO_message("Extracting data vectors") ; imar = THD_extract_many_series( masknum, ivox, inset ) ; DSET_unload(inset) ; if( imar == NULL ) ERROR_exit("Can't get data vector?!") ; /*-- detrending --*/ if( polort >= 0 || nyort > 0 || do_bpass ){ float **polref=NULL ; float *tsar ; int nort=IMARR_COUNT(ortar) , nref=0 ; if( polort >= 0 ){ /* polynomials */ nref = polort+1 ; polref = THD_build_polyref(nref,nt) ; } if( nort > 0 ){ /* other orts */ float *oar , *par ; int nx,ny , qq,tt ; for( kk=0 ; kk < nort ; kk++ ){ /* loop over input -ort files */ ortim = IMARR_SUBIM(ortar,kk) ; nx = ortim->nx ; ny = ortim->ny ; if( nx < nt ) ERROR_exit("-ort '%s' length %d shorter than dataset length %d" , ortim->name , nx , nt ) ; polref = (float **)realloc(polref,(nref+ny)*sizeof(float *)) ; oar = MRI_FLOAT_PTR(ortim) ; for( qq=0 ; qq < ny ; qq++,oar+=nx ){ par = polref[nref+qq] = (float *)malloc(sizeof(float)*nt) ; for( tt=0 ; tt < nt ; tt++ ) par[tt] = oar[tt] ; if( polort == 0 ) THD_const_detrend (nt,par,NULL) ; else if( polort > 0 ) THD_linear_detrend(nt,par,NULL,NULL) ; } nref += ny ; } DESTROY_IMARR(ortar) ; } if( !do_bpass ){ /* old style ort-ification */ MRI_IMAGE *imq , *imp ; float *qar ; INFO_message("Detrending data vectors") ; #if 1 imq = mri_new( nt , nref , MRI_float) ; qar = MRI_FLOAT_PTR(imq) ; for( kk=0 ; kk < nref ; kk++ ) memcpy( qar+kk*nt , polref[kk] , sizeof(float)*nt ) ; imp = mri_matrix_psinv( imq , NULL , 1.e-8 ) ; for( kk=0 ; kk < IMARR_COUNT(imar) ; kk++ ){ mri_matrix_detrend( IMARR_SUBIM(imar,kk) , imq , imp ) ; } mri_free(imp) ; mri_free(imq) ; #else for( kk=0 ; kk < IMARR_COUNT(imar) ; kk++ ){ tsar = MRI_FLOAT_PTR(IMARR_SUBIM(imar,kk)) ; THD_generic_detrend_LSQ( nt , tsar , -1 , nref , polref , NULL ) ; } #endif } else { /* bandpass plus (maybe) orts */ float **vec = (float **)malloc(sizeof(float *)*IMARR_COUNT(imar)) ; INFO_message("Bandpassing data vectors") ; for( kk=0 ; kk < IMARR_COUNT(imar) ; kk++ ) vec[kk] = MRI_FLOAT_PTR(IMARR_SUBIM(imar,kk)) ; (void)THD_bandpass_vectors( nt , IMARR_COUNT(imar) , vec , dtime , bpass_L , bpass_H , 2 , nref , polref ) ; free(vec) ; } for( kk=0 ; kk < nref; kk++ ) free(polref[kk]) ; free(polref) ; } /* end of detrendization */ /*--- the actual work ---*/ INFO_message("Computing SVD") ; pim = mri_principal_vector( imar ) ; DESTROY_IMARR(imar) ; if( pim == NULL ) ERROR_exit("SVD failure!?!") ; ev = mri_principal_getev() ; switch(sval_itop+1){ case 1: INFO_message("First singular value: %g",ev[0]) ; break ; case 2: INFO_message("First 2 singular values: %g %g",ev[0],ev[1]) ; break ; case 3: INFO_message("First 3 singular values: %g %g %g",ev[0],ev[1],ev[2]) ; break ; case 4: INFO_message("First 4 singular values: %g %g %g %g",ev[0],ev[1],ev[2],ev[3]) ; break ; default: case 5: INFO_message("First 5 singular values: %g %g %g %g %g",ev[0],ev[1],ev[2],ev[3],ev[4]) ; break ; } mri_write_1D(NULL,pim) ; exit(0) ; }
int main( int argc , char *argv[] ) { THD_3dim_dataset *dset_in=NULL , *dset_out ; int Lxx=-1 , Lyy=-1 , Lzz=-1 , Mode=FFT_ABS , Sign=-1 , do_alt=0 ; char *prefix = "FFTout" ; int iarg ; MRI_IMAGE *inim , *outim ; float fac ; int nx,ny,nz ; THD_ivec3 iv ; if( argc < 2 || strcasecmp(argv[1],"-help") == 0 ){ printf( "Usage: 3dFFT [options] dataset\n" "\n" "* Does the FFT of the input dataset in 3 directions (x,y,z) and\n" " produces the output dataset.\n" "\n" "* Why you'd want to do this is an interesting question.\n" "\n" "* Program 3dcalc can operate on complex-valued datasets, but\n" " only on one component at a time (cf. the '-cx2r' option).\n" "\n" "* Most other AFNI programs can only operate on real-valued\n" " datasets.\n" "\n" "* You could use 3dcalc (twice) to split a complex-valued dataset\n" " into two real-valued datasets, do your will on those with other\n" " AFNI programs, then merge the results back into a complex-valued\n" " dataset with 3dTwotoComplex.\n" "\n" "Options\n" "=======\n" " -abs = Outputs the magnitude of the FFT [default]\n" " -phase = Outputs the phase of the FFT (-PI..PI == no unwrapping!)\n" " -complex = Outputs the complex-valued FFT\n" " -inverse = Does the inverse FFT instead of the forward FFT\n" "\n" " -Lx xx = Use FFT of length 'xx' in the x-direction\n" " -Ly yy = Use FFT of length 'yy' in the y-direction\n" " -Lz zz = Use FFT of length 'zz' in the z-direction\n" " * Set a length to 0 to skip the FFT in that direction\n" "\n" " -altIN = Alternate signs of input data before FFT, to bring\n" " zero frequency from edge of FFT-space to center of grid\n" " for cosmetic purposes.\n" " -altOUT = Alternate signs of output data after FFT. If you\n" " use '-altI' on the forward transform, then you should\n" " use '-altO' an the inverse transform, to get the\n" " signs of the recovered image correct.\n" " **N.B.: You cannot use '-altIN' and '-altOUT' in the same run!\n" "\n" " -input dd = Read the input dataset from 'dd', instead of\n" " from the last argument on the command line.\n" "\n" " -prefix pp = Use 'pp' for the output dataset prefix.\n" "\n" "Notes\n" "=====\n" " * In the present avatar, only 1 sub-brick will be processed.\n" "\n" " * The program can only do FFT lengths that are factorable\n" " into a product of powers of 2, 3, and 5, and are even.\n" " + The largest power of 3 that is allowed is 3^3 = 27.\n" " + The largest power of 5 that is allowed is 5^3 = 125.\n" " + e.g., FFT of length 3*5*8=120 is possible.\n" " + e.g., FFT of length 4*31 =124 is not possible.\n" "\n" " * The 'x', 'y', and 'z' axes here refer to the order the\n" " data is stored, not DICOM coordinates; cf. 3dinfo.\n" "\n" " * If you force (via '-Lx' etc.) an FFT length that is not\n" " allowed, the program will stop with an error message.\n" "\n" " * If you force an FFT length that is shorter than an dataset\n" " axis dimension, the program will stop with an error message.\n" "\n" " * If you don't force an FFT length along a particular axis,\n" " the program will pick the smallest legal value that is\n" " greater than or equal to the corresponding dataset dimension.\n" " + e.g., 124 would be increased to 128.\n" "\n" " * If an FFT length is longer than an axis length, then the\n" " input data in that direction is zero-padded at the end.\n" "\n" " * For -abs and -phase, the output dataset is in float format.\n" "\n" " * If you do the forward and inverse FFT, then you should get back\n" " the original dataset, except for roundoff error and except that\n" " the new dataset axis dimensions may be longer than the original.\n" "\n" " * Forward FFT = sum_{k=0..N-1} [ exp(-2*PI*i*k/N) * data(k) ]\n" "\n" " * Inverse FFT = sum_{k=0..N-1} [ exp(+2*PI*i*k/N) * data(k) ] / N\n" "\n" " * Started a long time ago, but only finished in Aug 2009 at the\n" " request of John Butman, because he asked so nicely. (Now pay up!)\n" ) ; PRINT_COMPILE_DATE ; exit(0) ; } PRINT_VERSION("3dFFT") ; mainENTRY("3dFFT main") ; machdep() ; AUTHOR("RW Cox") ; AFNI_logger("3dFFT",argc,argv) ; /*--- scan args ---*/ iarg = 1 ; while( iarg < argc && argv[iarg][0] == '-' ){ if( strncasecmp(argv[iarg],"-altI",5) == 0 ){ do_alt = 1 ; iarg++ ; continue ; } if( strncasecmp(argv[iarg],"-altOUT",5) == 0 ){ do_alt = -1 ; iarg++ ; continue ; } if( strncasecmp(argv[iarg],"-inverse",4) == 0 ){ Sign = +1 ; iarg++ ; continue ; } if( strncasecmp(argv[iarg],"-abs",4) == 0 ){ Mode = FFT_ABS ; iarg++ ; continue ; } if( strncasecmp(argv[iarg],"-phase",4) == 0 ){ Mode = FFT_PHASE ; iarg++ ; continue ; } if( strncasecmp(argv[iarg],"-complex",4) == 0 ){ Mode = FFT_COMPLEX ; iarg++ ; continue ; } if( strlen(argv[iarg]) == 3 && strncmp(argv[iarg],"-L",2) == 0 ){ int lll=-1 , mmm ; char *ept ; iarg++ ; if( iarg >= argc ) ERROR_exit("need an argument after option %s",argv[iarg-1]) ; lll = strtol( argv[iarg] , &ept , 10 ) ; if( *ept != '\0' ) ERROR_exit("bad argument after option %s",argv[iarg-1]) ; if( lll > 0 && (mmm = csfft_nextup_even(lll)) != lll ) ERROR_exit( "'%s %d' is not a legal FFT length here: next largest legal value = %d" , argv[iarg-1] , lll , mmm ) ; switch( argv[iarg-1][2] ){ case 'x': case 'X': Lxx = lll ; break ; case 'y': case 'Y': Lyy = lll ; break ; case 'z': case 'Z': Lzz = lll ; break ; default: ERROR_exit("unknown option '%s'",argv[iarg-1]) ; } iarg++ ; continue ; } if( strncasecmp(argv[iarg],"-prefix",4) == 0 ){ iarg++ ; if( iarg >= argc ) ERROR_exit("need an argument after %s\n",argv[iarg-1]) ; prefix = strdup( argv[iarg] ) ; if( !THD_filename_ok(prefix) ) ERROR_exit("bad argument after %s\n",argv[iarg-1]) ; iarg++ ; continue ; } if( strncasecmp(argv[iarg],"-input",4) == 0 ){ iarg++ ; if( iarg >= argc ) ERROR_exit("need an argument after %s\n",argv[iarg-1]) ; dset_in = THD_open_dataset(argv[iarg]); CHECK_OPEN_ERROR(dset_in,argv[iarg]); iarg++ ; continue ; } ERROR_exit("unknown option '%s'\n",argv[iarg]) ; } /* check for simple errors */ if( Lxx == 0 && Lyy == 0 && Lzz == 0 ) ERROR_exit("-Lx, -Ly, -Lz all given as zero?!") ; /* open input dataset */ if( dset_in == NULL ){ if( iarg >= argc ) ERROR_exit("no input dataset on command line?!\n") ; dset_in = THD_open_dataset(argv[iarg]); CHECK_OPEN_ERROR(dset_in,argv[iarg]); } nx = DSET_NX(dset_in) ; ny = DSET_NY(dset_in) ; nz = DSET_NZ(dset_in) ; if( DSET_NVALS(dset_in) > 1 ) WARNING_message("only 3dFFT-ing sub-brick #0 of input dataset") ; /* establish actual FFT lengths now (0 ==> no FFT) */ if( nx == 1 ) Lxx = 0 ; /* can't FFT if dataset is shrimpy! */ if( ny == 1 ) Lyy = 0 ; if( nz == 1 ) Lzz = 0 ; if( Lxx < 0 ) Lxx = csfft_nextup_even(nx) ; /* get FFT length from */ if( Lyy < 0 ) Lyy = csfft_nextup_even(ny) ; /* dataset dimensions */ if( Lzz < 0 ) Lzz = csfft_nextup_even(nz) ; INFO_message("x-axis length=%d ; FFT length=%d %s",nx,Lxx,(Lxx==0)?"==> none":"\0") ; INFO_message("y-axis length=%d ; FFT length=%d %s",ny,Lyy,(Lyy==0)?"==> none":"\0") ; INFO_message("z-axis length=%d ; FFT length=%d %s",nz,Lzz,(Lzz==0)?"==> none":"\0") ; if( Lxx > 0 && Lxx < nx ) ERROR_exit("x-axis FFT length too short for data!") ; if( Lyy > 0 && Lyy < ny ) ERROR_exit("y-axis FFT length too short for data!") ; if( Lzz > 0 && Lzz < nz ) ERROR_exit("z-axis FFT length too short for data!") ; /* extract sub-brick #0 */ DSET_load(dset_in) ; CHECK_LOAD_ERROR(dset_in) ; inim = mri_to_complex( DSET_BRICK(dset_in,0) ) ; /* convert input to complex */ fac = DSET_BRICK_FACTOR(dset_in,0) ; if( fac > 0.0f && fac != 1.0f ){ /* scale it if needed */ int ii , nvox = nx*ny*nz ; complex *car = MRI_COMPLEX_PTR(inim) ; for( ii=0 ; ii < nvox ; ii++ ){ car[ii].r *= fac ; car[ii].i *= fac ; } } DSET_unload(dset_in) ; /* input data is all copied now */ /* FFT to get output image */ csfft_scale_inverse(1) ; /* scale by 1/N for inverse FFTs */ outim = mri_fft_3D( Sign , inim , Lxx,Lyy,Lzz , do_alt ) ; mri_free(inim) ; /* post-process output? */ switch( Mode ){ case FFT_ABS:{ MRI_IMAGE *qim = mri_complex_abs(outim) ; mri_free(outim) ; outim = qim ; } break ; case FFT_PHASE:{ MRI_IMAGE *qim = mri_complex_phase(outim) ; mri_free(outim) ; outim = qim ; } break ; } /* create and write output dataset */ dset_out = EDIT_empty_copy( dset_in ) ; tross_Copy_History( dset_in , dset_out ) ; tross_Make_History( "3dFFT" , argc,argv , dset_out ) ; LOAD_IVEC3( iv , outim->nx , outim->ny , outim->nz ) ; EDIT_dset_items( dset_out , ADN_prefix , prefix , ADN_nvals , 1 , ADN_ntt , 0 , ADN_nxyz , iv , /* change dimensions, possibly */ ADN_none ) ; EDIT_BRICK_FACTOR( dset_out , 0 , 0.0 ) ; EDIT_substitute_brick( dset_out , 0 , outim->kind , mri_data_pointer(outim) ) ; DSET_write(dset_out) ; WROTE_DSET(dset_out) ; DSET_unload(dset_out) ; exit(0) ; }
int main( int argc , char *argv[] ) { THD_3dim_dataset *old_dset , *new_dset ; /* input and output datasets */ THD_3dim_dataset *mask_dset=NULL ; float mask_bot=666.0 , mask_top=-666.0 ; byte *cmask=NULL ; int ncmask=0 ; byte *mmm = NULL ; int mcount=0, verb=0; int nopt, nbriks, ii ; int addBriks = 0 ; /* n-1 sub-bricks out */ int fullBriks = 0 ; /* n sub-bricks out */ int tsout = 0 ; /* flag to output a time series (not a stat bucket) */ int numMultBriks,methIndex,brikIndex; /*----- Help the pitiful user? -----*/ /* bureaucracy */ mainENTRY("3dTstat main"); machdep(); AFNI_logger("3dTstat",argc,argv); PRINT_VERSION("3dTstat"); AUTHOR("KR Hammett & RW Cox"); /*--- scan command line for options ---*/ if (argc == 1) { usage_3dTstat(1); exit(0); } /* Bob's help shortcut */ nopt = 1 ; nbriks = 0 ; nmeths = 0 ; verb = 0; while( nopt < argc && argv[nopt][0] == '-' ){ if (strcmp(argv[nopt], "-h") == 0 || strcmp(argv[nopt], "-help") == 0) { usage_3dTstat(strlen(argv[nopt]) > 3 ? 2:1); exit(0); } if( strcmp(argv[nopt],"-verb") == 0 ){ verb++ ; nopt++ ; continue ; } /*-- methods --*/ if( strcasecmp(argv[nopt],"-centromean") == 0 ){ /* 01 Nov 2010 */ meth[nmeths++] = METH_CENTROMEAN ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-bmv") == 0 ){ meth[nmeths++] = METH_BMV ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-median") == 0 ){ meth[nmeths++] = METH_MEDIAN ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-nzmedian") == 0 ){ meth[nmeths++] = METH_NZMEDIAN ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-DW") == 0 ){ meth[nmeths++] = METH_DW ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-zcount") == 0 ){ meth[nmeths++] = METH_ZCOUNT ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-nzcount") == 0 ){ meth[nmeths++] = METH_NZCOUNT ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-MAD") == 0 ){ meth[nmeths++] = METH_MAD ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-mean") == 0 ){ meth[nmeths++] = METH_MEAN ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-sum") == 0 ){ meth[nmeths++] = METH_SUM ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-sos") == 0 ){ meth[nmeths++] = METH_SUM_SQUARES ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-abssum") == 0 ){ meth[nmeths++] = METH_ABSSUM ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-slope") == 0 ){ meth[nmeths++] = METH_SLOPE ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-stdev") == 0 || strcasecmp(argv[nopt],"-sigma") == 0 ){ meth[nmeths++] = METH_SIGMA ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-cvar") == 0 ){ meth[nmeths++] = METH_CVAR ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-cvarinv") == 0 ){ meth[nmeths++] = METH_CVARINV ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-stdevNOD") == 0 || strcasecmp(argv[nopt],"-sigmaNOD") == 0 ){ /* 07 Dec 2001 */ meth[nmeths++] = METH_SIGMA_NOD ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-cvarNOD") == 0 ){ /* 07 Dec 2001 */ meth[nmeths++] = METH_CVAR_NOD ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-cvarinvNOD") == 0 ){ meth[nmeths++] = METH_CVARINVNOD ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-min") == 0 ){ meth[nmeths++] = METH_MIN ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-max") == 0 ){ meth[nmeths++] = METH_MAX ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-absmax") == 0 ){ meth[nmeths++] = METH_ABSMAX ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-signed_absmax") == 0 ){ meth[nmeths++] = METH_SIGNED_ABSMAX ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-argmin") == 0 ){ meth[nmeths++] = METH_ARGMIN ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-argmin1") == 0 ){ meth[nmeths++] = METH_ARGMIN1 ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-argmax") == 0 ){ meth[nmeths++] = METH_ARGMAX ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-argmax1") == 0 ){ meth[nmeths++] = METH_ARGMAX1 ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-argabsmax") == 0 ){ meth[nmeths++] = METH_ARGABSMAX ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-argabsmax1") == 0 ){ meth[nmeths++] = METH_ARGABSMAX1; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-duration") == 0 ){ meth[nmeths++] = METH_DURATION ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-onset") == 0 ){ meth[nmeths++] = METH_ONSET ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-offset") == 0 ){ meth[nmeths++] = METH_OFFSET ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-centroid") == 0 ){ meth[nmeths++] = METH_CENTROID ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-centduration") == 0 ){ meth[nmeths++] = METH_CENTDURATION ; nbriks++ ; nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-nzmean") == 0 ){ meth[nmeths++] = METH_NZMEAN ; nbriks++ ; nopt++ ; continue ; } if( strncmp(argv[nopt],"-mask",5) == 0 ){ if( mask_dset != NULL ) ERROR_exit("Cannot have two -mask options!\n") ; if( nopt+1 >= argc ) ERROR_exit("-mask option requires a following argument!\n"); mask_dset = THD_open_dataset( argv[++nopt] ) ; if( mask_dset == NULL ) ERROR_exit("Cannot open mask dataset!\n") ; if( DSET_BRICK_TYPE(mask_dset,0) == MRI_complex ) ERROR_exit("Cannot deal with complex-valued mask dataset!\n"); nopt++ ; continue ; } if( strncmp(argv[nopt],"-mrange",5) == 0 ){ if( nopt+2 >= argc ) ERROR_exit("-mrange option requires 2 following arguments!\n"); mask_bot = strtod( argv[++nopt] , NULL ) ; mask_top = strtod( argv[++nopt] , NULL ) ; if( mask_top < mask_top ) ERROR_exit("-mrange inputs are illegal!\n") ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-cmask") == 0 ){ /* 16 Mar 2000 */ if( nopt+1 >= argc ) ERROR_exit("-cmask option requires a following argument!\n"); cmask = EDT_calcmask( argv[++nopt] , &ncmask, 0 ) ; if( cmask == NULL ) ERROR_exit("Can't compute -cmask!\n"); nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-autocorr") == 0 ){ meth[nmeths++] = METH_AUTOCORR ; if( ++nopt >= argc ) ERROR_exit("-autocorr needs an argument!\n"); meth[nmeths++] = atoi(argv[nopt++]); if (meth[nmeths - 1] == 0) { addBriks++; } else { nbriks+=meth[nmeths - 1] ; } continue ; } if( strcasecmp(argv[nopt],"-autoreg") == 0 ){ meth[nmeths++] = METH_AUTOREGP ; if( ++nopt >= argc ) ERROR_exit("-autoreg needs an argument!\n"); meth[nmeths++] = atoi(argv[nopt++]); if (meth[nmeths - 1] == 0) { addBriks++; } else { nbriks+=meth[nmeths - 1] ; } continue ; } if( strcasecmp(argv[nopt],"-accumulate") == 0 ){ /* 4 Mar 2008 [rickr] */ meth[nmeths++] = METH_ACCUMULATE ; meth[nmeths++] = -1; /* flag to add N (not N-1) output bricks */ fullBriks++; tsout = 1; /* flag to output a timeseries */ nopt++ ; continue ; } if( strcasecmp(argv[nopt],"-l2norm") == 0 ){ /* 07 Jan 2013 [rickr] */ meth[nmeths++] = METH_L2_NORM ; nbriks++ ; nopt++ ; continue ; } /*-- prefix --*/ if( strcasecmp(argv[nopt],"-prefix") == 0 ){ if( ++nopt >= argc ) ERROR_exit("-prefix needs an argument!\n"); MCW_strncpy(prefix,argv[nopt],THD_MAX_PREFIX) ; if( !THD_filename_ok(prefix) ) ERROR_exit("%s is not a valid prefix!\n",prefix); nopt++ ; continue ; } /*-- tdiff --*/ if( strcasecmp(argv[nopt],"-tdiff") == 0 ){ /* 25 May 2011 */ do_tdiff = 1 ; nopt++ ; continue ; } /*-- nscale --*/ if( strcasecmp(argv[nopt],"-nscale") == 0 ){ /* 25 May 2011 */ nscale = 1 ; nopt++ ; continue ; } /*-- datum --*/ if( strcasecmp(argv[nopt],"-datum") == 0 ){ if( ++nopt >= argc ) ERROR_exit("-datum needs an argument!\n"); if( strcasecmp(argv[nopt],"short") == 0 ){ datum = MRI_short ; } else if( strcasecmp(argv[nopt],"float") == 0 ){ datum = MRI_float ; } else if( strcasecmp(argv[nopt],"byte") == 0 ){ datum = MRI_byte ; } else { ERROR_exit("-datum of type '%s' is not supported!\n", argv[nopt] ) ; } nopt++ ; continue ; } /* base percentage for duration calcs */ if (strcasecmp (argv[nopt], "-basepercent") == 0) { if( ++nopt >= argc ) ERROR_exit("-basepercent needs an argument!\n"); basepercent = strtod(argv[nopt], NULL); if(basepercent>1) basepercent /= 100.0; /* assume integer percent if >1*/ nopt++; continue; } /*-- Quien sabe'? --*/ ERROR_message("Unknown option: %s\n",argv[nopt]) ; suggest_best_prog_option(argv[0], argv[nopt]); exit(1); } if (argc < 2) { ERROR_message("Too few options, use -help for details"); exit(1); } /*--- If no options selected, default to single stat MEAN -- KRH ---*/ if (nmeths == 0) nmeths = 1; if (nbriks == 0 && addBriks == 0 && fullBriks == 0) nbriks = 1; /*----- read input dataset -----*/ if( nopt >= argc ) ERROR_exit(" No input dataset!?") ; old_dset = THD_open_dataset( argv[nopt] ) ; if( !ISVALID_DSET(old_dset) ) ERROR_exit("Can't open dataset %s\n",argv[nopt]); nopt++ ; if( nopt < argc ) WARNING_message("Trailing datasets on command line ignored: %s ...",argv[nopt]) ; if( DSET_NVALS(old_dset) == 1 ){ WARNING_message("Input dataset has 1 sub-brick ==> -tdiff is turned off") ; do_tdiff = 0 ; } /* no input volumes is bad, 1 volume applies to only certain methods */ /* 2 Nov 2010 [rickr] */ if( DSET_NVALS(old_dset) == 0 ) { ERROR_exit("Time series is of length 0?\n") ; } else if( DSET_NVALS(old_dset) == 1 || (do_tdiff && DSET_NVALS(old_dset)==2) ) { int methOK, OK = 1; /* see if each method is valid for nvals == 1 */ for( methIndex = 0; methIndex < nmeths; methIndex++ ) { methOK = 0; for( ii = 0; ii < NUM_1_INPUT_METHODS; ii++ ) { if( meth[methIndex] == valid_1_input_methods[ii] ) { methOK = 1; break; } } if( ! methOK ) ERROR_exit("Can't use dataset with %d values per voxel!" , DSET_NVALS(old_dset) ) ; } /* tell the library function that this case is okay */ g_thd_maker_allow_1brick = 1; } if( DSET_NUM_TIMES(old_dset) < 2 ){ WARNING_message("Input dataset is not 3D+time; assuming TR=1.0") ; EDIT_dset_items( old_dset , ADN_ntt , DSET_NVALS(old_dset) , ADN_ttorg , 0.0 , ADN_ttdel , 1.0 , ADN_tunits , UNITS_SEC_TYPE , NULL ) ; } /* If one or more of the -autocorr/-autoreg options was called with */ /* an argument of 0, then I'll now add extra BRIKs for the N-1 data */ /* output points for each. */ nbriks += ((DSET_NVALS(old_dset)-1) * addBriks); nbriks += ((DSET_NVALS(old_dset) ) * fullBriks); /* ------------- Mask business -----------------*/ if( mask_dset == NULL ){ mmm = NULL ; if( verb ) INFO_message("%d voxels in the entire dataset (no mask)\n", DSET_NVOX(old_dset)) ; } else { if( DSET_NVOX(mask_dset) != DSET_NVOX(old_dset) ) ERROR_exit("Input and mask datasets are not same dimensions!\n"); mmm = THD_makemask( mask_dset , 0 , mask_bot, mask_top ) ; mcount = THD_countmask( DSET_NVOX(old_dset) , mmm ) ; if( mcount <= 0 ) ERROR_exit("No voxels in the mask!\n") ; if( verb ) INFO_message("%d voxels in the mask\n",mcount) ; DSET_delete(mask_dset) ; } if( cmask != NULL ){ if( ncmask != DSET_NVOX(old_dset) ) ERROR_exit("Input and cmask datasets are not same dimensions!\n"); if( mmm != NULL ){ for( ii=0 ; ii < DSET_NVOX(old_dset) ; ii++ ) mmm[ii] = (mmm[ii] && cmask[ii]) ; free(cmask) ; mcount = THD_countmask( DSET_NVOX(old_dset) , mmm ) ; if( mcount <= 0 ) ERROR_exit("No voxels in the mask+cmask!\n") ; if( verb ) INFO_message("%d voxels in the mask+cmask\n",mcount) ; } else { mmm = cmask ; mcount = THD_countmask( DSET_NVOX(old_dset) , mmm ) ; if( mcount <= 0 ) ERROR_exit("No voxels in the cmask!\n") ; if( verb ) INFO_message("%d voxels in the cmask\n",mcount) ; } } /*------------- ready to compute new dataset -----------*/ new_dset = MAKER_4D_to_typed_fbuc( old_dset , /* input dataset */ prefix , /* output prefix */ datum , /* output datum */ 0 , /* ignore count */ 0 , /* can't detrend in maker function KRH 12/02*/ nbriks , /* number of briks */ STATS_tsfunc , /* timeseries processor */ NULL, /* data for tsfunc */ mmm, nscale ) ; if( new_dset != NULL ){ tross_Copy_History( old_dset , new_dset ) ; tross_Make_History( "3dTstat" , argc,argv , new_dset ) ; for (methIndex = 0,brikIndex = 0; methIndex < nmeths; methIndex++, brikIndex++) { if ((meth[methIndex] == METH_AUTOCORR) || (meth[methIndex] == METH_ACCUMULATE) || (meth[methIndex] == METH_AUTOREGP)) { numMultBriks = meth[methIndex+1]; /* note: this looks like it should be NV-1 4 Mar 2008 [rickr] */ if (numMultBriks == 0) numMultBriks = DSET_NVALS(old_dset)-1; /* new flag for NVALS [rickr] */ if (numMultBriks == -1) numMultBriks = DSET_NVALS(old_dset); for (ii = 1; ii <= numMultBriks; ii++) { char tmpstr[25]; if (meth[methIndex] == METH_AUTOREGP) { sprintf(tmpstr,"%s[%d](%d)",meth_names[meth[methIndex]], numMultBriks,ii); } else { sprintf(tmpstr,"%s(%d)",meth_names[meth[methIndex]],ii); } EDIT_BRICK_LABEL(new_dset, (brikIndex + ii - 1), tmpstr) ; } methIndex++; brikIndex += numMultBriks - 1; } else { EDIT_BRICK_LABEL(new_dset, brikIndex, meth_names[meth[methIndex]]) ; } } if( tsout ) /* then change output to a time series */ EDIT_dset_items( new_dset , ADN_ntt , brikIndex , ADN_ttorg , DSET_TIMEORIGIN(old_dset) , ADN_ttdel , DSET_TIMESTEP(old_dset) , ADN_tunits , DSET_TIMEUNITS(old_dset) , NULL ) ; DSET_write( new_dset ) ; WROTE_DSET( new_dset ) ; } else { ERROR_exit("Unable to compute output dataset!\n") ; } exit(0) ; }
int main( int argc , char *argv[] ) { int nopt , nbad=0 ; char *vlist, *expr , *mess ; int showgood=1; /* 21 Mar 2016 [rickr] */ /*-------------------------------------------------------------------------*/ if( argc < 2 || strcasecmp(argv[1],"-help") == 0 ){ printf("\n" "The function of program GLTsymtest is to test a set of '-gltsym'\n" "strings -- for use with 3dDeconvolve or 3dREMLfit -- for validity.\n" "\n" "Usage: GLTsymtest [options] varlist expr [expr ...]\n" "\n" " options (only 1 so far):\n" "\n" " -badonly : output only BAD messages, rather than all\n" "\n" "* 'varlist' is a list of allowed variable names in the expression.\n" " These names can be separated by commans, semicolons, and/or\n" " spaces (varlist would have to be in quotes if it contains spaces).\n" "\n" "* Each 'expr' is a GLT symbolic expression, which should be in quotes\n" " since different components are separated by blanks.\n" "\n" "EXAMPLES\n" "-------\n" " GLTsymtest -badonly 'Vrel Arel' 'Vrel -Arel' 'Verl + +aud'\n" "\n" " GLTsymtest 'Vrel Arel' 'Vrel -Arel' 'Verl + +aud'\n" "\n" " The first expression is good, but the second has both variable names\n" " mis-typed; the output from this program would include these messages:\n" "\n" " ***** Scanned GLT messages *****\n" " ++ -gltsym is: 'Vrel -Arel'\n" " ++ INFO: Allowed variable list is 'Vrel Arel'\n" " ++ INFO: This gltsym appears to be OKAY :-)\n" "\n" " ***** Scanned GLT messages *****\n" " ++ -gltsym is: 'Verl + +aud'\n" " ++ INFO: Allowed variable list is 'Vrel Arel'\n" " ++ INFO: -gltsym: isolated '+' is being ignored\n" " ** ERROR: -gltsym: can't match symbolic name 'Verl'\n" " ** ERROR: -gltsym: can't match symbolic name 'aud'\n" " ** SORRY: This gltsym appears to be BAD :-(\n" "\n" "NOTES\n" "-----\n" "* GLTsymtest does not check subscripts on variable names against the legal\n" " range for the name, since the information about the dimensionality of\n" " the beta vector associated with each name is not available here.\n" "\n" "* The exit status for this program is the number of expressions that had\n" " at least one ERROR message. In the example above, this status would be 1.\n" "\n" "* The text output goes to stdout.\n" "\n" "\n" "* Authored by RWCox on May Day 2015 to aid Rick Reynolds in detecting such\n" " problems, induced for example when his boss does someting stupid during\n" " an AFNI bootcamp in South Africa (a purely hypothetical case, I assure you).\n" "\n" ) ; exit(0) ; } /*-------------------------------------------------------------------------*/ mainENTRY("GLTsymtest"); machdep(); /* 21 Mar 2016 */ for( nopt=1; nopt < argc; nopt++ ) { if( ! strcmp(argv[nopt], "-badonly" ) ) showgood = 0; else break; } if( argc-nopt < 2 ) ERROR_exit("GLTsymtest: missing labels or GLTs (too few args)") ; vlist = argv[nopt] ; for( nopt++ ; nopt < argc ; nopt++ ){ expr = argv[nopt] ; mess = SYM_test_gltsym(vlist,expr) ; if( mess != NULL ){ if( strstr(mess,"** ERROR:") != NULL ) { nbad++ ; puts(mess) ; } else if ( showgood ) puts(mess) ; free(mess) ; } } exit(nbad) ; }
int main( int argc , char *argv[] ) { char *prefix = "Deghost" ; int iarg ; int fe=1 , pe=2 , se=3 , nvals ; THD_3dim_dataset *inset=NULL , *outset , *filset=NULL ; if( argc < 2 || strcmp(argv[1],"-help") == 0 ) { printf( "Usage: 3dDeghost [options] dataset\n" "\n" "* This program tries do remove N/2 (AKA Nyquist) ghosts from an EPI\n" " magnitude time series dataset.\n" "* If you apply it to some other kind of dataset (e.g., spiral), weird\n" " things will probably transpire.\n" "* The input EPI dataset should NOT be filtered, masked, cropped,\n" " registered, or pre-processed in any way!\n" "* This program will not work well if the input EPI dataset is heavily\n" " 'shaded' -- that is, its intensity varies dramatically inside the brain.\n" "* The output dataset is always stored in float format.\n" "* Only the Amitabha Buddha knows if this program is actually useful.\n" "\n" "========\n" "OPTIONS:\n" "========\n" " -input dataset = Another way to specify the input dataset\n" " -prefix pp = Use 'pp' for prefix of output dataset\n" " -FPS abc = Define the Frequency, Phase, and Slice\n" " directions in the dataset based on the\n" " axis orientations inside the dataset header\n" " (e.g., see the output of 3dinfo). The 'abc'\n" " code is a permutaton of the digits '123'.\n" " * The first digit 'a' specifies which dataset\n" " axis/index is the Frequency encoding direction.\n" " * The second digit 'b' specifies which dataset\n" " direction is the Phase encoding direction.\n" " * The third digit 'c' specifies which dataset\n" " direction is the Slice encoding direction.\n" " -->>** The default value for 'abc' is '123'; that is,\n" " the dataset is ordered so that the first index\n" " (x-axis) is frequency, the second index is phase,\n" " and the third index is slice. In most cases,\n" " this is how the reconstruction software will\n" " store the images. Only in unusual cases should\n" " you need the '-FPS' option!\n" " -filt N = Length of time series filter to apply when\n" " estimating ghosting parameters. Set N to 0 or 1\n" " to turn this feature off; otherwise, N should be an\n" " odd positive integer from 3 to 19 [default N=%d].\n" " * Longer filter lengths ARE allowed, but will be slow\n" " (cases with N <= 19 are hand coded for speed).\n" " * Datasets with fewer than 4 time points will not\n" " be filtered. For longer datasets, if the filter\n" " length is too big, it will be shortened ruthlessly.\n" "=======\n" "METHOD:\n" "=======\n" "Would you believe me if I said magic? Would you accept secret algorithms\n" "known only to the Olmecs? How about something so ad hoc that it cannot\n" "be described without embarrasment and shame?\n" "\n" "-- Feb 2014 - Zhark the Phantasmal\n" , orfilt_len ) ; PRINT_COMPILE_DATE ; exit(0) ; } mainENTRY("3dDeghost main"); machdep(); AFNI_logger("3dDeghost",argc,argv); PRINT_VERSION("3dDeghost") ; /*-- scan command line --*/ iarg = 1 ; while( iarg < argc && argv[iarg][0] == '-' ) { /*---*/ if( strcasecmp(argv[iarg],"-quiet") == 0 ) { verb = 0 ; iarg++ ; continue ; } if( strcasecmp(argv[iarg],"-verb") == 0 ) { verb++ ; iarg++ ; continue ; } /*---*/ if( strcasecmp(argv[iarg],"-filt") == 0 ) { if( ++iarg >= argc ) ERROR_exit("Need argument after option '%s'",argv[iarg-1]) ; orfilt_len = (int)strtod(argv[iarg],NULL) ; if( orfilt_len > 1 && orfilt_len%2 == 0 ) { orfilt_len++ ; INFO_message("-filt %d has been adjusted to %d (must be odd)" , orfilt_len-1 , orfilt_len) ; } if( orfilt_len > 19 ) WARNING_message("-filt %d is over the recommended limit of 19",orfilt_len) ; iarg++ ; continue ; } /*---*/ if( strcasecmp(argv[iarg],"-prefix") == 0 ) { if( ++iarg >= argc ) ERROR_exit("Need argument after option '%s'",argv[iarg-1]) ; prefix = argv[iarg] ; if( !THD_filename_ok(prefix) ) ERROR_exit("Illegal value after -prefix!\n"); iarg++ ; continue ; } /*---*/ if( strcasecmp(argv[iarg],"-input") == 0 || strcasecmp(argv[iarg],"-inset") == 0 ) { if( ++iarg >= argc ) ERROR_exit("Need argument after option '%s'",argv[iarg-1]) ; if( inset != NULL ) ERROR_exit("You can't give the input dataset twice!") ; inset = THD_open_dataset( argv[iarg] ) ; CHECK_OPEN_ERROR(inset,argv[iarg]) ; DSET_load(inset) ; CHECK_LOAD_ERROR(inset) ; iarg++ ; continue ; } /*---*/ if( strcasecmp(argv[iarg],"-FPS") == 0 ) { /* stolen from 3dAllineate.c */ char *fps ; if( ++iarg >= argc ) ERROR_exit("Need argument after option '%s'",argv[iarg-1]) ; fps = argv[iarg] ; if( strlen(fps) < 3 ) ERROR_exit("Code '%s' after '%s' is too short", fps , argv[iarg-1] ) ; switch( fps[0] ) { default: ERROR_exit("Illegal '%s' F code '%c' :-(" , argv[iarg-1],fps[0] ); case 'i': case 'I': case 'x': case 'X': case '1': fe = 1; break; case 'j': case 'J': case 'y': case 'Y': case '2': fe = 2; break; case 'k': case 'K': case 'z': case 'Z': case '3': fe = 3; break; } switch( fps[1] ) { default: ERROR_exit("Illegal '%s' P code '%c' :-(" , argv[iarg-1],fps[1] ); case 'i': case 'I': case 'x': case 'X': case '1': pe = 1; break; case 'j': case 'J': case 'y': case 'Y': case '2': pe = 2; break; case 'k': case 'K': case 'z': case 'Z': case '3': pe = 3; break; } switch( fps[2] ) { default: ERROR_exit("Illegal '%s' S code '%c' :-(" , argv[iarg-1],fps[2] ); case 'i': case 'I': case 'x': case 'X': case '1': se = 1; break; case 'j': case 'J': case 'y': case 'Y': case '2': se = 2; break; case 'k': case 'K': case 'z': case 'Z': case '3': se = 3; break; } if( fe+pe+se != 6 ) ERROR_exit("Code '%s' after '%s' is nonsensical", fps , argv[iarg-1] ) ; iarg++ ; continue ; } /*---*/ ERROR_exit("Unknown option: %s\n",argv[iarg]); } if( inset == NULL && iarg >= argc ) ERROR_exit("No dataset name on command line?\n"); /*-- read input if needed --*/ if( inset == NULL ) { inset = THD_open_dataset( argv[iarg] ) ; CHECK_OPEN_ERROR(inset,argv[iarg]) ; DSET_load( inset ) ; CHECK_LOAD_ERROR(inset) ; } /*-- filter input? --*/ nvals = DSET_NVALS(inset) ; if( orfilt_len > nvals/2 ) { orfilt_len = nvals/2 ; if( orfilt_len%2 == 0 ) orfilt_len++ ; } if( orfilt_len > 1 && nvals > 1 ) { MRI_vectim *invect ; int ii ; if( verb ) INFO_message("Filtering input dataset: filter length=%d",orfilt_len) ; invect = THD_dset_to_vectim(inset,NULL,0) ; THD_vectim_applyfunc( invect , orfilt_vector ) ; filset = EDIT_empty_copy( inset ) ; for( ii=0 ; ii < nvals ; ii++ ) EDIT_substitute_brick( filset , ii , MRI_float , NULL ) ; THD_vectim_to_dset( invect , filset ) ; VECTIM_destroy(invect) ; } else { if( verb ) INFO_message("Time series filtering is turned off") ; } /***** outsource the work *****/ outset = THD_deghoster( inset , (filset!=NULL)?filset:inset , pe,fe,se ) ; if( outset == NULL ) ERROR_exit("THD_deghoster fails :-(((") ; if( filset != NULL ) DSET_delete(filset) ; EDIT_dset_items( outset , ADN_prefix,prefix , ADN_none ) ; tross_Copy_History( inset , outset ) ; tross_Make_History( "3dDeghost" , argc,argv , outset ) ; DSET_write(outset) ; WROTE_DSET(outset) ; exit(0) ; }
int main(int argc, char **argv) { char *ppp=NULL , *sin ; int ii, iarg=1 , do_sin=0 , do_printf=0 , do_mul=0 , do_length=1 ; int do_stimes=0, do_stimes_verb=0 ; if( argc < 2 || strcmp(argv[1],"-help") == 0 ){ printf("Usage: dicom_hdr [options] fname [...]\n" "Prints information from the DICOM file 'fname' to stdout.\n" "Multiple files can be given on the command line.\n" "\n" "OPTIONS:\n" " -hex = Include hexadecimal printout for integer values.\n" " -noname = Don't include element names in the printout.\n" " -sexinfo = Dump Siemens EXtra INFO text (0029 1020), if present\n" " (can be VERY lengthy).\n" " -mulfram = Dump multi-frame information, if present\n" " (1 line per frame, plus an XML-style header/footer)\n" " [-mulfram also implies -noname]\n" " -v n = Dump n words of binary data also.\n" #if 0 " -printf = Use 'printf' directly, instead of an intermediate string.\n" #endif "\n" " -no_length = Skip lengths and offsets (helps diffs).\n" " -slice_times = Show slice times from Siemens mosaic images.\n" " -slice_times_verb = Same, but be more verbose about it.\n" "\n" "Based on program dcm_dump_file from the RSNA, developed at\n" "the Mallinckrodt Institute of Radiology. See the source\n" "code file mri_dicom_hdr.c for their Copyright and license.\n" "\n" "SOME SAMPLE OUTPUT LINES:\n" "\n" "0028 0010 2 [1234 ] // IMG Rows// 512\n" "0028 0011 2 [1244 ] // IMG Columns// 512\n" "0028 0030 18 [1254 ] // IMG Pixel Spacing//0.488281\\0.488281\n" "0028 0100 2 [1280 ] // IMG Bits Allocated// 16\n" "0028 0101 2 [1290 ] // IMG Bits Stored// 12\n" "0028 0102 2 [1300 ] // IMG High Bit// 11\n" "\n" "* The first 2 numbers on each line are the DICOM group and element tags,\n" " in hexadecimal.\n" "* The next number is the number of data bytes, in decimal.\n" "* The next number [in brackets] is the offset in the file of the data,\n" " in decimal. This is where the data bytes start, and does not include\n" " the tag, Value Representation, etc.\n" "* If -noname is NOT given, then the string in the '// ... //' region is\n" " the standard DICOM dictionary name for this data element. If this string\n" " is blank, then this element isn't in the dictionary (e.g., is a private\n" " tag, or an addition to DICOM that the program doesn't know about, etc.).\n" "* The value after the last '//' is the value of the data in the element.\n" "* In the example above, we have a 512x512 image with 0.488281 mm pixels,\n" " with 12 bits (stored in 16 bits) per pixel.\n" "* For vastly more detail on DICOM standard, you can start with the\n" " documents at ftp://afni.nimh.nih.gov/dicom/ (1000+ pages of PDF)!\n" "* Also see program dicom_hinfo -- which will print out just a few user-chosen\n" " values for each input file. It can be used in a script to sort through\n" " a lot of files at once.\n" ); exit(0); } mainENTRY("dicom_hdr main") ; machdep() ; mri_dicom_nohex( 1 ) ; while( argv[iarg] && argv[iarg][0] == '-' ){ if( strcmp(argv[iarg],"-sexinfo") == 0 ){ /* 23 Dec 2002 */ do_sin++ ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-printf") == 0 ){ /* 02 May 2008 */ do_printf++ ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-no_length") == 0 ){ /* 17 Oct 2012 [rickr] */ do_length = 0 ; iarg++ ; continue ; } if( strncmp(argv[iarg],"-mulfram",4) == 0 ){ /* 05 May 2008 */ mri_dicom_noname(1) ; do_mul++ ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-hex") == 0 ){ mri_dicom_nohex(0) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-noname") == 0 ){ mri_dicom_noname(1) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-slice_times") == 0 ){ /* 14 Apr 2010 [rickr] */ do_stimes++ ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-slice_times_verb") == 0 ){ /* 15 Apr 2010 */ do_stimes++ ; /* redundant, but for complete output */ do_stimes_verb++ ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-v") == 0 ){ int vv = strtol( argv[++iarg] , NULL , 10 ) ; if( vv > 0 ) mri_dicom_setvm( vv ) ; else fprintf(stderr,"*** Illegal value after -v!\n") ; iarg++ ; continue ; } fprintf(stderr,"*** Unknown option: %s\n",argv[iarg]) ; iarg++ ; } if( iarg == argc ) { fprintf(stderr,"** no input files?\n"); return 0; } mri_dicom_header_use_printf(do_printf) ; /* 02 May 2008 */ mri_dicom_header_show_size_offset(do_length) ; /* 17 Oct 2012 [rickr] */ if( do_stimes_verb ) mri_sst_set_verb(1+do_stimes_verb); /* 02 May 2011 */ for( ii=iarg ; ii < argc ; ii++ ){ if( ii > iarg ) printf("---------------------------------------------------------------\n"); mri_dicom_seterr(-1) ; /* make sure all errors are printed - 07 May 2003 */ STATUS("calling funct mri_dicom_header()") ; if( ppp != NULL ) free(ppp) ; ppp = mri_dicom_header( argv[ii] ) ; /* show slice times (in lieu of header) 14 Apr 2011 [rickr] */ if( do_stimes ) { get_and_display_siemens_times(); continue; } if( !do_printf && ppp != NULL ){ off_t poff ; unsigned int plen ; printf("%s",ppp) ; mri_dicom_pxlarr( &poff , &plen ) ; if( plen > 0 ) printf("Pixel array offset = %u (bytes)\n" "Pixel array length = %u (bytes)\n" , (unsigned int)poff , plen ) ; if( do_sin ){ (void) mri_imcount_dicom( argv[ii] ) ; /* only to get the sexinfo */ sin = mri_dicom_sexinfo() ; if( sin ){ printf("................... Siemens Extra Info [0029 1020] ...................\n" "%s\n" , sin ) ; } else { printf("........... Siemens Extra Info [0029 1020] = NOT PRESENT .............\n"); } } if( do_mul ){ /* 05 May 2008 */ MultiFrame_info *mfi = AFD_scanfor_MultiFrame(ppp) ; if( mfi != NULL ){ int nz = mfi->nframe , jj ; printf("........... DICOM MultiFrame Information ...........\n"); printf("........... time_index stack_index xpos ypos zpos ...........\n"); printf("<DICOM_MultiFrame nframe='%d'>\n",nz) ; for( jj=0 ; jj < nz ; jj++ ){ printf(" %4d %4d" , mfi->time_index[jj] , mfi->stack_index[jj] ) ; if( mfi->xpos != NULL ) printf(" %.3f %.3f %.3f",mfi->xpos[jj],mfi->ypos[jj],mfi->zpos[jj]); printf("\n") ; } printf("</DICOM_MultiFrame>\n") ; KILL_MultiFrame(mfi) ; } else { printf("........... DICOM MultiFrame Information = ABSENT ...........\n"); } } } else if( !do_printf ) { printf("***\n*** ERROR: can't open %s as a DICOM file!\n***\n",argv[ii]) ; } } exit(0) ; }
int main( int argc , char * argv[] ) { int do_norm=0 , qdet=2 , have_freq=0 , do_automask=0 ; float dt=0.0f , fbot=0.0f,ftop=999999.9f , blur=0.0f ; MRI_IMARR *ortar=NULL ; MRI_IMAGE *ortim=NULL ; THD_3dim_dataset **ortset=NULL ; int nortset=0 ; THD_3dim_dataset *inset=NULL , *outset=NULL; char *prefix="RSFC" ; byte *mask=NULL ; int mask_nx=0,mask_ny=0,mask_nz=0,nmask , verb=1 , nx,ny,nz,nvox , nfft=0 , kk ; float **vec , **ort=NULL ; int nort=0 , vv , nopt , ntime ; MRI_vectim *mrv ; float pvrad=0.0f ; int nosat=0 ; int do_despike=0 ; // @@ non-BP variables float fbotALL=0.0f, ftopALL=999999.9f; // do full range version int NumDen = 0; // switch for doing numerator or denom THD_3dim_dataset *outsetALL=NULL ; int m, mm; float delf; // harmonics int ind_low,ind_high,N_ny, ctr; float sqnt,nt_fac; gsl_fft_real_wavetable *real1, *real2; // GSL stuff gsl_fft_real_workspace *work; double *series1, *series2; double *xx1,*xx2; float numer,denom,val; float *alff=NULL,*malff=NULL,*falff=NULL, *rsfa=NULL,*mrsfa=NULL,*frsfa=NULL; // values float meanALFF=0.0f,meanRSFA=0.0f; // will be for mean in brain region THD_3dim_dataset *outsetALFF=NULL; THD_3dim_dataset *outsetmALFF=NULL; THD_3dim_dataset *outsetfALFF=NULL; THD_3dim_dataset *outsetRSFA=NULL; THD_3dim_dataset *outsetmRSFA=NULL; THD_3dim_dataset *outsetfRSFA=NULL; char out_lff[300]; char out_alff[300]; char out_malff[300]; char out_falff[300]; char out_rsfa[300]; char out_mrsfa[300]; char out_frsfa[300]; char out_unBP[300]; int SERIES_OUT = 1; int UNBP_OUT = 0; int DO_RSFA = 1; int BP_LAST = 0; // option for only doing filter to LFFs at very end of proc float de_rsfa=0.0f,nu_rsfa=0.0f; double pow1=0.0,pow2=0.0; /*-- help? --*/ if( argc < 2 || strcmp(argv[1],"-help") == 0 ){ printf( "\n Program to calculate common resting state functional connectivity (RSFC)\n" " parameters (ALFF, mALFF, fALFF, RSFA, etc.) for resting state time\n" " series. This program is **heavily** based on the existing\n" " 3dBandPass by RW Cox, with the amendments to calculate RSFC\n" " parameters written by PA Taylor (July, 2012).\n" " This program is part of FATCAT (Taylor & Saad, 2013) in AFNI. Importantly,\n" " its functionality can be included in the `afni_proc.py' processing-script \n" " generator; see that program's help file for an example including RSFC\n" " and spectral parameter calculation via the `-regress_RSFC' option.\n" "\n" "* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *\n" "\n" " All options of 3dBandPass may be used here (with a couple other\n" " parameter options, as well): essentially, the motivation of this\n" " program is to produce ALFF, etc. values of the actual RSFC time\n" " series that you calculate. Therefore, all the 3dBandPass processing\n" " you normally do en route to making your final `resting state time\n" " series' is done here to generate your LFFs, from which the\n" " amplitudes in the LFF band are calculated at the end. In order to\n" " calculate fALFF, the same initial time series are put through the\n" " same processing steps which you have chosen but *without* the\n" " bandpass part; the spectrum of this second time series is used to\n" " calculate the fALFF denominator.\n" " \n" " For more information about each RSFC parameter, see, e.g.: \n" " ALFF/mALFF -- Zang et al. (2007),\n" " fALFF -- Zou et al. (2008),\n" " RSFA -- Kannurpatti & Biswal (2008).\n" "\n" "* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *\n" "\n" " + USAGE: 3dRSFC [options] fbot ftop dataset\n" "\n" "* One function of this program is to prepare datasets for input\n" " to 3dSetupGroupInCorr. Other uses are left to your imagination.\n" "\n" "* 'dataset' is a 3D+time sequence of volumes\n" " ++ This must be a single imaging run -- that is, no discontinuities\n" " in time from 3dTcat-ing multiple datasets together.\n" "\n" "* fbot = lowest frequency in the passband, in Hz\n" " ++ fbot can be 0 if you want to do a lowpass filter only;\n" " HOWEVER, the mean and Nyquist freq are always removed.\n" "\n" "* ftop = highest frequency in the passband (must be > fbot)\n" " ++ if ftop > Nyquist freq, then it's a highpass filter only.\n" "\n" "* Set fbot=0 and ftop=99999 to do an 'allpass' filter.\n" " ++ Except for removal of the 0 and Nyquist frequencies, that is.\n" "\n" "* You cannot construct a 'notch' filter with this program!\n" " ++ You could use 3dRSFC followed by 3dcalc to get the same effect.\n" " ++ If you are understand what you are doing, that is.\n" " ++ Of course, that is the AFNI way -- if you don't want to\n" " understand what you are doing, use Some other PrograM, and\n" " you can still get Fine StatisticaL maps.\n" "\n" "* 3dRSFC will fail if fbot and ftop are too close for comfort.\n" " ++ Which means closer than one frequency grid step df,\n" " where df = 1 / (nfft * dt) [of course]\n" "\n" "* The actual FFT length used will be printed, and may be larger\n" " than the input time series length for the sake of efficiency.\n" " ++ The program will use a power-of-2, possibly multiplied by\n" " a power of 3 and/or 5 (up to and including the 3rd power of\n" " each of these: 3, 9, 27, and 5, 25, 125).\n" "\n" "* Note that the results of combining 3dDetrend and 3dRSFC will\n" " depend on the order in which you run these programs. That's why\n" " 3dRSFC has the '-ort' and '-dsort' options, so that the\n" " time series filtering can be done properly, in one place.\n" "\n" "* The output dataset is stored in float format.\n" "\n" "* The order of processing steps is the following (most are optional), and\n" " for the LFFs, the bandpass is done between the specified fbot and ftop,\n" " while for the `whole spectrum' (i.e., fALFF denominator) the bandpass is:\n" " done only to exclude the time series mean and the Nyquist frequency:\n" " (0) Check time series for initial transients [does not alter data]\n" " (1) Despiking of each time series\n" " (2) Removal of a constant+linear+quadratic trend in each time series\n" " (3) Bandpass of data time series\n" " (4) Bandpass of -ort time series, then detrending of data\n" " with respect to the -ort time series\n" " (5) Bandpass and de-orting of the -dsort dataset,\n" " then detrending of the data with respect to -dsort\n" " (6) Blurring inside the mask [might be slow]\n" " (7) Local PV calculation [WILL be slow!]\n" " (8) L2 normalization [will be fast.]\n" " (9) Calculate spectrum and amplitudes, for RSFC parameters.\n" "\n" "* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *\n" "--------\n" "OPTIONS:\n" "--------\n" " -despike = Despike each time series before other processing.\n" " ++ Hopefully, you don't actually need to do this,\n" " which is why it is optional.\n" " -ort f.1D = Also orthogonalize input to columns in f.1D\n" " ++ Multiple '-ort' options are allowed.\n" " -dsort fset = Orthogonalize each voxel to the corresponding\n" " voxel time series in dataset 'fset', which must\n" " have the same spatial and temporal grid structure\n" " as the main input dataset.\n" " ++ At present, only one '-dsort' option is allowed.\n" " -nodetrend = Skip the quadratic detrending of the input that\n" " occurs before the FFT-based bandpassing.\n" " ++ You would only want to do this if the dataset\n" " had been detrended already in some other program.\n" " -dt dd = set time step to 'dd' sec [default=from dataset header]\n" " -nfft N = set the FFT length to 'N' [must be a legal value]\n" " -norm = Make all output time series have L2 norm = 1\n" " ++ i.e., sum of squares = 1\n" " -mask mset = Mask dataset\n" " -automask = Create a mask from the input dataset\n" " -blur fff = Blur (inside the mask only) with a filter\n" " width (FWHM) of 'fff' millimeters.\n" " -localPV rrr = Replace each vector by the local Principal Vector\n" " (AKA first singular vector) from a neighborhood\n" " of radius 'rrr' millimiters.\n" " ++ Note that the PV time series is L2 normalized.\n" " ++ This option is mostly for Bob Cox to have fun with.\n" "\n" " -input dataset = Alternative way to specify input dataset.\n" " -band fbot ftop = Alternative way to specify passband frequencies.\n" "\n" " -prefix ppp = Set prefix name of output dataset. Name of filtered time\n" " series would be, e.g., ppp_LFF+orig.*, and the parameter\n" " outputs are named with obvious suffices.\n" " -quiet = Turn off the fun and informative messages. (Why?)\n" " -no_rs_out = Don't output processed time series-- just output\n" " parameters (not recommended, since the point of\n" " calculating RSFC params here is to have them be quite\n" " related to the time series themselves which are used for\n" " further analysis)." " -un_bp_out = Output the un-bandpassed series as well (default is not \n" " to). Name would be, e.g., ppp_unBP+orig.* .\n" " with suffix `_unBP'.\n" " -no_rsfa = If you don't want RSFA output (default is to do so).\n" " -bp_at_end = A (probably unnecessary) switch to have bandpassing be \n" " the very last processing step that is done in the\n" " sequence of steps listed above; at Step 3 above, only \n" " the time series mean and nyquist are BP'ed out, and then\n" " the LFF series is created only after Step 9. NB: this \n" " probably makes only very small changes for most\n" " processing sequences (but maybe not, depending usage).\n" "\n" " -notrans = Don't check for initial positive transients in the data:\n" " *OR* ++ The test is a little slow, so skipping it is OK,\n" " -nosat if you KNOW the data time series are transient-free.\n" " ++ Or set AFNI_SKIP_SATCHECK to YES.\n" " ++ Initial transients won't be handled well by the\n" " bandpassing algorithm, and in addition may seriously\n" " contaminate any further processing, such as inter-\n" " voxel correlations via InstaCorr.\n" " ++ No other tests are made [yet] for non-stationary \n" " behavior in the time series data.\n" "\n" "* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *\n" "\n" " If you use this program, please reference the introductory/description\n" " paper for the FATCAT toolbox:\n" " Taylor PA, Saad ZS (2013). FATCAT: (An Efficient) Functional\n" " And Tractographic Connectivity Analysis Toolbox. Brain \n" " Connectivity 3(5):523-535.\n" "____________________________________________________________________________\n" ); PRINT_AFNI_OMP_USAGE( " 3dRSFC" , " * At present, the only part of 3dRSFC that is parallelized is the\n" " '-blur' option, which processes each sub-brick independently.\n" ) ; PRINT_COMPILE_DATE ; exit(0) ; } /*-- startup --*/ mainENTRY("3dRSFC"); machdep(); AFNI_logger("3dRSFC",argc,argv); PRINT_VERSION("3dRSFC (from 3dBandpass by RW Cox): version THETA"); AUTHOR("PA Taylor"); nosat = AFNI_yesenv("AFNI_SKIP_SATCHECK") ; nopt = 1 ; while( nopt < argc && argv[nopt][0] == '-' ){ if( strcmp(argv[nopt],"-despike") == 0 ){ /* 08 Oct 2010 */ do_despike++ ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-nfft") == 0 ){ int nnup ; if( ++nopt >= argc ) ERROR_exit("need an argument after -nfft!") ; nfft = (int)strtod(argv[nopt],NULL) ; nnup = csfft_nextup_even(nfft) ; if( nfft < 16 || nfft != nnup ) ERROR_exit("value %d after -nfft is illegal! Next legal value = %d",nfft,nnup) ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-blur") == 0 ){ if( ++nopt >= argc ) ERROR_exit("need an argument after -blur!") ; blur = strtod(argv[nopt],NULL) ; if( blur <= 0.0f ) WARNING_message("non-positive blur?!") ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-localPV") == 0 ){ if( ++nopt >= argc ) ERROR_exit("need an argument after -localpv!") ; pvrad = strtod(argv[nopt],NULL) ; if( pvrad <= 0.0f ) WARNING_message("non-positive -localpv?!") ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-prefix") == 0 ){ if( ++nopt >= argc ) ERROR_exit("need an argument after -prefix!") ; prefix = strdup(argv[nopt]) ; if( !THD_filename_ok(prefix) ) ERROR_exit("bad -prefix option!") ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-automask") == 0 ){ if( mask != NULL ) ERROR_exit("Can't use -mask AND -automask!") ; do_automask = 1 ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-mask") == 0 ){ THD_3dim_dataset *mset ; if( ++nopt >= argc ) ERROR_exit("Need argument after '-mask'") ; if( mask != NULL || do_automask ) ERROR_exit("Can't have two mask inputs") ; mset = THD_open_dataset( argv[nopt] ) ; CHECK_OPEN_ERROR(mset,argv[nopt]) ; DSET_load(mset) ; CHECK_LOAD_ERROR(mset) ; mask_nx = DSET_NX(mset); mask_ny = DSET_NY(mset); mask_nz = DSET_NZ(mset); mask = THD_makemask( mset , 0 , 0.5f, 0.0f ) ; DSET_delete(mset) ; if( mask == NULL ) ERROR_exit("Can't make mask from dataset '%s'",argv[nopt]) ; nmask = THD_countmask( mask_nx*mask_ny*mask_nz , mask ) ; if( verb ) INFO_message("Number of voxels in mask = %d",nmask) ; if( nmask < 1 ) ERROR_exit("Mask is too small to process") ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-norm") == 0 ){ do_norm = 1 ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-quiet") == 0 ){ verb = 0 ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-no_rs_out") == 0 ){ // @@ SERIES_OUT = 0 ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-un_bp_out") == 0 ){ // @@ UNBP_OUT = 1 ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-no_rsfa") == 0 ){ // @@ DO_RSFA = 0 ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-bp_at_end") == 0 ){ // @@ BP_LAST = 1 ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-notrans") == 0 || strcmp(argv[nopt],"-nosat") == 0 ){ nosat = 1 ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-ort") == 0 ){ if( ++nopt >= argc ) ERROR_exit("need an argument after -ort!") ; if( ortar == NULL ) INIT_IMARR(ortar) ; ortim = mri_read_1D( argv[nopt] ) ; if( ortim == NULL ) ERROR_exit("can't read from -ort '%s'",argv[nopt]) ; mri_add_name(argv[nopt],ortim) ; ADDTO_IMARR(ortar,ortim) ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-dsort") == 0 ){ THD_3dim_dataset *qset ; if( ++nopt >= argc ) ERROR_exit("need an argument after -dsort!") ; if( nortset > 0 ) ERROR_exit("only 1 -dsort option is allowed!") ; qset = THD_open_dataset(argv[nopt]) ; CHECK_OPEN_ERROR(qset,argv[nopt]) ; ortset = (THD_3dim_dataset **)realloc(ortset, sizeof(THD_3dim_dataset *)*(nortset+1)) ; ortset[nortset++] = qset ; nopt++ ; continue ; } if( strncmp(argv[nopt],"-nodetrend",6) == 0 ){ qdet = 0 ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-dt") == 0 ){ if( ++nopt >= argc ) ERROR_exit("need an argument after -dt!") ; dt = (float)strtod(argv[nopt],NULL) ; if( dt <= 0.0f ) WARNING_message("value after -dt illegal!") ; nopt++ ; continue ; } if( strcmp(argv[nopt],"-input") == 0 ){ if( inset != NULL ) ERROR_exit("Can't have 2 -input options!") ; if( ++nopt >= argc ) ERROR_exit("need an argument after -input!") ; inset = THD_open_dataset(argv[nopt]) ; CHECK_OPEN_ERROR(inset,argv[nopt]) ; nopt++ ; continue ; } if( strncmp(argv[nopt],"-band",5) == 0 ){ if( ++nopt >= argc-1 ) ERROR_exit("need 2 arguments after -band!") ; if( have_freq ) WARNING_message("second -band option replaces first one!") ; fbot = strtod(argv[nopt++],NULL) ; ftop = strtod(argv[nopt++],NULL) ; have_freq = 1 ; continue ; } ERROR_exit("Unknown option: '%s'",argv[nopt]) ; } /** check inputs for reasonablositiness **/ if( !have_freq ){ if( nopt+1 >= argc ) ERROR_exit("Need frequencies on command line after options!") ; fbot = (float)strtod(argv[nopt++],NULL) ; ftop = (float)strtod(argv[nopt++],NULL) ; } if( inset == NULL ){ if( nopt >= argc ) ERROR_exit("Need input dataset name on command line after options!") ; inset = THD_open_dataset(argv[nopt]) ; CHECK_OPEN_ERROR(inset,argv[nopt]) ; nopt++ ; } DSET_UNMSEC(inset) ; if( fbot < 0.0f ) ERROR_exit("fbot value can't be negative!") ; if( ftop <= fbot ) ERROR_exit("ftop value %g must be greater than fbot value %g!",ftop,fbot) ; ntime = DSET_NVALS(inset) ; if( ntime < 9 ) ERROR_exit("Input dataset is too short!") ; if( nfft <= 0 ){ nfft = csfft_nextup_even(ntime) ; if( verb ) INFO_message("Data length = %d FFT length = %d",ntime,nfft) ; (void)THD_bandpass_set_nfft(nfft) ; } else if( nfft < ntime ){ ERROR_exit("-nfft %d is less than data length = %d",nfft,ntime) ; } else { kk = THD_bandpass_set_nfft(nfft) ; if( kk != nfft && verb ) INFO_message("Data length = %d FFT length = %d",ntime,kk) ; } if( dt <= 0.0f ){ dt = DSET_TR(inset) ; if( dt <= 0.0f ){ WARNING_message("Setting dt=1.0 since input dataset lacks a time axis!") ; dt = 1.0f ; } } ftopALL = 1./dt ;// Aug,2016: should solve problem of a too-large // value for THD_bandpass_vectors(), while still // being >f_{Nyquist} if( !THD_bandpass_OK(ntime,dt,fbot,ftop,1) ) ERROR_exit("Can't continue!") ; nx = DSET_NX(inset); ny = DSET_NY(inset); nz = DSET_NZ(inset); nvox = nx*ny*nz; /* check mask, or create it */ if( verb ) INFO_message("Loading input dataset time series" ) ; DSET_load(inset) ; if( mask != NULL ){ if( mask_nx != nx || mask_ny != ny || mask_nz != nz ) ERROR_exit("-mask dataset grid doesn't match input dataset") ; } else if( do_automask ){ mask = THD_automask( inset ) ; if( mask == NULL ) ERROR_message("Can't create -automask from input dataset?") ; nmask = THD_countmask( DSET_NVOX(inset) , mask ) ; if( verb ) INFO_message("Number of voxels in automask = %d",nmask); if( nmask < 1 ) ERROR_exit("Automask is too small to process") ; } else { mask = (byte *)malloc(sizeof(byte)*nvox) ; nmask = nvox ; memset(mask,1,sizeof(byte)*nvox) ; // if( verb ) // @@ alert if aaaalllllll vox are going to be analyzed! INFO_message("No mask ==> processing all %d voxels",nvox); } /* A simple check of dataset quality [08 Feb 2010] */ if( !nosat ){ float val ; INFO_message( "Checking dataset for initial transients [use '-notrans' to skip this test]") ; val = THD_saturation_check(inset,mask,0,0) ; kk = (int)(val+0.54321f) ; if( kk > 0 ) ININFO_message( "Looks like there %s %d non-steady-state initial time point%s :-(" , ((kk==1) ? "is" : "are") , kk , ((kk==1) ? " " : "s") ) ; else if( val > 0.3210f ) /* don't ask where this threshold comes from! */ ININFO_message( "MAYBE there's an initial positive transient of 1 point, but it's hard to tell\n") ; else ININFO_message("No widespread initial positive transient detected :-)") ; } /* check -dsort inputs for match to inset */ for( kk=0 ; kk < nortset ; kk++ ){ if( DSET_NX(ortset[kk]) != nx || DSET_NY(ortset[kk]) != ny || DSET_NZ(ortset[kk]) != nz || DSET_NVALS(ortset[kk]) != ntime ) ERROR_exit("-dsort %s doesn't match input dataset grid" , DSET_BRIKNAME(ortset[kk]) ) ; } /* convert input dataset to a vectim, which is more fun */ // @@ convert BP'ing ftop/bot into indices for the DFT (below) delf = 1.0/(ntime*dt); ind_low = (int) rint(fbot/delf); ind_high = (int) rint(ftop/delf); if( ntime % 2 ) // nyquist number N_ny = (ntime-1)/2; else N_ny = ntime/2; sqnt = sqrt(ntime); nt_fac = sqrt(ntime*(ntime-1)); // @@ if BP_LAST==0: // now we go through twice, doing LFF bandpass for NumDen==0 and // `full spectrum' processing for NumDen==1. // if BP_LAST==1: // now we go through once, doing only `full spectrum' processing for( NumDen=0 ; NumDen<2 ; NumDen++) { //if( NumDen==1 ){ // full spectrum // fbot = fbotALL; // ftop = ftopALL; //} // essentially, just doesn't BP here, and the perfect filtering at end // is used for both still; this makes the final output spectrum // contain only frequencies in range of 0.01-0.08 if( BP_LAST==1 ) INFO_message("Only doing filtering to LFFs at end!"); mrv = THD_dset_to_vectim( inset , mask , 0 ) ; if( mrv == NULL ) ERROR_exit("Can't load time series data!?") ; if( NumDen==1 ) DSET_unload(inset) ; // @@ only unload on 2nd pass /* similarly for the ort vectors */ if( ortar != NULL ){ for( kk=0 ; kk < IMARR_COUNT(ortar) ; kk++ ){ ortim = IMARR_SUBIM(ortar,kk) ; if( ortim->nx < ntime ) ERROR_exit("-ort file %s is shorter than input dataset time series", ortim->name ) ; ort = (float **)realloc( ort , sizeof(float *)*(nort+ortim->ny) ) ; for( vv=0 ; vv < ortim->ny ; vv++ ) ort[nort++] = MRI_FLOAT_PTR(ortim) + ortim->nx * vv ; } } /* all the real work now */ if( do_despike ){ int_pair nsp ; if( verb ) INFO_message("Testing data time series for spikes") ; nsp = THD_vectim_despike9( mrv ) ; if( verb ) ININFO_message(" -- Squashed %d spikes from %d voxels",nsp.j,nsp.i) ; } if( verb ) INFO_message("Bandpassing data time series") ; if( (BP_LAST==0) && (NumDen==0) ) (void)THD_bandpass_vectim( mrv , dt,fbot,ftop , qdet , nort,ort ) ; else (void)THD_bandpass_vectim( mrv , dt,fbotALL,ftopALL, qdet,nort,ort ) ; /* OK, maybe a little more work */ if( nortset == 1 ){ MRI_vectim *orv ; orv = THD_dset_to_vectim( ortset[0] , mask , 0 ) ; if( orv == NULL ){ ERROR_message("Can't load -dsort %s",DSET_BRIKNAME(ortset[0])) ; } else { float *dp , *mvv , *ovv , ff ; if( verb ) INFO_message("Orthogonalizing to bandpassed -dsort") ; //(void)THD_bandpass_vectim( orv , dt,fbot,ftop , qdet , nort,ort ) ; //@@ if( (BP_LAST==0) && (NumDen==0) ) (void)THD_bandpass_vectim(orv,dt,fbot,ftop,qdet,nort,ort); else (void)THD_bandpass_vectim(orv,dt,fbotALL,ftopALL,qdet,nort,ort); THD_vectim_normalize( orv ) ; dp = malloc(sizeof(float)*mrv->nvec) ; THD_vectim_vectim_dot( mrv , orv , dp ) ; for( vv=0 ; vv < mrv->nvec ; vv++ ){ ff = dp[vv] ; if( ff != 0.0f ){ mvv = VECTIM_PTR(mrv,vv) ; ovv = VECTIM_PTR(orv,vv) ; for( kk=0 ; kk < ntime ; kk++ ) mvv[kk] -= ff*ovv[kk] ; } } VECTIM_destroy(orv) ; free(dp) ; } } if( blur > 0.0f ){ if( verb ) INFO_message("Blurring time series data spatially; FWHM=%.2f",blur) ; mri_blur3D_vectim( mrv , blur ) ; } if( pvrad > 0.0f ){ if( verb ) INFO_message("Local PV-ing time series data spatially; radius=%.2f",pvrad) ; THD_vectim_normalize( mrv ) ; THD_vectim_localpv( mrv , pvrad ) ; } if( do_norm && pvrad <= 0.0f ){ if( verb ) INFO_message("L2 normalizing time series data") ; THD_vectim_normalize( mrv ) ; } /* create output dataset, populate it, write it, then quit */ if( (NumDen==0) ) { // @@ BP'ed version; will do filt if BP_LAST if(BP_LAST) // do bandpass here for BP_LAST (void)THD_bandpass_vectim(mrv,dt,fbot,ftop,qdet,0,NULL); if( verb ) INFO_message("Creating output dataset in memory, then writing it") ; outset = EDIT_empty_copy(inset) ; if(SERIES_OUT){ sprintf(out_lff,"%s_LFF",prefix); EDIT_dset_items( outset , ADN_prefix,out_lff , ADN_none ) ; tross_Copy_History( inset , outset ) ; tross_Make_History( "3dBandpass" , argc,argv , outset ) ; } for( vv=0 ; vv < ntime ; vv++ ) EDIT_substitute_brick( outset , vv , MRI_float , NULL ) ; #if 1 THD_vectim_to_dset( mrv , outset ) ; #else AFNI_OMP_START ; #pragma omp parallel { float *far , *var ; int *ivec=mrv->ivec ; int vv,kk ; #pragma omp for for( vv=0 ; vv < ntime ; vv++ ){ far = DSET_BRICK_ARRAY(outset,vv) ; var = mrv->fvec + vv ; for( kk=0 ; kk < nmask ; kk++ ) far[ivec[kk]] = var[kk*ntime] ; } } AFNI_OMP_END ; #endif VECTIM_destroy(mrv) ; if(SERIES_OUT){ // @@ DSET_write(outset) ; if( verb ) WROTE_DSET(outset) ; } } else{ // @@ non-BP'ed version if( verb ) INFO_message("Creating output dataset 2 in memory") ; // do this here because LFF version was also BP'ed at end. if(BP_LAST) // do bandpass here for BP_LAST (void)THD_bandpass_vectim(mrv,dt,fbotALL,ftopALL,qdet,0,NULL); outsetALL = EDIT_empty_copy(inset) ; if(UNBP_OUT){ sprintf(out_unBP,"%s_unBP",prefix); EDIT_dset_items( outsetALL, ADN_prefix, out_unBP, ADN_none ); tross_Copy_History( inset , outsetALL ) ; tross_Make_History( "3dRSFC" , argc,argv , outsetALL ) ; } for( vv=0 ; vv < ntime ; vv++ ) EDIT_substitute_brick( outsetALL , vv , MRI_float , NULL ) ; #if 1 THD_vectim_to_dset( mrv , outsetALL ) ; #else AFNI_OMP_START ; #pragma omp parallel { float *far , *var ; int *ivec=mrv->ivec ; int vv,kk ; #pragma omp for for( vv=0 ; vv < ntime ; vv++ ){ far = DSET_BRICK_ARRAY(outsetALL,vv) ; var = mrv->fvec + vv ; for( kk=0 ; kk < nmask ; kk++ ) far[ivec[kk]] = var[kk*ntime] ; } } AFNI_OMP_END ; #endif VECTIM_destroy(mrv) ; if(UNBP_OUT){ DSET_write(outsetALL) ; if( verb ) WROTE_DSET(outsetALL) ; } } }// end of NumDen loop // @@ INFO_message("Starting the (f)ALaFFel calcs") ; // allocations series1 = (double *)calloc(ntime,sizeof(double)); series2 = (double *)calloc(ntime,sizeof(double)); xx1 = (double *)calloc(2*ntime,sizeof(double)); xx2 = (double *)calloc(2*ntime,sizeof(double)); alff = (float *)calloc(nvox,sizeof(float)); malff = (float *)calloc(nvox,sizeof(float)); falff = (float *)calloc(nvox,sizeof(float)); if( (series1 == NULL) || (series2 == NULL) || (xx1 == NULL) || (xx2 == NULL) || (alff == NULL) || (malff == NULL) || (falff == NULL)) { fprintf(stderr, "\n\n MemAlloc failure.\n\n"); exit(122); } if(DO_RSFA) { rsfa = (float *)calloc(nvox,sizeof(float)); mrsfa = (float *)calloc(nvox,sizeof(float)); frsfa = (float *)calloc(nvox,sizeof(float)); if( (rsfa == NULL) || (mrsfa == NULL) || (frsfa == NULL)) { fprintf(stderr, "\n\n MemAlloc failure.\n\n"); exit(123); } } work = gsl_fft_real_workspace_alloc (ntime); real1 = gsl_fft_real_wavetable_alloc (ntime); real2 = gsl_fft_real_wavetable_alloc (ntime); gsl_complex_packed_array compl_freqs1 = xx1; gsl_complex_packed_array compl_freqs2 = xx2; // ********************************************************************* // ********************************************************************* // ************** Falafelling = ALFF/fALFF calcs ***************** // ********************************************************************* // ********************************************************************* // Be now have the BP'ed data set (outset) and the non-BP'ed one // (outsetALL). now we'll FFT both, get amplitudes in appropriate // ranges, and calculate: ALFF, mALFF, fALFF, ctr = 0; for( kk=0; kk<nvox ; kk++) { if(mask[kk]) { // BP one, and unBP one, either for BP_LAST or !BP_LAST for( m=0 ; m<ntime ; m++ ) { series1[m] = THD_get_voxel(outset,kk,m); series2[m] = THD_get_voxel(outsetALL,kk,m); } mm = gsl_fft_real_transform(series1, 1, ntime, real1, work); mm = gsl_fft_halfcomplex_unpack(series1, compl_freqs1, 1, ntime); mm = gsl_fft_real_transform(series2, 1, ntime, real2, work); mm = gsl_fft_halfcomplex_unpack(series2, compl_freqs2, 1, ntime); numer = 0.0f; denom = 0.0f; de_rsfa = 0.0f; nu_rsfa = 0.0f; for( m=1 ; m<N_ny ; m++ ) { mm = 2*m; pow2 = compl_freqs2[mm]*compl_freqs2[mm] + compl_freqs2[mm+1]*compl_freqs2[mm+1]; // power //pow2*=2;// factor of 2 since ampls are even funcs denom+= (float) sqrt(pow2); // amplitude de_rsfa+= (float) pow2; if( ( m>=ind_low ) && ( m<=ind_high ) ){ pow1 = compl_freqs1[mm]*compl_freqs1[mm]+ compl_freqs1[mm+1]*compl_freqs1[mm+1]; //pow1*=2; numer+= (float) sqrt(pow1); nu_rsfa+= (float) pow1; } } if( denom>0.000001 ) falff[kk] = numer/denom; else falff[kk] = 0.; alff[kk] = 2*numer/sqnt;// factor of 2 since ampl is even funct meanALFF+= alff[kk]; if(DO_RSFA){ nu_rsfa = sqrt(2*nu_rsfa); // factor of 2 since ampls de_rsfa = sqrt(2*de_rsfa); // are even funcs if( de_rsfa>0.000001 ) frsfa[kk] = nu_rsfa/de_rsfa; else frsfa[kk]=0.; rsfa[kk] = nu_rsfa/nt_fac; meanRSFA+= rsfa[kk]; } ctr+=1; } } meanALFF/= ctr; meanRSFA/= ctr; gsl_fft_real_wavetable_free(real1); gsl_fft_real_wavetable_free(real2); gsl_fft_real_workspace_free(work); // ALFFs divided by mean of brain value for( kk=0 ; kk<nvox ; kk++ ) if(mask[kk]){ malff[kk] = alff[kk]/meanALFF; if(DO_RSFA) mrsfa[kk] = rsfa[kk]/meanRSFA; } // ************************************************************** // ************************************************************** // Store and output // ************************************************************** // ************************************************************** outsetALFF = EDIT_empty_copy( inset ) ; sprintf(out_alff,"%s_ALFF",prefix); EDIT_dset_items( outsetALFF, ADN_nvals, 1, ADN_datum_all , MRI_float , ADN_prefix , out_alff, ADN_none ) ; if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetALFF)) ) ERROR_exit("Can't overwrite existing dataset '%s'", DSET_HEADNAME(outsetALFF)); EDIT_substitute_brick(outsetALFF, 0, MRI_float, alff); alff=NULL; THD_load_statistics(outsetALFF); tross_Make_History("3dRSFC", argc, argv, outsetALFF); THD_write_3dim_dataset(NULL, NULL, outsetALFF, True); outsetfALFF = EDIT_empty_copy( inset ) ; sprintf(out_falff,"%s_fALFF",prefix); EDIT_dset_items( outsetfALFF, ADN_nvals, 1, ADN_datum_all , MRI_float , ADN_prefix , out_falff, ADN_none ) ; if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetfALFF)) ) ERROR_exit("Can't overwrite existing dataset '%s'", DSET_HEADNAME(outsetfALFF)); EDIT_substitute_brick(outsetfALFF, 0, MRI_float, falff); falff=NULL; THD_load_statistics(outsetfALFF); tross_Make_History("3dRSFC", argc, argv, outsetfALFF); THD_write_3dim_dataset(NULL, NULL, outsetfALFF, True); outsetmALFF = EDIT_empty_copy( inset ) ; sprintf(out_malff,"%s_mALFF",prefix); EDIT_dset_items( outsetmALFF, ADN_nvals, 1, ADN_datum_all , MRI_float , ADN_prefix , out_malff, ADN_none ) ; if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetmALFF)) ) ERROR_exit("Can't overwrite existing dataset '%s'", DSET_HEADNAME(outsetmALFF)); EDIT_substitute_brick(outsetmALFF, 0, MRI_float, malff); malff=NULL; THD_load_statistics(outsetmALFF); tross_Make_History("3dRSFC", argc, argv, outsetmALFF); THD_write_3dim_dataset(NULL, NULL, outsetmALFF, True); if(DO_RSFA){ outsetRSFA = EDIT_empty_copy( inset ) ; sprintf(out_rsfa,"%s_RSFA",prefix); EDIT_dset_items( outsetRSFA, ADN_nvals, 1, ADN_datum_all , MRI_float , ADN_prefix , out_rsfa, ADN_none ) ; if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetRSFA)) ) ERROR_exit("Can't overwrite existing dataset '%s'", DSET_HEADNAME(outsetRSFA)); EDIT_substitute_brick(outsetRSFA, 0, MRI_float, rsfa); rsfa=NULL; THD_load_statistics(outsetRSFA); tross_Make_History("3dRSFC", argc, argv, outsetRSFA); THD_write_3dim_dataset(NULL, NULL, outsetRSFA, True); outsetfRSFA = EDIT_empty_copy( inset ) ; sprintf(out_frsfa,"%s_fRSFA",prefix); EDIT_dset_items( outsetfRSFA, ADN_nvals, 1, ADN_datum_all , MRI_float , ADN_prefix , out_frsfa, ADN_none ) ; if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetfRSFA)) ) ERROR_exit("Can't overwrite existing dataset '%s'", DSET_HEADNAME(outsetfRSFA)); EDIT_substitute_brick(outsetfRSFA, 0, MRI_float, frsfa); frsfa=NULL; THD_load_statistics(outsetfRSFA); tross_Make_History("3dRSFC", argc, argv, outsetfRSFA); THD_write_3dim_dataset(NULL, NULL, outsetfRSFA, True); outsetmRSFA = EDIT_empty_copy( inset ) ; sprintf(out_mrsfa,"%s_mRSFA",prefix); EDIT_dset_items( outsetmRSFA, ADN_nvals, 1, ADN_datum_all , MRI_float , ADN_prefix , out_mrsfa, ADN_none ) ; if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outsetmRSFA)) ) ERROR_exit("Can't overwrite existing dataset '%s'", DSET_HEADNAME(outsetmRSFA)); EDIT_substitute_brick(outsetmRSFA, 0, MRI_float, mrsfa); mrsfa=NULL; THD_load_statistics(outsetmRSFA); tross_Make_History("3dRSFC", argc, argv, outsetmRSFA); THD_write_3dim_dataset(NULL, NULL, outsetmRSFA, True); } // ************************************************************ // ************************************************************ // Freeing // ************************************************************ // ************************************************************ DSET_delete(inset); DSET_delete(outsetALL); DSET_delete(outset); DSET_delete(outsetALFF); DSET_delete(outsetmALFF); DSET_delete(outsetfALFF); DSET_delete(outsetRSFA); DSET_delete(outsetmRSFA); DSET_delete(outsetfRSFA); free(inset); free(outsetALL); free(outset); free(outsetALFF); free(outsetmALFF); free(outsetfALFF); free(outsetRSFA); free(outsetmRSFA); free(outsetfRSFA); free(rsfa); free(mrsfa); free(frsfa); free(alff); free(malff); free(falff); free(mask); free(series1); free(series2); free(xx1); free(xx2); exit(0) ; }
/*! Replace a voxel's value by the value's rank in the entire set of input datasets */ int main( int argc , char * argv[] ) { THD_3dim_dataset ** dsets_in = NULL, *dset=NULL; /*input and output datasets*/ int nopt=0, nbriks=0, nsubbriks=0, ib=0, isb=0; byte *cmask=NULL; int *all_uniques=NULL, **uniques=NULL, *final_unq=NULL, *N_uniques=NULL; int N_final_unq=0, iun=0, total_unq=0; INT_HASH_DATUM *rmap=NULL, *hd=NULL; int imax=0, iunq=0, ii=0, id = 0; long int off=0; char *prefix=NULL; char stmp[THD_MAX_PREFIX+1]={""}; FILE *fout=NULL; /*----- Read command line -----*/ if( argc < 2 || strcmp(argv[1],"-help") == 0 ){ Rank_help (); exit(0) ; } mainENTRY("3dRank main"); machdep(); AFNI_logger("3dRank",argc,argv); nopt = 1 ; while( nopt < argc && argv[nopt][0] == '-' ){ if( strcmp(argv[nopt],"-ver") == 0 ){ PRINT_VERSION("3dRank"); AUTHOR("Ziad Saad"); nopt++; continue; } if( strcmp(argv[nopt],"-help") == 0 ){ Rank_help(); exit(0) ; } if( strcmp(argv[nopt],"-prefix") == 0 ){ ++nopt; if (nopt>=argc) { fprintf(stderr,"**ERROR: Need string after -prefix\n"); exit(1); } prefix = argv[nopt] ; ++nopt; continue; } if( strcmp(argv[nopt],"-input") == 0 ){ dsets_in = (THD_3dim_dataset**) calloc(argc-nopt+1, sizeof(THD_3dim_dataset*)); ++nopt; nbriks=0; while (nopt < argc ) { dsets_in[nbriks] = THD_open_dataset( argv[nopt] ); if( !ISVALID_DSET(dsets_in[nbriks]) ){ fprintf(stderr,"**ERROR: can't open dataset %s\n",argv[nopt]) ; exit(1); } ++nopt; ++nbriks; } continue; } ERROR_exit( " Error - unknown option %s", argv[nopt]); } if (nopt < argc) { ERROR_exit( " Error unexplained trailing option: %s\n", argv[nopt]); } if (!nbriks) { ERROR_exit( " Error no volumes entered on command line?"); } /* some checks and inits*/ nsubbriks = 0; for (ib = 0; ib<nbriks; ++ib) { if (!is_integral_dset(dsets_in[ib], 0)) { ERROR_exit("Dset %s is not of an integral data type.", DSET_PREFIX(dsets_in[ib])); } nsubbriks += DSET_NVALS(dsets_in[ib]); } /* Now get unique arrays */ uniques = (int **)calloc(nsubbriks, sizeof(int*)); N_uniques = (int *)calloc(nsubbriks, sizeof(int)); total_unq = 0; iun = 0; for (ib = 0; ib<nbriks; ++ib) { DSET_mallocize(dsets_in[ib]); DSET_load(dsets_in[ib]); for (isb=0; isb<DSET_NVALS(dsets_in[ib]); ++isb) { uniques[iun] = THD_unique_vals(dsets_in[ib], isb, &(N_uniques[iun]), cmask); total_unq += N_uniques[iun]; ++iun; } } /* put all the arrays together and get the unique of the uniques */ all_uniques = (int *)calloc(total_unq, sizeof(int)); off=0; for (iun=0; iun<nsubbriks; ++iun) { memcpy(all_uniques+off, uniques[iun], N_uniques[iun]*sizeof(int)); off += N_uniques[iun]; } /* free intermediate unique arrays */ for (iun=0; iun<nsubbriks; ++iun) { free(uniques[iun]); } free(uniques); uniques=NULL; free(N_uniques); N_uniques=NULL; /* get unique of catenated array */ if (!(final_unq = UniqueInt (all_uniques, total_unq, &N_final_unq, 0 ))) { ERROR_exit( " Failed to get unique list (%d, %d, %d) ", total_unq, N_final_unq, nsubbriks); } free(all_uniques); all_uniques=NULL; if (prefix) { snprintf(stmp, sizeof(char)*THD_MAX_PREFIX, "%s.rankmap.1D", prefix); } else { if (nbriks == 1) { snprintf(stmp, sizeof(char)*THD_MAX_PREFIX, "%s.rankmap.1D", DSET_PREFIX(dsets_in[0])); } else { snprintf(stmp, sizeof(char)*THD_MAX_PREFIX, "%s+.rankmap.1D", DSET_PREFIX(dsets_in[0])); } } if (stmp[0]) { if ((fout = fopen(stmp,"w"))) { fprintf(fout, "#Rank Map (%d unique values)\n", N_final_unq); fprintf(fout, "#Col. 0: Rank\n"); fprintf(fout, "#Col. 1: Input Dset Value\n"); } } /* get the maximum integer in the unique array */ imax = 0; for (iunq=0; iunq<N_final_unq; ++iunq) { if (final_unq[iunq] > imax) imax = final_unq[iunq]; if (fout) fprintf(fout, "%d %d\n", iunq, final_unq[iunq]); hd = (INT_HASH_DATUM*)calloc(1,sizeof(INT_HASH_DATUM)); hd->id = final_unq[iunq]; hd->index = iunq; HASH_ADD_INT(rmap, id, hd); } fclose(fout); fout=NULL; /* now cycle over all dsets and replace their voxel values with rank */ for (ib = 0; ib<nbriks; ++ib) { for (isb=0; isb<DSET_NVALS(dsets_in[ib]); ++isb) { EDIT_BRICK_LABEL( dsets_in[ib],isb, "rank" ) ; EDIT_BRICK_TO_NOSTAT( dsets_in[ib],isb ) ; EDIT_BRICK_FACTOR( dsets_in[ib],isb, 0.0);/* no factors for rank*/ switch (DSET_BRICK_TYPE(dsets_in[ib],isb) ){ default: fprintf(stderr, "** Bad dset type for unique operation.\n" "Only Byte, Short, and float dsets are allowed.\n"); break ; /* this should not happen here, so don't bother returning*/ case MRI_short:{ short *mar = (short *) DSET_ARRAY(dsets_in[ib],isb) ; if (imax > MRI_TYPE_maxval[MRI_short]) { WARNING_message("Maximum rank value of %d is\n" "than maximum value for dset datatype of %d\n", imax, MRI_TYPE_maxval[MRI_short]); } for( ii=0 ; ii < DSET_NVOX(dsets_in[ib]) ; ii++ ) if (!cmask || cmask[ii]) { id = (int)mar[ii]; HASH_FIND_INT(rmap,&id ,hd); if (hd) mar[ii] = (short)(hd->index); else ERROR_exit("** Failed to find key %d in hash table\n",id); } else mar[ii] = 0; } break ; case MRI_byte:{ byte *mar ; if (imax > MRI_TYPE_maxval[MRI_short]) { WARNING_message("Maximum rank value of %d is\n" "than maximum value for dset datatype of %d\n", imax, MRI_TYPE_maxval[MRI_byte]); } mar = (byte *) DSET_ARRAY(dsets_in[ib],isb) ; for( ii=0 ; ii < DSET_NVOX(dsets_in[ib]) ; ii++ ) if (!cmask || cmask[ii]) { id = (int)mar[ii]; HASH_FIND_INT(rmap,&id ,hd); if (hd) mar[ii] = (byte)(hd->index); else ERROR_exit("** Failed to find key %d in hash table\n",id); } else mar[ii] = 0; } break ; case MRI_float:{ float *mar = (float *) DSET_ARRAY(dsets_in[ib],isb) ; for( ii=0 ; ii < DSET_NVOX(dsets_in[ib]) ; ii++ ) if (!cmask || cmask[ii]) { id = (int)mar[ii]; /* Assuming float is integral valued */ HASH_FIND_INT(rmap,&id ,hd); if (hd) mar[ii] = (float)(hd->index); else ERROR_exit("** Failed to find key %d in hash table\n",id); } else mar[ii] = 0; } break ; } } /* update range, etc. */ THD_load_statistics(dsets_in[ib]); /* Now write the bricks */ if (prefix) { if (nbriks == 1) { snprintf(stmp, sizeof(char)*THD_MAX_PREFIX, "%s", prefix); } else { snprintf(stmp, sizeof(char)*THD_MAX_PREFIX, "r%02d.%s", ib, prefix); } } else { snprintf(stmp, sizeof(char)*THD_MAX_PREFIX, "rank.%s", DSET_PREFIX(dsets_in[ib])); } EDIT_dset_items( dsets_in[ib] , ADN_prefix , stmp , ADN_none ) ; /* change storage mode, this way prefix will determine format of output dset */ dsets_in[ib]->dblk->diskptr->storage_mode = STORAGE_BY_BRICK; tross_Make_History( "3dRank" , argc, argv , dsets_in[ib] ) ; if (DSET_IS_MASTERED(dsets_in[ib])) { /* THD_write_3dim_dataset won't write a mastered dude */ dset = EDIT_full_copy(dsets_in[ib],stmp); } else { dset = dsets_in[ib]; } /* New ID */ ZERO_IDCODE(dset->idcode); dset->idcode = MCW_new_idcode() ; if (!THD_write_3dim_dataset( NULL, stmp, dset,True )) { ERROR_message("Failed to write %s", stmp); exit(1); } else { WROTE_DSET(dsets_in[ib]); if (dset != dsets_in[ib]) DSET_deletepp(dset); DSET_deletepp(dsets_in[ib]); } } /* destroy hash */ while (rmap) { hd = rmap; HASH_DEL(rmap,hd); free(hd); } free(final_unq); final_unq=NULL; exit(0); }
int main( int argc , char *argv[] ) { int vstep=0 , ii,nvox , ntin , ntout , do_one=0 , nup=-1 ; THD_3dim_dataset *inset=NULL , *outset ; char *prefix="Upsam", *dsetname=NULL ; int verb=0 , iarg=1, datum = MRI_float; float *ivec , *ovec , trin , trout, *fac=NULL, *ofac=NULL, top=0.0, maxtop=0.0; /*------- help the pitifully ignorant user? -------*/ if( argc < 2 || strcmp(argv[1],"-help") == 0 ){ printf( "Usage: 3dUpsample [options] n dataset\n" "\n" "* Upsamples a 3D+time dataset, in the time direction,\n" " by a factor of 'n'.\n" "* The value of 'n' must be between 2 and 320 (inclusive).\n" "* The output dataset is in float format by default.\n" "\n" "Options:\n" "--------\n" " -1 or -one = Use linear interpolation. Otherwise,\n" " or -linear 7th order polynomial interpolation is used.\n" "\n" " -prefix pp = Define the prefix name of the output dataset.\n" " [default prefix is 'Upsam']\n" "\n" " -verb = Be eloquently and mellifluosly verbose.\n" "\n" " -n n = An alternate way to specify n\n" " -input dataset = An alternate way to specify dataset\n" "\n" " -datum ddd = Use datatype ddd at output. Choose from\n" " float (default), short, byte.\n" "Example:\n" "--------\n" " 3dUpsample -prefix LongFred 5 Fred+orig\n" "\n" "Nota Bene:\n" "----------\n" "* You should not use this for files that were 3dTcat-ed across\n" " imaging run boundaries, since that will result in interpolating\n" " between non-contiguous time samples!\n" "* If the input has M time points, the output will have n*M time\n" " points. The last n-1 of them will be past the end of the original\n" " time series.\n" "* This program gobbles up memory and diskspace as a function of n.\n" " You can reduce output file size with -datum option.\n" "\n" "--- RW Cox - April 2008\n" ) ; PRINT_COMPILE_DATE ; exit(0) ; } mainENTRY("3dUpsample"); machdep(); PRINT_VERSION("3dUpsample"); AUTHOR("RWCox") ; AFNI_logger("3dUpsample",argc,argv); /*------- read command line args -------*/ datum = MRI_float; iarg = 1 ; while( iarg < argc && argv[iarg][0] == '-' ){ if( strncasecmp(argv[iarg],"-prefix",5) == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '%s'",argv[iarg-1]); prefix = argv[iarg] ; if( !THD_filename_ok(prefix) ) ERROR_exit("Illegal string after -prefix: '%s'",prefix) ; iarg++ ; continue ; } if( strncasecmp(argv[iarg],"-one",4) == 0 || strcmp (argv[iarg],"-1" ) == 0 || strncasecmp(argv[iarg],"-lin",4) == 0 ){ do_one = 1 ; iarg++ ; continue ; } if( strncasecmp(argv[iarg],"-verb",3) == 0 ){ verb = 1 ; iarg++ ; continue ; } if( strcasecmp(argv[iarg],"-n") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '%s'",argv[iarg-1]); nup = (int)strtod(argv[iarg],NULL) ; if( nup < 2 || nup > 320 ) ERROR_exit("3dUpsample rate '%d' is outside range 2..320",nup) ; iarg++ ; continue ; } if( strcasecmp(argv[iarg],"-input") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '%s'",argv[iarg-1]); dsetname = argv[iarg]; iarg++ ; continue ; } if( strcasecmp(argv[iarg],"-datum") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '%s'",argv[iarg-1]); if( strcmp(argv[iarg],"short") == 0 ){ datum = MRI_short ; } else if( strcmp(argv[iarg],"float") == 0 ){ datum = MRI_float ; } else if( strcmp(argv[iarg],"byte") == 0 ){ datum = MRI_byte ; } else { ERROR_message("-datum of type '%s' not supported in 3dUpsample!\n", argv[iarg] ) ; exit(1) ; } iarg++ ; continue ; } ERROR_message("Unknown argument on command line: '%s'",argv[iarg]) ; suggest_best_prog_option(argv[0], argv[iarg]); exit (1); } /*------- check options for completeness and consistency -----*/ if (nup == -1) { if( iarg+1 >= argc ) ERROR_exit("need 'n' and 'dataset' on command line!") ; nup = (int)strtod(argv[iarg++],NULL) ; if( nup < 2 || nup > 320 ) ERROR_exit("3dUpsample rate '%d' is outside range 2..320",nup) ; } if (!dsetname) { if( iarg >= argc ) ERROR_exit("need 'dataset' on command line!") ; dsetname = argv[iarg]; } inset = THD_open_dataset(dsetname) ; if( !ISVALID_DSET(inset) ) ERROR_exit("3dUpsample can't open dataset '%s'", dsetname) ; ntin = DSET_NVALS(inset) ; trin = DSET_TR(inset) ; if( ntin < 2 ) ERROR_exit("dataset '%s' has only 1 value per voxel?!",dsetname) ; nvox = DSET_NVOX(inset) ; if( verb ) INFO_message("loading input dataset into memory") ; DSET_load(inset) ; CHECK_LOAD_ERROR(inset) ; /*------ create output dataset ------*/ ntout = ntin * nup ; trout = trin / nup ; /* scaling factor for output */ fac = NULL; maxtop = 0.0; if (MRI_IS_INT_TYPE(datum)) { fac = (float *)calloc(DSET_NVALS(inset), sizeof(float)); ofac = (float *)calloc(ntout, sizeof(float)); for (ii=0; ii<DSET_NVALS(inset); ++ii) { top = MCW_vol_amax( DSET_NVOX(inset),1,1 , DSET_BRICK_TYPE(inset,ii), DSET_BRICK_ARRAY(inset,ii) ) ; if (DSET_BRICK_FACTOR(inset, ii)) top = top * DSET_BRICK_FACTOR(inset,ii); fac[ii] = (top > MRI_TYPE_maxval[datum]) ? top/MRI_TYPE_maxval[datum] : 0.0 ; if (top > maxtop) maxtop = top; } if (storage_mode_from_filename(prefix) != STORAGE_BY_BRICK) { fac[0] = (maxtop > MRI_TYPE_maxval[datum]) ? maxtop/MRI_TYPE_maxval[datum] : 0.0 ; for (ii=0; ii<ntout; ++ii) ofac[ii] = fac[0]; if (verb) INFO_message("Forcing global scaling, Max = %f, fac = %f\n", maxtop, fac[0]); } else { if (verb) INFO_message("Reusing scaling factors of input dset\n"); upsample_1( nup, DSET_NVALS(inset), fac, ofac); } } free(fac); fac = NULL; outset = EDIT_empty_copy(inset) ; EDIT_dset_items( outset , ADN_nvals , ntout , ADN_ntt , DSET_NUM_TIMES(inset) > 1 ? ntout : 0 , ADN_datum_all , datum , ADN_brick_fac , ofac , ADN_prefix , prefix , ADN_none ) ; tross_Copy_History( inset , outset ) ; tross_Make_History( "3dUpsample" , argc,argv , outset ) ; free(ofac); ofac = NULL; if( outset->taxis != NULL ){ outset->taxis->ttdel /= nup ; outset->taxis->ttdur /= nup ; if( outset->taxis->toff_sl != NULL ){ for( ii=0 ; ii < outset->taxis->nsl ; ii++ ) outset->taxis->toff_sl[ii] /= nup ; } } for( ii=0 ; ii < ntout ; ii++ ){ /* create empty bricks to be filled below */ EDIT_substitute_brick( outset , ii , datum , NULL ) ; } /*------- loop over voxels and process them one at a time ---------*/ if( verb ) INFO_message("Upsampling time series from %d to %d: %s interpolation", ntin , ntout , (do_one) ? "linear" : "heptic" ) ; if( verb && nvox > 499 ) vstep = nvox / 50 ; if( vstep > 0 ) fprintf(stderr,"++ voxel loop: ") ; ivec = (float *)malloc(sizeof(float)*ntin) ; ovec = (float *)malloc(sizeof(float)*ntout) ; for( ii=0 ; ii < nvox ; ii++ ){ if( vstep > 0 && ii%vstep==vstep-1 ) vstep_print() ; THD_extract_array( ii , inset , 0 , ivec ) ; if( do_one ) upsample_1( nup , ntin , ivec , ovec ) ; else upsample_7( nup , ntin , ivec , ovec ) ; THD_insert_series( ii , outset , ntout , MRI_float , ovec , datum==MRI_float ? 1:0 ) ; } /* end of loop over voxels */ if( vstep > 0 ) fprintf(stderr," Done!\n") ; /*----- clean up and go away -----*/ DSET_write(outset) ; if( verb ) WROTE_DSET(outset) ; if( verb ) INFO_message("Total CPU time = %.1f s",COX_cpu_time()) ; exit(0); }
int main( int argc , char *argv[] ) { THD_3dim_dataset *dset=NULL; int iarg , verbose = -1 ; char *outbuf, *stmp=NULL; char *labelName = NULL; char *sbdelim = {"|"}; char *NAflag = {"NA"}; char *atrdelim = {"\t"}, *form=NULL; INFO_FIELDS sing[512]; int iis=0, N_sing = 0, isb=0, withhead = 0, itmp=0; int ip=0, needpair = 0, namelen=0, monog_pairs = 0; THD_3dim_dataset *tttdset=NULL, *dsetp=NULL; char *tempstr = NULL; int extinit = 0; float RL_AP_IS[6]; mainENTRY("3dinfo main") ; machdep() ; if( argc < 2) { Syntax(TXT,1) ; RETURN(0); } iarg = 1 ; while (iarg < argc && argv[iarg][0] == '-') { CHECK_HELP(argv[iarg],Syntax); if( strncmp(argv[iarg],"-verb" ,5) == 0 ){ verbose = 0; iarg++; continue; } else if( strncmp(argv[iarg],"-VERB" ,5) == 0 ){ verbose = 1; iarg++; continue; } else if( strncmp(argv[iarg],"-short",5) == 0 ){ verbose = -1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-header_line") == 0 || strcasecmp(argv[iarg],"-hdr") == 0 ){ withhead = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-monog_pairs") == 0 ){ monog_pairs = 1; iarg++; continue; } else if ( strncmp(argv[iarg],"-label2",7) == 0 ) { iarg++; if (iarg >= argc) ERROR_exit( "3dinfo needs an argument after -label2number\n"); labelName = malloc(sizeof(char) * 2048); strcpy(labelName, argv[iarg]); iarg++; continue; } else if( strcasecmp(argv[iarg],"-sb_delim") == 0) { iarg++; if (iarg >= argc) ERROR_exit( "3dinfo needs a string after -sb_delim\n"); sbdelim = argv[iarg]; iarg++; continue; } else if( strcasecmp(argv[iarg],"-NA_flag") == 0) { iarg++; if (iarg >= argc) ERROR_exit( "3dinfo needs a string after -NA_flag\n"); NAflag = argv[iarg]; iarg++; continue; } else if( strcasecmp(argv[iarg],"-atr_delim") == 0) { iarg++; if (iarg >= argc) ERROR_exit( "3dinfo needs a string after -atr_delim\n"); atrdelim = argv[iarg]; iarg++; continue; } else if( strcasecmp(argv[iarg],"-space") == 0) { sing[N_sing++] = DSET_SPACE; iarg++; continue; } else if( strcasecmp(argv[iarg],"-av_space") == 0) { sing[N_sing++] = AV_DSET_SPACE; iarg++; continue; } else if( strcasecmp(argv[iarg],"-gen_space") == 0) { sing[N_sing++] = DSET_GEN_SPACE; iarg++; continue; } else if( strcasecmp(argv[iarg],"-is_nifti") == 0) { sing[N_sing++] = IS_NIFTI; iarg++; continue; } else if( strcasecmp(argv[iarg],"-is_atlas") == 0) { sing[N_sing++] = IS_ATLAS; iarg++; continue; } else if( strcasecmp(argv[iarg],"-exists") == 0) { sing[N_sing++] = DSET_EXISTS; iarg++; continue; } else if( strcasecmp(argv[iarg],"-is_oblique") == 0) { sing[N_sing++] = IS_OBLIQUE; iarg++; continue; } else if( strcasecmp(argv[iarg],"-obliquity") == 0) { sing[N_sing++] = OBLIQUITY; iarg++; continue; } else if( strcasecmp(argv[iarg],"-handedness") == 0) { sing[N_sing++] = HANDEDNESS; iarg++; continue; } else if( strcasecmp(argv[iarg],"-prefix") == 0) { sing[N_sing++] = PREFIX; iarg++; continue; } else if( strcasecmp(argv[iarg],"-prefix_noext") == 0) { sing[N_sing++] = PREFIX_NOEXT; iarg++; continue; } else if( strcasecmp(argv[iarg],"-ni") == 0) { sing[N_sing++] = NI; iarg++; continue; } else if( strcasecmp(argv[iarg],"-nj") == 0) { sing[N_sing++] = NJ; iarg++; continue; } else if( strcasecmp(argv[iarg],"-nk") == 0) { sing[N_sing++] = NK; iarg++; continue; } else if( strcasecmp(argv[iarg],"-n4") == 0) { sing[N_sing++] = NI; sing[N_sing++] = NJ; sing[N_sing++] = NK; sing[N_sing++] = NV; iarg++; continue; } else if( strcasecmp(argv[iarg],"-Rextent") == 0) { sing[N_sing++] = EXTENT_R; iarg++; continue; } else if( strcasecmp(argv[iarg],"-Lextent") == 0) { sing[N_sing++] = EXTENT_L; iarg++; continue; } else if( strcasecmp(argv[iarg],"-Aextent") == 0) { sing[N_sing++] = EXTENT_A; iarg++; continue; } else if( strcasecmp(argv[iarg],"-Pextent") == 0) { sing[N_sing++] = EXTENT_P; iarg++; continue; } else if( strcasecmp(argv[iarg],"-Iextent") == 0) { sing[N_sing++] = EXTENT_I; iarg++; continue; } else if( strcasecmp(argv[iarg],"-Sextent") == 0) { sing[N_sing++] = EXTENT_S; iarg++; continue; } else if( strcasecmp(argv[iarg],"-extent") == 0) { sing[N_sing++] = EXTENT_R; sing[N_sing++] = EXTENT_L; sing[N_sing++] = EXTENT_A; sing[N_sing++] = EXTENT_P; sing[N_sing++] = EXTENT_I; sing[N_sing++] = EXTENT_S; iarg++; continue; } else if( strcasecmp(argv[iarg],"-di") == 0) { sing[N_sing++] = DI; iarg++; continue; } else if( strcasecmp(argv[iarg],"-dj") == 0) { sing[N_sing++] = DJ; iarg++; continue; } else if( strcasecmp(argv[iarg],"-dk") == 0) { sing[N_sing++] = DK; iarg++; continue; } else if( strcasecmp(argv[iarg],"-d3") == 0) { sing[N_sing++] = DI; sing[N_sing++] = DJ; sing[N_sing++] = DK; iarg++; continue; } else if( strcasecmp(argv[iarg],"-adi") == 0) { sing[N_sing++] = ADI; iarg++; continue; } else if( strcasecmp(argv[iarg],"-adj") == 0) { sing[N_sing++] = ADJ; iarg++; continue; } else if( strcasecmp(argv[iarg],"-adk") == 0) { sing[N_sing++] = ADK; iarg++; continue; } else if( strcasecmp(argv[iarg],"-ad3") == 0) { sing[N_sing++] = ADI; sing[N_sing++] = ADJ; sing[N_sing++] = ADK; iarg++; continue; } else if( strcasecmp(argv[iarg],"-voxvol") == 0) { sing[N_sing++] = VOXVOL; iarg++; continue; } else if( strcasecmp(argv[iarg],"-iname") == 0) { sing[N_sing++] = INAME; iarg++; continue; } else if( strcasecmp(argv[iarg],"-oi") == 0) { sing[N_sing++] = OI; iarg++; continue; } else if( strcasecmp(argv[iarg],"-oj") == 0) { sing[N_sing++] = OJ; iarg++; continue; } else if( strcasecmp(argv[iarg],"-ok") == 0) { sing[N_sing++] = OK; iarg++; continue; } else if( strcasecmp(argv[iarg],"-o3") == 0) { sing[N_sing++] = OI; sing[N_sing++] = OJ; sing[N_sing++] = OK; iarg++; continue; }else if( strcasecmp(argv[iarg],"-nt") == 0) { sing[N_sing++] = NT; iarg++; continue; } else if( strcasecmp(argv[iarg],"-nti") == 0) { sing[N_sing++] = NTI; iarg++; continue; } else if( strcasecmp(argv[iarg],"-nv") == 0) { sing[N_sing++] = NV; iarg++; continue; } else if( strcasecmp(argv[iarg],"-nvi") == 0) { sing[N_sing++] = NVI; iarg++; continue; } else if( strcasecmp(argv[iarg],"-ntimes") == 0) { sing[N_sing++] = NTIMES; iarg++; continue; } else if( strcasecmp(argv[iarg],"-max_node") == 0) { sing[N_sing++] = MAX_NODE; iarg++; continue; } else if( strcasecmp(argv[iarg],"-nijk") == 0) { sing[N_sing++] = NIJK; iarg++; continue; } else if( strcasecmp(argv[iarg],"-labeltable") == 0) { sing[N_sing++] = LTABLE; iarg++; continue; } else if( strcasecmp(argv[iarg],"-labeltable_as_atlas_points") == 0) { sing[N_sing++] = LTABLE_AS_ATLAS_POINT_LIST; iarg++; continue; } else if( strcasecmp(argv[iarg],"-atlas_points") == 0) { sing[N_sing++] = ATLAS_POINTS; iarg++; continue; } else if( strcasecmp(argv[iarg],"-fac") == 0) { sing[N_sing++] = FAC; iarg++; continue; } else if( strcasecmp(argv[iarg],"-datum") == 0) { sing[N_sing++] = DATUM; iarg++; continue; } else if( strcasecmp(argv[iarg],"-label") == 0) { sing[N_sing++] = LABEL; iarg++; continue; } else if( strcasecmp(argv[iarg],"-min") == 0) { sing[N_sing++] = MIN; iarg++; continue; } else if( strcasecmp(argv[iarg],"-max") == 0) { sing[N_sing++] = MAX; iarg++; continue; } else if( strcasecmp(argv[iarg],"-minus") == 0) { sing[N_sing++] = MINUS; iarg++; continue; } else if( strcasecmp(argv[iarg],"-maxus") == 0) { sing[N_sing++] = MAXUS; iarg++; continue; } else if( strcasecmp(argv[iarg],"-dmin") == 0) { sing[N_sing++] = DMIN; iarg++; continue; } else if( strcasecmp(argv[iarg],"-dmax") == 0) { sing[N_sing++] = DMAX; iarg++; continue; } else if( strcasecmp(argv[iarg],"-dminus") == 0) { sing[N_sing++] = DMINUS; iarg++; continue; } else if( strcasecmp(argv[iarg],"-dmaxus") == 0) { sing[N_sing++] = DMAXUS; iarg++; continue; } else if( strcasecmp(argv[iarg],"-TR") == 0) { sing[N_sing++] = TR; iarg++; continue; } else if( strcasecmp(argv[iarg],"-header_name") == 0) { sing[N_sing++] = HEADER_NAME; iarg++; continue; } else if( strcasecmp(argv[iarg],"-brick_name") == 0) { sing[N_sing++] = BRICK_NAME; iarg++; continue; } else if( strcasecmp(argv[iarg],"-history") == 0) { sing[N_sing++] = HISTORY; iarg++; continue; } else if( strcasecmp(argv[iarg],"-all_names") == 0) { sing[N_sing++] = ALL_NAMES; iarg++; continue; } else if( strcasecmp(argv[iarg],"-orient") == 0) { sing[N_sing++] = ORIENT; iarg++; continue; } else if( strcasecmp(argv[iarg],"-same_grid") == 0) { sing[N_sing++] = SAME_GRID; needpair = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-same_dim") == 0) { sing[N_sing++] = SAME_DIM; needpair = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-same_delta") == 0) { sing[N_sing++] = SAME_DELTA; needpair = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-same_orient") == 0) { sing[N_sing++] = SAME_ORIENT; needpair = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-same_center") == 0) { sing[N_sing++] = SAME_CENTER; needpair = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-same_obl") == 0) { sing[N_sing++] = SAME_OBL; needpair = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-slice_timing") == 0) { sing[N_sing++] = SLICE_TIMING; iarg++; continue; } else if( strcasecmp(argv[iarg],"-sval_diff") == 0) { sing[N_sing++] = SVAL_DIFF; needpair = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-val_diff") == 0) { sing[N_sing++] = VAL_DIFF; needpair = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-same_all_grid") == 0) { sing[N_sing++] = SAME_DIM; sing[N_sing++] = SAME_DELTA; sing[N_sing++] = SAME_ORIENT; sing[N_sing++] = SAME_CENTER; sing[N_sing++] = SAME_OBL; needpair = 1; iarg++; continue; } else if( strcasecmp(argv[iarg],"-id") == 0) { sing[N_sing++] = ID; iarg++; continue; } else if( strcasecmp(argv[iarg],"-smode") == 0) { sing[N_sing++] = SMODE; iarg++; continue; } else { ERROR_message("Option %s unknown", argv[iarg]); suggest_best_prog_option(argv[0], argv[iarg]); exit(1); } } if (N_sing == 0) { sing[N_sing++] = CLASSIC; } if (sing[iis] == CLASSIC) PRINT_VERSION("3dinfo") ; THD_allow_empty_dataset(1) ; /* 21 Mar 2007 */ if (iarg == argc) { ERROR_message("No dsets on command line? I have nothing to do.\n"); exit(1); } if (needpair && monog_pairs) needpair = 2; /* pair each couple separately */ if (needpair==2 && (argc-iarg) % 2) { ERROR_message("Using options requiring dset pairs but have odd number\n" "of dsets (%d) on command line.\n", (argc-iarg)); exit (1); } else if (needpair==1 && (argc-iarg) < 2) { ERROR_message("Using options requiring dset pairs but have less than\n" "two dsets (%d) on command line.\n", (argc-iarg)); exit (1); } ip = 0; for( ; iarg < argc ; iarg++ ){ if (ip == 0) { int kkk, nml; char *etr; namelen = 0; for (kkk=iarg; kkk<argc; ++kkk) { if ((etr = THD_trailname(argv[kkk],0))) { nml=strlen(etr); if (nml < 48 && nml > namelen) namelen = nml; } } if (namelen < 6) namelen = 6; if (withhead) { int havenew=0; for (iis = 0; iis < N_sing; ++iis) { if (sing[iis] != CLASSIC) { ++havenew; form = PrintForm(sing[iis], namelen, 1); /*fprintf(stderr,"ZSS: %d %s >%s<\n", sing[iis], Field_Names[sing[iis]], form);*/ fprintf(stdout, form, Field_Names[sing[iis]]); } if (havenew) { if (N_sing > 1 && iis < N_sing-1) fprintf(stdout,"%s",atrdelim); else fprintf(stdout,"\n"); } } } } if( argv[iarg][0] == '\0' ) continue ; /* bad filename */ set_obliquity_report(0); /* silence obliquity */ if (!needpair) { if (!(dset = load_3dinfo_dataset(argv[iarg]))) { /* exit(1); */ } } else { if (needpair == 2) { /* Crazy idea of comparing each pair separately */ if (ip % 2 == 0) { if (!(dset = load_3dinfo_dataset(argv[iarg] ))) { /* exit(1); */ } if (iarg+1==argc || argv[iarg+1][0] == '\0') { ERROR_message("Bad dset pair for %s\n", argv[iarg]); exit(1); } if (!(dsetp = load_3dinfo_dataset(argv[iarg+1] ))) { /* exit(1); */ } } else { /* swap the pair - this allows non pair requiring functions to work as before.*/ tttdset = dsetp; dsetp = dset; dset = tttdset; tttdset=NULL; } } else { /* always compare to very first dset */ if (ip==0) { if (!(dset = load_3dinfo_dataset(argv[iarg] ))) { /*exit(1);*/ } if (!(dsetp = load_3dinfo_dataset(argv[iarg+1] ))) { /*exit(1);*/ } } else if (ip==1) { /* switch order of first two */ tttdset = dsetp; dsetp = dset; /* now dsetp is the very first dset */ dset = tttdset; tttdset=NULL; } else { /* pair with very first, which is dsetp */ if (!(dset = load_3dinfo_dataset(argv[iarg] ))) { /*exit(1);*/ } } } } ++ip; if (0 && !dset) { /* allow for DSET_EXISTS option */ ERROR_exit("Should not get here"); } /* we should re-capture this per dataset 5 Feb 2019 [rickr] */ extinit = 0; for (iis = 0; iis < N_sing; ++iis) { if (!dset) { if (sing[iis] == CLASSIC) { if( dset == NULL ){ /* still not open? */ ERROR_exit("Can't open dataset %s\n", argv[iarg]) ; } } else if (sing[iis] != DSET_EXISTS && sing[iis] != INAME) { fprintf(stdout, "NO-DSET"); SPIT_DELIM(iis, N_sing, atrdelim); continue; } } switch (sing[iis]) { case CLASSIC: if (labelName == NULL ) /*** get and output info ***/ { outbuf = THD_dataset_info( dset , verbose ) ; if( outbuf != NULL ){ printf("\n") ; puts(outbuf) ; free(outbuf) ; outbuf = NULL ; } else { ERROR_exit("Can't get info for dataset %s",argv[iarg]) ; } } else /*** get and output label ***/ { int nval_per = dset->dblk->nvals; int foundLabel = 0; int ival=0; for (ival=0 ; ival < nval_per && !foundLabel; ival++ ) { if (strcmp(DSET_BRICK_LAB(dset,ival), labelName) == 0) { printf("%d\n", ival); foundLabel = 1; } } /* end of for (ival=0 ; ival < nval_per ; ival++ ) */ if (!foundLabel) printf("\n"); } THD_delete_3dim_dataset( dset , False ) ; free(labelName); break; case DSET_EXISTS: fprintf(stdout, "%d", dset ? 1:0); break; case DSET_SPACE: tempstr = THD_get_space(dset); if(tempstr==NULL) fprintf(stdout, "-----"); else fprintf(stdout, "%s", tempstr); break; case DSET_GEN_SPACE: tempstr = THD_get_generic_space(dset); if(tempstr==NULL) fprintf(stdout, "-----"); else fprintf(stdout, "%s", tempstr); break; case AV_DSET_SPACE: /* don't allow anything but the three AFNI views */ tempstr = THD_get_view_space(dset); if(tempstr==NULL) fprintf(stdout, "+orig"); else if (!strncasecmp(tempstr,"ORIG",4)) fprintf(stdout, "+orig"); else if (!strncasecmp(tempstr,"ACPC",4)) fprintf(stdout, "+acpc"); else if (!strncasecmp(tempstr,"TLRC",4)) fprintf(stdout, "+tlrc"); else /* shouldn't get here */ fprintf(stdout, "+orig"); break; case IS_NIFTI: if ( dset->dblk->diskptr && dset->dblk->diskptr->storage_mode == STORAGE_BY_NIFTI ) { fprintf(stdout,"1"); } else { fprintf(stdout,"0"); } break; case IS_ATLAS: if ( is_Dset_Atlasy(dset, NULL) ) { fprintf(stdout,"1"); } else { fprintf(stdout,"0"); } break; case IS_OBLIQUE: if (dset_obliquity(dset,NULL) > 0) { fprintf(stdout,"1"); } else { fprintf(stdout,"0"); } break; case HANDEDNESS: if (THD_handedness(dset) > 0) { fprintf(stdout,"R"); } else { fprintf(stdout,"L"); } break; case OBLIQUITY: fprintf(stdout,"%.3f", THD_compute_oblique_angle(dset->daxes->ijk_to_dicom_real, 0)); break; case PREFIX: form = PrintForm(sing[iis], namelen, 1); fprintf(stdout,form, DSET_PREFIX(dset)); break; case PREFIX_NOEXT: { form = PrintForm(sing[iis], namelen, 1); stmp=DSET_prefix_noext(dset); fprintf(stdout,form, stmp); free(stmp); stmp=NULL; } break; case HEADER_NAME: fprintf(stdout,"%s", dset->dblk->diskptr->header_name); break; case BRICK_NAME: fprintf(stdout,"%s", dset->dblk->diskptr->brick_name); break; case ALL_NAMES: THD_show_dataset_names(dset, "FOR_3DINFO", stdout); break; case HISTORY: stmp = tross_Get_History(dset); fprintf(stdout,"%s", stmp ? stmp:NAflag); if (stmp) free(stmp); stmp=NULL; break; case NI: fprintf(stdout,"%d", DSET_NX(dset)); break; case NJ: fprintf(stdout,"%d", DSET_NY(dset)); break; case NK: fprintf(stdout,"%d", DSET_NZ(dset)); break; case NIJK: fprintf(stdout,"%d", DSET_NVOX(dset)); break; case NTIMES: fprintf(stdout,"%d", DSET_NUM_TIMES(dset)); break; case MAX_NODE: DSET_MAX_NODE(dset,itmp); fprintf(stdout,"%d", itmp); break; case NT: case NV: fprintf(stdout,"%d", DSET_NVALS(dset)); break; case NTI: case NVI: fprintf(stdout,"%d", DSET_NVALS(dset)-1); break; case DI: fprintf(stdout,"%f", DSET_DX(dset)); break; case DJ: fprintf(stdout,"%f", DSET_DY(dset)); break; case DK: fprintf(stdout,"%f", DSET_DZ(dset)); break; case OI: fprintf(stdout,"%f", DSET_XORG(dset)); break; case OJ: fprintf(stdout,"%f", DSET_YORG(dset)); break; case OK: fprintf(stdout,"%f", DSET_ZORG(dset)); break; case ADI: fprintf(stdout,"%f", fabs(DSET_DX(dset))); break; case EXTENT_R: case EXTENT_L: case EXTENT_A: case EXTENT_P: case EXTENT_I: case EXTENT_S: { if (!extinit) { THD_dset_extent(dset, '-', RL_AP_IS); extinit = 1; } fprintf(stdout,"%f", RL_AP_IS[sing[iis]-EXTENT_R]); } break; case ADJ: fprintf(stdout,"%f", fabs(DSET_DY(dset))); break; case ADK: fprintf(stdout,"%f", fabs(DSET_DZ(dset))); break; case VOXVOL: fprintf(stdout,"%f", fabs(DSET_DX(dset))* fabs(DSET_DY(dset))*fabs(DSET_DZ(dset))); break; case INAME: fprintf(stdout,"%s", argv[iarg]); break; case LTABLE: { char *str; if ((str = Dtable_to_nimlstring(DSET_Label_Dtable(dset), "VALUE_LABEL_DTABLE"))) { fprintf(stdout,"%s", str); free(str); } else { fprintf(stdout,"NO_LABEL_TABLE"); } } break; case LTABLE_AS_ATLAS_POINT_LIST: { ATLAS_POINT_LIST *apl=NULL; if ((apl = label_table_to_atlas_point_list(DSET_Label_Dtable(dset)))) { atlas_list_to_niml(apl,NULL); free_atlas_point_list(apl); } else { fprintf(stdout,"NO_LABEL_TABLE"); } } break; case ATLAS_POINTS: { ATR_string *atr = THD_find_string_atr( dset->dblk, "ATLAS_LABEL_TABLE"); if (atr) { fprintf(stdout,"%s", atr->ch); } else { fprintf(stdout,"NO_APL"); } } break; case FAC: { for (isb=0; isb<DSET_NVALS(dset); ++isb) { fprintf(stdout,"%f%s", DSET_BRICK_FACTOR(dset,isb), (isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim); } break; } case DATUM: { for (isb=0; isb<DSET_NVALS(dset); ++isb) { fprintf(stdout,"%s%s", MRI_TYPE_name[DSET_BRICK_TYPE(dset,isb)], (isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim); } break; } case LABEL: { for (isb=0; isb<DSET_NVALS(dset); ++isb) { fprintf(stdout,"%s%s", DSET_BRICK_LABEL(dset,isb) ? DSET_BRICK_LABEL(dset,isb):NAflag, (isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim); } break; } case MIN: case MINUS: case MAX: case MAXUS: { float vv=0.0, min, max; for (isb=0; isb<DSET_NVALS(dset); ++isb) { if (!THD_subbrick_minmax(dset, isb, (sing[iis] == MINUS || sing[iis] == MAXUS) ? 0:1, &min, &max)) { fprintf(stdout,"%s%s", NAflag, (isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim); } else { if (sing[iis] == MINUS) vv = min; else if (sing[iis] == MAXUS) vv = max; else if (sing[iis] == MIN) vv = min; else if (sing[iis] == MAX) vv = max; fprintf(stdout,"%g%s", vv, (isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim); } } break; } case DMIN: case DMINUS: case DMAX: case DMAXUS: { float vv=0.0, min, max; if (!THD_dset_minmax(dset, (sing[iis] == DMINUS || sing[iis] == DMAXUS) ? 0:1, &min, &max)) { fprintf(stdout,"%s%s", NAflag, (isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim); } else { if (sing[iis] == DMINUS) vv = min; else if (sing[iis] == DMAXUS) vv = max; else if (sing[iis] == DMIN) vv = min; else if (sing[iis] == DMAX) vv = max; fprintf(stdout,"%g%s", vv, (isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim); } break; } case TR: #if 0 fprintf(stdout,"%f", DSET_TR_SEC(dset)); #else fprintf(stdout,"%f", DSET_TR(dset)); #endif break; case ORIENT: { /* fprintf(stdout,"%c%c%c", * ORIENT_typestr[dset->daxes->xxorient][0], ... ); */ char ostr[4]; /* just to show 23 Jan 2013 [rickr] */ THD_fill_orient_str_3(dset->daxes, ostr); fprintf(stdout,"%3s", ostr); } break; case SAME_GRID: fprintf(stdout,"%d", !THD_dataset_mismatch( dset , dsetp )); break; case SAME_DIM: fprintf(stdout,"%d", !(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_DIMEN)); break; case SAME_DELTA: fprintf(stdout,"%d", !(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_DELTA)); break; case SAME_ORIENT: fprintf(stdout,"%d", !(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_ORIENT)); break; case SAME_CENTER: fprintf(stdout,"%d", !(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_CENTER)); break; case SAME_OBL: fprintf(stdout,"%d", !(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_OBLIQ)); break; case SLICE_TIMING: /* 6 May 2013 [rickr] */ { if( DSET_HAS_SLICE_TIMING(dset) ) { DSET_UNMSEC(dset); /* make sure times are in seconds */ for (isb=0; isb<dset->taxis->nsl; ++isb) { fprintf(stdout,"%s%f", (isb > 0) ? sbdelim : "", dset->taxis->toff_sl[isb]); } } else { /* all slices times are at t=0.0 */ for (isb=0; isb<DSET_NZ(dset); ++isb) { fprintf(stdout,"%s%f", (isb > 0) ? sbdelim : "", 0.0); } } } break; case SVAL_DIFF: fprintf(stdout,"%f",THD_diff_vol_vals(dset, dsetp, 1)); break; case VAL_DIFF: fprintf(stdout,"%f",THD_diff_vol_vals(dset, dsetp, 0)); break; case ID: fprintf(stdout,"%s", DSET_IDCODE_STR(dset)); break; case SMODE: fprintf(stdout,"%s", DSET_STORAGE_MODE_STR(dset)); break; default: ERROR_message("Info field not set properly (%d)\n", sing[iis]); exit(1); } if (sing[iis] != CLASSIC) { SPIT_DELIM(iis, N_sing, atrdelim); } } } exit(0) ; }
int main( int argc , char *argv[] ) { int iarg , ii,jj,kk,mm , nvec , nx=0,ny , ff , vlen=4 ; MRI_IMAGE *tim , *vsim=NULL ; MRI_IMARR *tar ; char **vecnam , *tnam ; float *far , **tvec , *vsig=NULL , xsig,ysig ; float_quad qcor ; float_pair pci ; float corst, cor025, cor500, cor975 ; char fmt[256] ; int cormeth=0 ; /* 0=Pearson, 1=Spearman, 2=Quadrant, 3=Kendall tau_b */ float (*corfun)(int,float *,float *) ; /*-- start the AFNI machinery --*/ mainENTRY("1dCorrelate main") ; machdep() ; /* check for options */ iarg = 1 ; nvec = 0 ; while( iarg < argc && argv[iarg][0] == '-' ){ /* I get by with a little help from my friends? */ if( strcmp(argv[iarg],"-help") == 0 || strcmp(argv[iarg],"-h") == 0){ usage_1dCorrelate(strlen(argv[iarg])>3 ? 2:1); exit(0) ; } /*--- methods ---*/ if( toupper(argv[iarg][1]) == 'P' ){ cormeth = 0 ; iarg++ ; continue ; } if( toupper(argv[iarg][1]) == 'S' ){ cormeth = 1 ; iarg++ ; continue ; } if( toupper(argv[iarg][1]) == 'Q' ){ cormeth = 2 ; iarg++ ; continue ; } if( toupper(argv[iarg][1]) == 'K' ){ cormeth = 3 ; iarg++ ; continue ; } if( toupper(argv[iarg][1]) == 'T' ){ cormeth = 4 ; iarg++ ; continue ; } if( toupper(argv[iarg][1]) == 'U' ){ cormeth = 5 ; iarg++ ; continue ; } /*--- set nboot ---*/ if( strcasecmp(argv[iarg],"-nboot") == 0 || strcasecmp(argv[iarg],"-num") == 0 ){ iarg++ ; if( iarg >= argc ) ERROR_exit("Need argument after '-nboot'") ; nboot = (int)strtod(argv[iarg],NULL) ; if( nboot < NBMIN ){ WARNING_message("Replacing -nboot %d with %d",nboot,NBMIN) ; nboot = NBMIN ; } iarg++ ; continue ; } /*--- set alpha ---*/ if( strcasecmp(argv[iarg],"-alpha") == 0 ){ iarg++ ; if( iarg >= argc ) ERROR_exit("Need argument after '-alpha'") ; alpha = (float)strtod(argv[iarg],NULL) ; if( alpha < 1.0f ){ WARNING_message("Replacing -alpha %.1f with 1",alpha) ; alpha = 0.01f ; } else if( alpha > 20.0f ){ WARNING_message("Replacing -alpha %.1f with 20",alpha) ; alpha = 0.20f ; } else { alpha *= 0.01f ; /* convert from percent to fraction */ } iarg++ ; continue ; } /*--- block resampling ---*/ if( strcasecmp(argv[iarg],"-blk") == 0 || strcasecmp(argv[iarg],"-block") == 0 ){ doblk = 1 ; iarg++ ; continue ; } if( strcasecmp(argv[iarg],"-vsig") == 0 ){ if( vsim != NULL ) ERROR_exit("Can't use -vsig twice!") ; if( ++iarg >= argc ) ERROR_exit("Need argument after -vsig") ; vsim = mri_read_1D(argv[iarg]) ; if( vsim == NULL ) ERROR_exit("Can't read -vsig file '%s'",argv[iarg]) ; iarg++ ; continue ; } /*--- user should be flogged ---*/ ERROR_message("Monstrously illegal option '%s'",argv[iarg]) ; suggest_best_prog_option(argv[0], argv[iarg]); exit(1); } /*--- user should be flogged twice ---*/ if( argc < 2 ){ usage_1dCorrelate(1) ; exit(0) ; } if( iarg == argc ) ERROR_exit("No 1D files on command line!?\n") ; /* the function to compute the correlation */ corfun = cor_func[cormeth] ; /* check and assemble list of input 1D files */ ff = iarg ; INIT_IMARR(tar) ; for( ; iarg < argc ; iarg++ ){ tim = mri_read_1D( argv[iarg] ) ; if( tim == NULL ) ERROR_exit("Can't read 1D file '%s'",argv[iarg]) ; if( nx == 0 ){ nx = tim->nx ; if( nx < 3 ) ERROR_exit("1D file '%.77s' length=%d is less than 3",argv[iarg],nx) ; else if( nx < 7 ) WARNING_message("1D file '%.77s' length=%d is less than 7",argv[iarg],nx) ; } else if( tim->nx != nx ){ ERROR_exit("Length of 1D file '%.77s' [%d] doesn't match first file [%d]", argv[iarg] , tim->nx , nx ); } nvec += tim->ny ; ADDTO_IMARR(tar,tim) ; } /* user is really an idiot -- flogging's too good for him */ if( nvec < 2 ) ERROR_exit("Must have at least 2 input columns!") ; if( nx < 20 && doblk ){ doblk = 0 ; WARNING_message("Column length %d < 20 ==> cannot use block resampling",nx) ; } if( vsim != NULL ){ if( vsim->nvox < nvec ) ERROR_exit("-vsig file only has %d entries, but needs at least %d",vsim->nvox,nvec) ; vsig = MRI_FLOAT_PTR(vsim) ; } /* create vectors from 1D files */ tvec = (float **)malloc( sizeof(float *)*nvec ) ; vecnam = (char **)malloc( sizeof(char *)*nvec ) ; for( jj=0 ; jj < nvec ; jj++ ){ tvec[jj] = (float *)malloc( sizeof(float)*nx ) ; vecnam[jj] = (char *)malloc(sizeof(char)*THD_MAX_NAME) ; } /* copy data into new space, create output labels, check for stoopiditees */ for( kk=mm=0 ; mm < IMARR_COUNT(tar) ; mm++ ){ tim = IMARR_SUBIM(tar,mm) ; far = MRI_FLOAT_PTR(tim) ; tnam = tim->name ; if( tnam == NULL ) tnam = "File" ; for( jj=0 ; jj < tim->ny ; jj++,kk++ ){ for( ii=0 ; ii < nx ; ii++ ) tvec[kk][ii] = far[ii+jj*nx] ; sprintf(vecnam[kk],"%s[%d]",THD_trailname(tnam,0),jj) ; /* vector name */ iarg = strlen(vecnam[kk]) ; vlen = MAX(vlen,iarg) ; if( THD_is_constant(nx,tvec[kk]) ) ERROR_exit("Column %s is constant!",vecnam[kk]) ; } } DESTROY_IMARR(tar) ; /*--- Print a beeyootiful header ---*/ printf("# %s correlation [n=%d #col=%d]\n",cor_name[cormeth],nx,nvec) ; sprintf(fmt,"# %%-%ds %%-%ds",vlen,vlen) ; printf(fmt,"Name","Name") ; printf(" Value BiasCorr %5.2f%% %5.2f%%",50.0f*alpha,100.0f-50.0f*alpha) ; if( cormeth == 0 ) /* Pearson */ printf(" N:%5.2f%% N:%5.2f%%",50.0f*alpha,100.0f-50.0f*alpha) ; printf("\n") ; printf("# ") ; for( ii=0 ; ii < vlen ; ii++ ) printf("-") ; printf(" ") ; for( ii=0 ; ii < vlen ; ii++ ) printf("-") ; printf(" ") ; printf(" --------") ; printf(" --------") ; printf(" --------") ; printf(" --------") ; if( cormeth == 0 ){ printf(" --------") ; printf(" --------") ; } printf("\n") ; if( cormeth != 0 ) /* non-Pearson */ sprintf(fmt," %%-%ds %%-%ds %%+8.5f %%+8.5f %%+8.5f %%+8.5f\n",vlen,vlen) ; else /* Pearson */ sprintf(fmt," %%-%ds %%-%ds %%+8.5f %%+8.5f %%+8.5f %%+8.5f %%+8.5f %%+8.5f\n",vlen,vlen) ; /*--- Do some actual work for a suprising change ---*/ for( jj=0 ; jj < nvec ; jj++ ){ /* loops over column pairs */ for( kk=jj+1 ; kk < nvec ; kk++ ){ if( vsig != NULL ){ xsig = vsig[jj]; ysig = vsig[kk]; } else { xsig = ysig = 0.0f; } qcor = Corrboot( nx, tvec[jj], tvec[kk], xsig, ysig, corfun ) ; /* outsourced */ corst = qcor.a ; cor025 = qcor.b ; cor500 = qcor.c ; cor975 = qcor.d ; if( cormeth == 0 ){ /* Pearson */ pci = PCorrCI( nx , corst , alpha ) ; printf(fmt, vecnam[jj], vecnam[kk], corst, cor500, cor025, cor975, pci.a,pci.b ) ; } else { /* all other methods */ printf(fmt, vecnam[jj], vecnam[kk], corst, cor500, cor025, cor975 ) ; } } } /* Finished -- go back to watching Star Trek reruns -- Tribbles ahoy, Cap'n! */ exit(0) ; }
int main( int argc , char * argv[] ) { int iarg=1 , dcode=0 , maxgap=2 , nftot=0 ; char * prefix="zfillin" , * dstr=NULL; THD_3dim_dataset * inset , * outset ; MRI_IMAGE * brim ; int verb=0 ; if( argc < 2 || strcmp(argv[1],"-help") == 0 ){ printf("Usage: 3dZFillin [options] dataset\n" "Extracts 1D rows in the given direction from a 3D dataset,\n" "searches for zeros that are 'close' to nonzero values in the row,\n" "and replaces the zeros with the closest nonzero neighbor.\n" "\n" "OPTIONS:\n" " -maxstep N = set the maximum distance to a neighbor\n" " [default=2].\n" " -dir D = set the direction of fill to 'D', which can\n" " be one of the following:\n" " A-P, P-A, I-S, S-I, L-R, R-L, x, y, z\n" " The first 6 are anatomical directions;\n" " the last 3 are reference to the dataset\n" " internal axes [no default value].\n" " -prefix P = set the prefix to 'P' for the output dataset.\n" "\n" "N.B.: * If the input dataset has more than one sub-brick,\n" " only the first one will be processed.\n" " * At this time, 3dZFillin only works on byte-valued datasets\n" "\n" "This program's only purpose is to fill up the Talairach Daemon\n" "bricks obtained from the UT San Antonio database.\n" "\n" ) ; PRINT_COMPILE_DATE ; exit(0) ; } mainENTRY("3dZFillin main") ; machdep() ; AFNI_logger("3dZfillin",argc,argv) ; PRINT_VERSION(3dZFillin") ; /*-- scan args --*/ while( iarg < argc && argv[iarg][0] == '-' ){ if( strncmp(argv[iarg],"-verb",5) == 0 ){ verb++ ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-prefix") == 0 ){ prefix = argv[++iarg] ; if( !THD_filename_ok(prefix) ){ fprintf(stderr,"*** Illegal string after -prefix!\n"); exit(1) ; } iarg++ ; continue ; } if( strcmp(argv[iarg],"-maxstep") == 0 ){ maxgap = strtol( argv[++iarg] , NULL , 10 ) ; if( maxgap < 1 ){ fprintf(stderr,"*** Illegal value after -maxgap!\n"); exit(1); } iarg++ ; continue ; } if( strcmp(argv[iarg],"-dir") == 0 ){ dstr = argv[++iarg] ; iarg++ ; continue ; } fprintf(stderr,"*** Illegal option: %s\n",argv[iarg]) ; exit(1) ; } if( dstr == NULL ){ fprintf(stderr,"*** No -dir option on command line!\n"); exit(1); } if( iarg >= argc ){ fprintf(stderr,"*** No input dataset on command line!\n"); exit(1); } inset = THD_open_dataset( argv[iarg] ) ; if( inset == NULL ){ fprintf(stderr,"*** Can't open dataset %s\n",argv[iarg]); exit(1); } outset = EDIT_empty_copy( inset ) ; EDIT_dset_items( outset , ADN_prefix , prefix , ADN_none ) ; if( THD_deathcon() && THD_is_file( DSET_HEADNAME(outset) ) ){ fprintf(stderr,"** Output file %s exists -- cannot overwrite!\n", DSET_HEADNAME(outset) ) ; exit(1) ; } tross_Copy_History( inset , outset ) ; tross_Make_History( "3dZFillin" , argc,argv , outset ) ; if( DSET_NVALS(inset) > 1 ){ fprintf(stderr,"++ WARNING: input dataset has more than one sub-brick!\n"); EDIT_dset_items( outset , ADN_ntt , 0 , ADN_nvals , 1 , ADN_none ) ; } if( DSET_BRICK_TYPE(outset,0) != MRI_byte ){ fprintf(stderr,"*** This program only works on byte datasets!\n"); exit(1) ; } switch( *dstr ){ case 'x': dcode = 1 ; break ; case 'y': dcode = 2 ; break ; case 'z': dcode = 3 ; break ; default: if( *dstr == ORIENT_tinystr[outset->daxes->xxorient][0] || *dstr == ORIENT_tinystr[outset->daxes->xxorient][1] ) dcode = 1 ; if( *dstr == ORIENT_tinystr[outset->daxes->yyorient][0] || *dstr == ORIENT_tinystr[outset->daxes->yyorient][1] ) dcode = 2 ; if( *dstr == ORIENT_tinystr[outset->daxes->zzorient][0] || *dstr == ORIENT_tinystr[outset->daxes->zzorient][1] ) dcode = 3 ; break ; } if( dcode == 0 ){ fprintf(stderr,"*** Illegal -dir direction!\n") ; exit(1) ; } if( verb ) fprintf(stderr,"++ Direction = axis %d in dataset\n",dcode) ; DSET_load(inset) ; CHECK_LOAD_ERROR(inset) ; brim = mri_copy( DSET_BRICK(inset,0) ) ; DSET_unload(inset) ; EDIT_substitute_brick( outset , 0 , brim->kind , mri_data_pointer(brim) ) ; nftot = THD_dataset_zfillin( outset , 0 , dcode , maxgap ) ; fprintf(stderr,"++ Number of voxels filled = %d\n",nftot) ; if (DSET_write(outset) != False) { fprintf(stderr,"++ output dataset: %s\n",DSET_BRIKNAME(outset)) ; exit(0) ; } else { fprintf(stderr, "** 3dZFillin: Failed to write output!\n" ) ; exit(1) ; } }
int main( int argc , char *argv[] ) { MRI_IMAGE *imin, *imout , *imout_orig; THD_3dim_dataset *iset, *oset , *ooset; char *prefix = "SpatNorm", *bottom_cuts = NULL; int iarg , verb=0, OrigSpace = 0 , specie = HUMAN; float SpatNormDxyz= 0.0, iset_scaled=1.0; THD_ivec3 orixyz , nxyz ; THD_fvec3 dxyz , orgxyz, originRAIfv, fv2; mainENTRY("3dSpatNorm main") ; machdep() ; if (argc == 1) { usage_3dSpatNorm(1); exit(0); } /*--- options ---*/ iarg = 1 ; OrigSpace = 0; while( iarg < argc && argv[iarg][0] == '-' ){ if (strcmp(argv[iarg],"-h") == 0 || strcmp(argv[iarg],"-help") == 0 ) { usage_3dSpatNorm(strlen(argv[iarg]) > 3 ? 2:1); exit(0); } /* -prefix */ if( strcmp(argv[iarg],"-prefix") == 0 ){ if( ++iarg >= argc ){ fprintf(stderr,"**ERROR: -prefix requires another argument!\n") ; exit(1) ; } prefix = strdup(argv[iarg]) ; if( !THD_filename_ok(prefix) ){ fprintf(stderr,"**ERROR: -prefix value contains forbidden characters!\n") ; exit(1) ; } iarg++ ; continue ; } if( strcmp(argv[iarg],"-dxyz") == 0 ){ if( ++iarg >= argc ){ fprintf(stderr,"**ERROR: -dxyz requires another argument!\n") ; exit(1) ; } SpatNormDxyz = atof(argv[iarg]) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-bottom_cuts") == 0 ){ if( ++iarg >= argc ){ fprintf(stderr,"**ERROR: -bottom_cuts requires another argument!\n") ; exit(1) ; } bottom_cuts = argv[iarg] ; iarg++ ; continue ; } if( strncmp(argv[iarg],"-verb",5) == 0 ){ verb++ ; iarg++ ; continue ; } if( strncmp(argv[iarg],"-human",5) == 0 ){ specie = HUMAN ; iarg++ ; continue ; } if( strncmp(argv[iarg],"-monkey",5) == 0 ){ specie = MONKEY ; iarg++ ; continue ; } if( strncmp(argv[iarg],"-marmoset",5) == 0 ){ specie = MARMOSET ; iarg++ ; continue ; } if( strncmp(argv[iarg],"-rat",5) == 0 ){ specie = RAT ; iarg++ ; continue ; } if( strncmp(argv[iarg],"-orig_space",10) == 0 ){ OrigSpace = 1 ; iarg++ ; continue ; } fprintf(stderr,"**ERROR: %s is unknown option!\n",argv[iarg]) ; suggest_best_prog_option(argv[0], argv[iarg]); exit(1) ; } if( iarg >= argc ){ fprintf(stderr,"**ERROR: no input dataset name on command line?!\n") ; exit(1) ; } /*--- read dataset ---*/ iset = THD_open_dataset( argv[iarg] ) ; if( !ISVALID_DSET(iset) ){ fprintf(stderr,"**ERROR: can't open dataset %s\n",argv[iarg]) ; exit(1) ; } /*--- get median brick --*/ if( verb ) fprintf(stderr,"++3dSpatNorm: loading dataset\n") ; if (specie == MARMOSET) { iset_scaled = 2.5; THD_volDXYZscale(iset->daxes, iset_scaled, 0); specie = MONKEY; } imin = THD_median_brick( iset ) ; if( imin == NULL ){ fprintf(stderr,"**ERROR: can't load dataset %s\n",argv[iarg]) ; exit(1) ; } imin->dx = fabs(iset->daxes->xxdel) ; imin->dy = fabs(iset->daxes->yydel) ; imin->dz = fabs(iset->daxes->zzdel) ; mri_speciebusiness(specie); mri_brain_normalize_cuts(bottom_cuts); if (SpatNormDxyz) { if (verb) fprintf(stderr,"Overriding default resampling\n"); mri_brainormalize_initialize(SpatNormDxyz, SpatNormDxyz, SpatNormDxyz); } else { float xxdel, yydel, zzdel, minres; if (specie == MONKEY) minres = 0.5; else if (specie == MARMOSET) minres = 0.2; else if (specie == RAT) minres = 0.1; else minres = 0.5; /* don't allow for too low a resolution, please */ if (imin->dx < minres) xxdel = minres; else xxdel = imin->dx; if (imin->dy < minres) yydel = minres; else yydel = imin->dy; if (imin->dz < minres) zzdel = minres; else zzdel = imin->dz; if (verb) { fprintf(stderr, "%s:\n" " Original resolution %f, %f, %f\n" " SpatNorm resolution %f, %f, %f\n", "3dSpatnorm", imin->dx, imin->dy, imin->dz, xxdel, yydel, zzdel); } mri_brainormalize_initialize(xxdel, yydel, zzdel); } /* To get around the #define for voxel counts and dimensions */ mri_brainormalize_initialize(imin->dz, imin->dy, imin->dz); /* me needs the origin of this dset in RAI world */ LOAD_FVEC3( originRAIfv , iset->daxes->xxorg , iset->daxes->yyorg , iset->daxes->zzorg) ; originRAIfv = THD_3dmm_to_dicomm( iset , originRAIfv ) ; LOAD_FVEC3(fv2, iset->daxes->xxorg + (iset->daxes->nxx-1)*iset->daxes->xxdel , iset->daxes->yyorg + (iset->daxes->nyy-1)*iset->daxes->yydel , iset->daxes->zzorg + (iset->daxes->nzz-1)*iset->daxes->zzdel); fv2 = THD_3dmm_to_dicomm( iset , fv2 ) ; if( originRAIfv.xyz[0] > fv2.xyz[0] ) { float tf; tf = originRAIfv.xyz[0]; originRAIfv.xyz[0] = fv2.xyz[0]; fv2.xyz[0] = tf; } if( originRAIfv.xyz[1] > fv2.xyz[1] ) { float tf; tf = originRAIfv.xyz[1]; originRAIfv.xyz[1] = fv2.xyz[1]; fv2.xyz[1] = tf; } if( originRAIfv.xyz[2] > fv2.xyz[2] ) { float tf; tf = originRAIfv.xyz[2]; originRAIfv.xyz[2] = fv2.xyz[2]; fv2.xyz[2] = tf; } if (verb) { fprintf(stderr,"++3dSpatNorm (ZSS): RAI origin info: %f %f %f\n", originRAIfv.xyz[0], originRAIfv.xyz[1], originRAIfv.xyz[2]); } DSET_unload( iset ) ; /* don't need this data no more */ /*-- convert image to shorts, if appropriate --*/ if( DSET_BRICK_TYPE(iset,0) == MRI_short || DSET_BRICK_TYPE(iset,0) == MRI_byte ){ imout = mri_to_short(0.0,imin) ; /* ZSS Oct 2012: Let function set scaling*/ mri_free(imin) ; imin = imout ; } /*--- normalize image spatially ---*/ mri_brainormalize_verbose( verb ) ; if (OrigSpace) { imout = mri_brainormalize( imin , iset->daxes->xxorient, iset->daxes->yyorient, iset->daxes->zzorient , &imout_orig, NULL) ; } else { imout = mri_brainormalize( imin , iset->daxes->xxorient, iset->daxes->yyorient, iset->daxes->zzorient , NULL, NULL) ; } mri_free( imin ) ; if( imout == NULL ){ fprintf(stderr,"**ERROR: normalization fails!?\n"); exit(1); } if (OrigSpace) { if( verb ) fprintf(stderr,"++3dSpatNorm: Output in Orignal space\n") ; mri_free( imout ) ; imout = imout_orig; imout->xo = originRAIfv.xyz[0]; imout->yo = originRAIfv.xyz[1]; imout->zo = originRAIfv.xyz[2]; imout_orig = NULL; } else { if( verb ) fprintf(stderr,"++3dSpatNorm: Output in SpatNorm space\n") ; } #if 0 if( AFNI_yesenv("WATERSHED") ){ imin = mri_watershedize( imout , 0.10 ) ; if( imin != NULL ){ mri_free(imout); imout = imin; } } #endif /*--- create output dataset ---*/ if( verb ) fprintf(stderr,"++3dSpatNorm: Creating output dset\n") ; oset = EDIT_empty_copy( NULL ) ; tross_Copy_History( iset , oset ) ; tross_Make_History( "3dSpatNorm" , argc,argv , oset ) ; LOAD_IVEC3( nxyz , imout->nx , imout->ny , imout->nz ) ; LOAD_FVEC3( dxyz , imout->dx , imout->dy , imout->dz ) ; LOAD_FVEC3( orgxyz , imout->xo , imout->yo , imout->zo ) ; LOAD_IVEC3( orixyz , ORI_R2L_TYPE , ORI_A2P_TYPE , ORI_I2S_TYPE ) ; if( verb ) fprintf(stderr,"++3dSpatNorm: EDIT_dset_items\n") ; EDIT_dset_items( oset , ADN_prefix , prefix , ADN_datum_all , imout->kind , ADN_nxyz , nxyz , ADN_xyzdel , dxyz , ADN_xyzorg , orgxyz , ADN_xyzorient , orixyz , ADN_malloc_type , DATABLOCK_MEM_MALLOC , ADN_view_type , VIEW_ORIGINAL_TYPE , ADN_type , HEAD_ANAT_TYPE , ADN_func_type , ANAT_BUCK_TYPE , ADN_none ) ; if( verb ) fprintf(stderr,"++3dSpatNorm: EDIT_substitute_brick\n") ; EDIT_substitute_brick( oset , 0 , imout->kind , mri_data_pointer(imout) ) ; if (OrigSpace) { if( verb ) fprintf(stderr,"++3dSpatNorm: Changing orientation from RAI\n") ; ooset = r_new_resam_dset ( oset, iset, 0, 0, 0, NULL, MRI_NN, NULL, 1, 0); if (!ooset) { fprintf(stderr,"**ERROR: Failed to reslice!?\n"); exit(1); } /* put prefix back, r_new_resam_dset puts dummy prefix */ EDIT_dset_items( ooset , ADN_prefix , prefix, ADN_none ) ; DSET_delete(oset); oset = ooset; ooset = NULL; } if (iset_scaled != 1.0f) THD_volDXYZscale(oset->daxes, 1/iset_scaled, 0); DSET_write(oset) ; if( verb ) fprintf(stderr,"++3dSpatNorm: wrote dataset %s\n",DSET_BRIKNAME(oset)) ; exit(0) ; }