int GenFeatureDist(SEG_OPTS *Opt)
{
ENTRY("GenFeatureDist");
/* get the probability maps */
if (!Opt->pset && Opt->DO_p) {
if (!(Opt->pset = p_C_GIV_A(Opt))) {
ERROR_message("Failed miserably");
RETURN(0);
}
}
/* Get the classes */
if (!Opt->cset && Opt->crefix && Opt->DO_c) {
if (!(SUMA_assign_classes_eng(Opt->pset,
Opt->clss->str, Opt->clss->num, Opt->keys,
Opt->cmask, &Opt->cset))) {
ERROR_message("Failed aimlessly");
RETURN(0);
}
EDIT_dset_items(Opt->cset, ADN_prefix, Opt->crefix, ADN_none);
if( !THD_ok_overwrite() && THD_is_file( DSET_HEADNAME(Opt->cset) ) ){
ERROR_exit("Output file %s already exists -- cannot continue!\n",
DSET_HEADNAME(Opt->cset) ) ;
}
}
/* group classes ? */
if (Opt->group_classes) {
THD_3dim_dataset *gcset=NULL;
THD_3dim_dataset *gpset=NULL;
if (!SUMA_Regroup_classes (Opt,
Opt->clss->str, Opt->clss->num, Opt->keys,
Opt->group_classes->str,
Opt->group_classes->num,
Opt->group_keys, Opt->cmask,
Opt->pset,
Opt->cset,
&gpset,
&gcset) ) {
ERROR_message("Failed to regroup");
RETURN(0);
}
DSET_write(gpset);
DSET_write(gcset);
}
RETURN(1);
}
int main( int argc , char * argv[] )
{
THD_3dim_dataset * dset ;
int iarg , all = 0, verbose = 0, cnt = 0;
if( argc < 2 || strncmp(argv[1],"-help",4) == 0 ) Syntax() ;
iarg = 1 ;
cnt = 1;
while (cnt < argc) {
if( strncmp(argv[iarg],"-all",4) == 0 ){ all = 1 ; iarg++ ; }
else if( strncmp(argv[iarg],"-verbose",5) == 0 ){ verbose = 1 ; iarg++ ; }
++cnt;
}
for( ; iarg < argc ; iarg++ ){
dset = THD_open_dataset( argv[iarg] ) ;
if( dset == NULL ){
printf("-1\n") ;
continue ;
}
if (!all) {
if (verbose) {
printf("%s: %d\n",
DSET_HEADNAME(dset),
DSET_NVALS(dset)) ;
} else {
printf("%d\n",DSET_NVALS(dset)) ;
}
} else {
if (verbose) {
printf("%s: %d %d %d %d\n",
DSET_HEADNAME(dset),
DSET_NX(dset), DSET_NY(dset), DSET_NZ(dset),
DSET_NVALS(dset)) ;
} else {
printf("%d %d %d %d\n",
DSET_NX(dset), DSET_NY(dset), DSET_NZ(dset),
DSET_NVALS(dset)) ;
}
}
THD_delete_3dim_dataset( dset , False ) ;
}
exit(0) ;
}
void RT_test_callback(void *junk)
{
RT_status *rts = GLOBAL_library.realtime_status ;
int cc , nval,nbr ;
if( rts == NULL ){ ERROR_message("bad call to RT_test_callback"); return; }
INFO_message("RT_test_callback: numchan=%d status=%d numdset=%d",
rts->numchan , rts->status , rts->numdset ) ;
for( cc=0 ; cc < rts->numdset ; cc++ ){ /* print out some dataset info */
if( !ISVALID_DSET(rts->dset[cc]) ){
ININFO_message(" dset[%d] invalid!",cc) ; /* should never happen */
} else {
nval = DSET_NVALS(rts->dset[cc]) ; /* number of bricks */
nbr = THD_count_databricks(rts->dset[cc]->dblk) ; /* number with data */
ININFO_message(" dset[%d] '%s': nvals=%d nbr=%d",
cc , DSET_HEADNAME(rts->dset[cc]) , nval,nbr ) ;
}
}
return ;
}
int main(int argc, char *argv[]) {
int i, k, ii;
int iarg;
char *prefix=NULL;
char *maskname=NULL;
char *gradsname=NULL;
char *dtsname=NULL;
THD_3dim_dataset *MASK=NULL;
THD_3dim_dataset *DTS=NULL;
MRI_IMAGE *GRADS=NULL, *GRADS_IN=NULL;
int Ngrads=0, Nfull=0;
int Nvox=-1; // tot number vox
int Dim[3]={0,0,0}; // dim in each dir
float NOISESCALE_DWI = -1.;
float NOISESCALE_B0 = -1;
float S0 = 1000.;
float bval = 1.;
int NOISE_IN_S0 = 0;
byte *mskd2=NULL; // not great, but another format of mask
float **dwi=NULL;
THD_3dim_dataset *DWI_OUT=NULL;
const gsl_rng_type * T;
gsl_rng *r;
long seed;
srand(time(0));
seed = time(NULL) ;
gsl_rng_env_setup();
T = gsl_rng_default;
r = gsl_rng_alloc (T);
gsl_rng_set (r, seed);
// ###################################################################
// ######################### load ##################################
// ###################################################################
mainENTRY("3dDTtoNoisyDWI"); machdep();
if (argc == 1) { usage_DTtoNoisyDWI(1); exit(0); }
iarg = 1;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-help") == 0 ||
strcmp(argv[iarg],"-h") == 0 ) {
usage_DTtoNoisyDWI(strlen(argv[iarg])>3 ? 2:1);
exit(0);
}
if( strcmp(argv[iarg],"-dt_in") == 0) {
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-eig_vecs'");
dtsname = strdup(argv[iarg]) ;
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],"-mask") == 0) {
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-mask'");
maskname = strdup(argv[iarg]) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-grads") == 0) {
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-mask'");
gradsname = strdup(argv[iarg]) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-noise_DWI") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need numerical argument after '-noise_DWI'");
NOISESCALE_DWI = atof(argv[iarg]);
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-noise_B0") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need numerical argument after '-noise_B0'");
NOISESCALE_B0 = atof(argv[iarg]);
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-S0") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need numerical argument after '-S0'");
S0 = atof(argv[iarg]);
if(S0 <= 0 )
ERROR_exit("The '-S0' value must be >0.");
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-bval") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need numerical argument after '-bval'");
bval = atof(argv[iarg]);
if(bval <= 0 )
ERROR_exit("The '-bval' value must be >0.");
iarg++ ; continue ;
}
ERROR_message("Bad option '%s'\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
// ###################################################################
// #################### some checks ###############################
// ###################################################################
if(!prefix)
ERROR_exit("Need to give a '-prefix'.");
if(!dtsname)
ERROR_exit("Need to input diffusion tensor file after '-dt_in'.");
if(!gradsname)
ERROR_exit("Need to input gradient file after '-grads'.");
if( NOISESCALE_DWI<0 )
ERROR_exit("Fractional noise value after '-snr0' needs to be >0. "
"It sets the noise scale of ref signal S0.");
if(NOISESCALE_DWI > 0)
INFO_message("You have chosen an SNR0 of approximately %.2f for DWIs",
1./NOISESCALE_DWI);
else
INFO_message("You have noiseless (i.e., infinite SNR) set of DWIs");
if( NOISESCALE_B0 < 0 )
NOISESCALE_B0 = NOISESCALE_DWI;
if(NOISESCALE_B0 > 0)
INFO_message("You have chosen an SNR0 of approximately %.2f for the B0",
1./NOISESCALE_B0);
else
INFO_message("You have noiseless (i.e., infinite SNR) reference B0.");
// ###################################################################
if(dtsname) {
DTS = THD_open_dataset(dtsname);
DSET_load(DTS); CHECK_LOAD_ERROR(DTS);
if( 6 != DSET_NVALS(DTS) )
ERROR_exit("DT file '%s' must have 6 bricks-- "
"it has %d bricks!",
dtsname, DSET_NVALS(DTS));
}
Nvox = DSET_NVOX(DTS);
Dim[0] = DSET_NX(DTS);
Dim[1] = DSET_NY(DTS);
Dim[2] = DSET_NZ(DTS);
if(Nvox<0)
ERROR_exit("Error reading Nvox from eigenvalue file.");
mskd2 = (byte *)calloc(Nvox,sizeof(byte));
if( (mskd2 == NULL)) {
fprintf(stderr, "\n\n MemAlloc failure (masks).\n\n");
exit(122);
}
if(maskname) {
MASK = THD_open_dataset(maskname);
DSET_load(MASK); CHECK_LOAD_ERROR(MASK);
if( 1 != DSET_NVALS(MASK) )
ERROR_exit("Mask file '%s' is not scalar-- "
"it has %d bricks!",
maskname, DSET_NVALS(MASK));
for( k=0 ; k<Nvox ; k++ )
if (THD_get_voxel(MASK, k, 0) > 0 )
mskd2[k] = 1;
DSET_delete(MASK);
free(MASK);
free(maskname);
}
else {
for( k=0 ; k<Nvox ; k++ )
if( fabs(THD_get_voxel(DTS,k,0) > EPS_V) )
mskd2[k] = 1;
}
GRADS_IN = mri_read_1D (gradsname);
GRADS = mri_transpose(GRADS_IN); // get rid of autotranspose...
if (GRADS == NULL)
ERROR_exit("Error reading gradient vector file");
mri_free(GRADS_IN);
Ngrads = GRADS->ny;
if(Ngrads < 6)
ERROR_exit("Too few grads (there appear to be only %d).",Ngrads);
if(GRADS->nx !=3 )
ERROR_exit("Wrong number of columns in the grad file: "
" am reading %d instead of 3.",GRADS->nx);
Nfull = Ngrads+1;
INFO_message("Have surmised there are %d total grads; "
"output file will have %d bricks", Ngrads,Nfull);
dwi = calloc(Nfull,sizeof(dwi));
for(i=0 ; i<Nfull ; i++)
dwi[i] = calloc( Nvox,sizeof(float));
INFO_message("Calculating the DWIs.");
i = RicianNoiseDWIs( dwi, Nvox, Ngrads, DTS,
NOISESCALE_DWI, NOISESCALE_B0,
GRADS, mskd2,
S0, bval, r);
INFO_message("Writing the DWIs.");
DWI_OUT = EDIT_empty_copy( DTS );
EDIT_dset_items(DWI_OUT,
ADN_nvals, Nfull,
ADN_datum_all, MRI_float ,
ADN_prefix, prefix,
ADN_none );
for( i=0; i<Nfull ; i++) {
EDIT_substitute_brick(DWI_OUT, i, MRI_float, dwi[i]);
dwi[i]=NULL;
}
THD_load_statistics( DWI_OUT );
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(DWI_OUT)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(DWI_OUT));
tross_Make_History("3dDTtoNoisyDWI", argc, argv, DWI_OUT);
THD_write_3dim_dataset(NULL, NULL, DWI_OUT, True);
DSET_delete(DWI_OUT);
free(DWI_OUT);
// #################################################################
// ########################## free ###############################
// #################################################################
DSET_delete(DTS);
free(DTS);
for( i=0 ; i<Nfull ; i++)
free(dwi[i]);
free(dwi);
free(prefix);
free(gradsname);
free(dtsname);
mri_free(GRADS);
return 0;
}
int main( int argc , char * argv[] )
{
THD_3dim_dataset *mask_dset=NULL, *iset=NULL,
*sset=NULL, *xset=NULL, *vset=NULL;
char *prefix="toy";
int iarg=1 , mcount, udatum = MRI_float;
byte *maskvox=NULL;
mainENTRY("3dToyProg main"); machdep(); AFNI_logger("3dToyProg",argc,argv);
#ifdef USING_MCW_MALLOC
enable_mcw_malloc() ;
#endif
/*-- options --*/
set_obliquity_report(0); /* silence obliquity */
while( iarg < argc && argv[iarg][0] == '-' ){
CHECK_HELP(argv[iarg], help_3dToyProg);
if( strncmp(argv[iarg],"-mask",5) == 0 ){
if (iarg >= argc) ERROR_exit("Need dset after -mask");
mask_dset = THD_open_dataset( argv[++iarg] ) ;
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");
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-input") == 0) {
if (iarg >= argc) ERROR_exit("Need dset after -mask");
if (!(iset = THD_open_dataset( argv[++iarg]))) {
ERROR_exit("Cannot open input dataset %s!\n", argv[iarg]) ;
}
DSET_mallocize(iset); DSET_load(iset); /* load data part of dataset */
iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-prefix",6) == 0) {
if (iarg >= argc) ERROR_exit("Need name after -prefix");
prefix = argv[++iarg];
iarg++ ; continue ;
continue ;
}
if( strcmp(argv[iarg],"-datum") == 0) {
if (iarg >= argc) ERROR_exit("Need datum type after -datum");
++iarg;
if (!strcmp(argv[iarg],"float")) udatum = MRI_float;
else if (!strcmp(argv[iarg],"short")) udatum = MRI_short;
else {
ERROR_exit(
"For the purpose of this demo, only float and short are allowed");
}
iarg++ ; continue ;
continue ;
}
ERROR_message("ILLEGAL option: %s\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
if( argc < 2 ){
help_3dToyProg(TXT, 0);
PRINT_COMPILE_DATE ; exit(0) ;
}
if( !iset )
ERROR_exit("No dataset on command line!?") ;
if (mask_dset) {
if (THD_dataset_mismatch(mask_dset, iset))
ERROR_exit("grid mismatch between input dset and mask dset");
maskvox = THD_makemask( mask_dset , 0 , 1.0, -1.0 ) ;
mcount = THD_countmask( DSET_NVOX(mask_dset) , maskvox ) ;
if( mcount <= 0 ) ERROR_exit("No voxels in the mask!\n") ;
INFO_message("%d voxels in the mask dset %s\n",
mcount, DSET_PREFIX(mask_dset)) ;
DSET_delete(mask_dset) ; mask_dset=NULL; /* Done with the mask dset */
}
/* An illustration of how volume navigation works */
Dataset_Navigation(iset);
/* Let us create a dataset from scratch */
sset = New_Dataset_From_Scratch(prefix);
/* Now for the output, add history, check for overwrite and write away */
tross_Copy_History( iset , sset );/* Copy the old history (not mandatory). */
tross_Make_History("3dToyProg", argc, argv ,sset) ; /* add the new */
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(sset)) ) {
ERROR_message(
"Output %s already exists, use -overwrite to do you know what",
DSET_HEADNAME(sset));
} else DSET_write(sset);
/* Now we'll do some voxelwise computations */
xset = Voxelwise_Operations(sset, maskvox, prefix);
tross_Copy_History( iset , xset ) ; /* Copy the old */
tross_Make_History("3dToyProg", argc, argv ,xset) ; /* add the new */
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(xset)) ) {
ERROR_message(
"Output %s already exists, use -overwrite to do you know what",
DSET_HEADNAME(xset));
} else DSET_write(xset);
/* Or some volumewise operations */
vset = Volumewise_Operations(sset, prefix, udatum);
tross_Copy_History( iset , vset ) ; /* Copy the old */
tross_Make_History("3dToyProg", argc, argv ,vset) ; /* add the new */
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(vset)) ) {
ERROR_message(
"Output %s already exists, use -overwrite to do you know what",
DSET_HEADNAME(vset));
} else DSET_write(vset);
/* cleanup */
DSET_delete(xset); xset = NULL;
DSET_delete(vset); vset = NULL;
DSET_delete(sset); sset = NULL;
exit(0) ;
}
int main( int argc , char * argv[] )
{
int narg=1, do_automask=0 , iv , nxyz , do_set=0 ,
*rois=NULL, N_rois=0, all_rois = 0;
THD_3dim_dataset *xset ;
byte *mmm=NULL ; int nmask=0 , nvox_mask=0 ;
THD_fvec3 cmv , setv ;
/*-- read command line arguments --*/
if( argc < 2 || strncmp(argv[1],"-help",5) == 0 ){
printf("Usage: 3dCM [options] dset\n"
"Output = center of mass of dataset, to stdout.\n"
" -mask mset Means to use the dataset 'mset' as a mask:\n"
" Only voxels with nonzero values in 'mset'\n"
" will be averaged from 'dataset'. Note\n"
" that the mask dataset and the input dataset\n"
" must have the same number of voxels.\n"
" -automask Generate the mask automatically.\n"
" -set x y z After computing the CM of the dataset, set the\n"
" origin fields in the header so that the CM\n"
" will be at (x,y,z) in DICOM coords.\n"
" -roi_vals v0 v1 v2 ... : Compute center of mass for each blob\n"
" with voxel value of v0, v1, v2, etc.\n"
" This option is handy for getting ROI \n"
" centers of mass.\n"
" -all_rois Don't bother listing the values of ROIs you want\n"
" the program will find all of them and produce a \n"
" full list.\n"
" NOTE: Masking options are ignored with -roi_vals and -all_rois\n"
) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
LOAD_FVEC3(setv,0,0,0) ; /* ZSS: To quiet init. warnings */
narg = 1 ;
while( narg < argc && argv[narg][0] == '-' ){
if( strcmp(argv[narg],"-set") == 0 ){
float xset,yset,zset ;
if( narg+3 >= argc ){
fprintf(stderr,"*** -set need 3 args following!\n") ; exit(1) ;
}
xset = strtod( argv[++narg] , NULL ) ;
yset = strtod( argv[++narg] , NULL ) ;
zset = strtod( argv[++narg] , NULL ) ;
LOAD_FVEC3(setv,xset,yset,zset) ; do_set = 1 ;
THD_set_write_compression(COMPRESS_NONE); /* do not alter compression*/
narg++ ; continue ;
}
if( strncmp(argv[narg],"-mask",5) == 0 ){
THD_3dim_dataset *mask_dset ;
if( mmm != NULL ){
fprintf(stderr,"*** Cannot have two -mask options!\n") ; exit(1) ;
}
if( do_automask ){
fprintf(stderr,"*** Can't have -mask and -automask!\n") ; exit(1) ;
}
if( narg+1 >= argc ){
fprintf(stderr,"*** -mask option requires a following argument!\n");
exit(1) ;
}
mask_dset = THD_open_dataset( argv[++narg] ) ;
CHECK_OPEN_ERROR(mask_dset,argv[narg]) ;
if( DSET_BRICK_TYPE(mask_dset,0) == MRI_complex ){
fprintf(stderr,"*** Cannot deal with complex-valued mask dataset!\n");
exit(1) ;
}
mmm = THD_makemask( mask_dset , 0 , 1.0,0.0 ) ;
nvox_mask = DSET_NVOX(mask_dset) ;
nmask = THD_countmask( nvox_mask , mmm ) ;
if( mmm == NULL || nmask <= 0 ){
fprintf(stderr,"*** Can't make mask from dataset %s\n",argv[narg-1]);
exit(1) ;
}
DSET_delete( mask_dset ) ;
narg++ ; continue ;
}
if( strncmp(argv[narg],"-roi_vals",5) == 0 ){
if( narg+1 >= argc ){
fprintf(stderr,"*** -mask option requires a following argument(s)!\n");
exit(1) ;
}
rois = (int *)calloc(argc, sizeof(int));
N_rois = 0;
++narg;
while (narg < argc-1 && argv[narg][0] != '-') {
rois[N_rois++] = atoi(argv[narg]);
++narg;
}
continue ;
}
if( strncmp(argv[narg],"-all_rois",5) == 0 ){
all_rois = 1;
narg++ ; continue ;
}
if( strcmp(argv[narg],"-automask") == 0 ){
if( mmm != NULL ){
fprintf(stderr,"*** Can't have -mask and -automask!\n") ; exit(1) ;
}
do_automask = 1 ; narg++ ; continue ;
}
fprintf(stderr,"*** Unknown option: %s\n",argv[narg]) ; exit(1) ;
}
/* should have at least 1 more argument */
if( argc <= narg ){
fprintf(stderr,"*** No input dataset!?\n") ; exit(1) ;
}
for( ; narg < argc ; narg++ ){
xset = THD_open_dataset( argv[narg] ) ;
if( xset == NULL ){
fprintf(stderr,"+++ Can't open dataset %s -- skipping\n",argv[narg]);
continue ;
}
DSET_load(xset) ;
if( !DSET_LOADED(xset) ){
fprintf(stderr,"+++ Can't load dataset %s -- skipping\n",argv[narg]);
DSET_delete(xset) ; continue ;
}
if( do_automask ){
if( mmm != NULL ){ free(mmm); mmm = NULL; }
mmm = THD_automask(xset) ;
nvox_mask = DSET_NVOX(xset) ;
nmask = THD_countmask( nvox_mask , mmm ) ;
if( mmm == NULL || nmask <= 0 ){
fprintf( stderr,
"+++ Can't make automask from dataset %s "
"-- skipping\n",argv[narg]) ;
DSET_delete(xset) ; continue ;
}
}
nxyz = DSET_NVOX(xset) ;
if( mmm != NULL && nxyz != nvox_mask ){
fprintf(stderr,"+++ Mask/Dataset grid size mismatch at %s\n -- skipping\n",argv[narg]) ;
DSET_delete(xset) ; continue ;
}
if (all_rois) {
if (!(rois = THD_unique_vals(xset, 0, &N_rois, NULL)) || N_rois == 0) {
ERROR_message("No rois or error in THD_unique_vals"); continue;
}
fprintf(stderr,"#%d distinct ROIs", N_rois);
}
if (!N_rois) {
cmv = THD_cmass( xset , 0 , mmm ) ;
printf("%g %g %g\n",cmv.xyz[0],cmv.xyz[1],cmv.xyz[2]) ;
DSET_unload(xset) ;
if( do_set ){
THD_fvec3 dv , ov ;
if( DSET_IS_MASTERED(xset) ){
fprintf(stderr,"+++ Can't modify CM of dataset %s\n",argv[narg]) ;
} else {
/* lose obliquity */
/* recompute Tc(Cardinal transformation matrix for new grid output */
THD_make_cardinal(xset);
LOAD_FVEC3(ov,DSET_XORG(xset),DSET_YORG(xset),DSET_ZORG(xset)) ;
ov = THD_3dmm_to_dicomm( xset , ov ) ;
dv = SUB_FVEC3(setv,cmv) ;
ov = ADD_FVEC3(dv,ov) ;
ov = THD_dicomm_to_3dmm( xset , ov ) ;
xset->daxes->xxorg = ov.xyz[0] ;
xset->daxes->yyorg = ov.xyz[1] ;
xset->daxes->zzorg = ov.xyz[2] ;
/* allow overwriting header for all types of output data */
putenv("AFNI_DECONFLICT=OVERWRITE") ;
tross_Make_History( "3dCM" , argc,argv , xset );/* ZSS Dec. 09 08 */
if(DSET_IS_BRIK(xset)) {
INFO_message("Rewriting header %s",DSET_HEADNAME(xset)) ;
DSET_overwrite_header( xset ) ;
}
else { /* for other dataset types like NIFTI, rewrite whole dset */
DSET_load( xset ) ;
DSET_overwrite(xset) ;
INFO_message("Wrote new dataset: %s",DSET_BRIKNAME(xset)) ;
}
}
}
} else {
float *xyz;
if ((xyz = THD_roi_cmass(xset , 0 , rois, N_rois))) {
printf("#Dset %s\n",DSET_BRIKNAME(xset));
for (iv=0; iv<N_rois; ++iv) {
printf("#ROI %d\n", rois[iv]);
printf("%g %g %g\n",xyz[3*iv],xyz[3*iv+1],xyz[3*iv+2]) ;
}
free(xyz); free(rois);
} else {
ERROR_message("Failed in THD_roi_cmass"); continue;
}
}
DSET_delete(xset) ;
}
exit(0);
}
int WB_netw_corr(int Do_r,
int Do_Z,
int HAVE_ROIS,
char *prefix,
int NIFTI_OUT,
int *NROI_REF,
int *Dim,
double ***ROI_AVE_TS,
int **ROI_LABELS_REF,
THD_3dim_dataset *insetTIME,
byte *mskd2,
int Nmask,
int argc,
char *argv[])
{
int i,j,k;
float **AVE_TS_fl=NULL; // not great, but another format of TS
char OUT_indiv0[300];
char OUT_indiv[300];
char OUT_indivZ[300];
MRI_IMAGE *mri=NULL;
THD_3dim_dataset *OUT_CORR_MAP=NULL;
THD_3dim_dataset *OUT_Z_MAP=NULL;
float *zscores=NULL;
int Nvox;
Nvox = Dim[0]*Dim[1]*Dim[2];
// make average time series per voxel
AVE_TS_fl = calloc( 1,sizeof(AVE_TS_fl));
for(i=0 ; i<1 ; i++)
AVE_TS_fl[i] = calloc(Dim[3],sizeof(float));
if( (AVE_TS_fl == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure (time series out).\n\n");
exit(123);
}
fprintf(stderr,"\nHAVE_ROIS=%d",HAVE_ROIS);
for( k=0 ; k<HAVE_ROIS ; k++) { // each netw gets own file
sprintf(OUT_indiv0,"%s_%03d_INDIV", prefix, k);
mkdir(OUT_indiv0, 0777);
for( i=0 ; i<NROI_REF[k] ; i++ ) {
fprintf(stderr,"\nNROI_REF[%d]= %d",k,NROI_REF[k]);
for( j=0 ; j<Dim[3] ; j++)
AVE_TS_fl[0][j] = (float) ROI_AVE_TS[k][i][j];
if( NIFTI_OUT )
sprintf(OUT_indiv,"%s/WB_CORR_ROI_%03d.nii.gz",
OUT_indiv0,ROI_LABELS_REF[k][i+1]);
else
sprintf(OUT_indiv,"%s/WB_CORR_ROI_%03d",
OUT_indiv0,ROI_LABELS_REF[k][i+1]);
mri = mri_float_arrays_to_image(AVE_TS_fl,Dim[3],1);
OUT_CORR_MAP = THD_Tcorr1D(insetTIME, mskd2, Nmask,
mri,
"pearson", OUT_indiv);
if(Do_r){
THD_load_statistics(OUT_CORR_MAP);
tross_Copy_History( insetTIME , OUT_CORR_MAP ) ;
tross_Make_History( "3dNetcorr", argc, argv, OUT_CORR_MAP );
if( !THD_ok_overwrite() &&
THD_is_ondisk(DSET_HEADNAME(OUT_CORR_MAP)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(OUT_CORR_MAP));
THD_write_3dim_dataset(NULL, NULL, OUT_CORR_MAP, True);
INFO_message("Wrote dataset: %s\n",DSET_BRIKNAME(OUT_CORR_MAP));
}
if(Do_Z){
if( NIFTI_OUT )
sprintf(OUT_indivZ,"%s/WB_Z_ROI_%03d.nii.gz",
OUT_indiv0,ROI_LABELS_REF[k][i+1]);
else
sprintf(OUT_indivZ,"%s/WB_Z_ROI_%03d",
OUT_indiv0,ROI_LABELS_REF[k][i+1]);
OUT_Z_MAP = EDIT_empty_copy(OUT_CORR_MAP);
EDIT_dset_items( OUT_Z_MAP,
ADN_nvals, 1,
ADN_datum_all , MRI_float ,
ADN_prefix , OUT_indivZ,
ADN_none ) ;
if( !THD_ok_overwrite() &&
THD_is_ondisk(DSET_HEADNAME(OUT_Z_MAP)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(OUT_Z_MAP));
zscores = (float *)calloc(Nvox,sizeof(float));
if( (zscores == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure (zscores).\n\n");
exit(123);
}
for( j=0 ; j<Nvox ; j++ )
if( mskd2[j] ) // control for r ==1
BOBatanhf( THD_get_voxel(OUT_CORR_MAP, j, 0) );
/*
if( THD_get_voxel(OUT_CORR_MAP, j, 0) > MAX_R )
zscores[j] = (float) atanh(MAX_R);
else if ( THD_get_voxel(OUT_CORR_MAP, j, 0) < -MAX_R )
zscores[j] = (float) atanh(-MAX_R);
else
zscores[j] = (float) atanh(THD_get_voxel(OUT_CORR_MAP, j, 0));*/
EDIT_substitute_brick(OUT_Z_MAP, 0, MRI_float, zscores);
zscores=NULL;
THD_load_statistics(OUT_Z_MAP);
tross_Copy_History(insetTIME, OUT_Z_MAP);
tross_Make_History("3dNetcorr", argc, argv, OUT_Z_MAP);
THD_write_3dim_dataset(NULL, NULL, OUT_Z_MAP, True);
INFO_message("Wrote dataset: %s\n",DSET_BRIKNAME(OUT_Z_MAP));
DSET_delete(OUT_Z_MAP);
free(OUT_Z_MAP);
OUT_Z_MAP=NULL;
}
DSET_delete(OUT_CORR_MAP);
free(OUT_CORR_MAP);
OUT_CORR_MAP=NULL;
}
}
free(zscores);
mri_free(mri);
for( i=0 ; i<1 ; i++)
free(AVE_TS_fl[i]);
free(AVE_TS_fl);
RETURN(1);
}
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[])
{
int CHECK = 0;
int iarg;
char *Fname_input = NULL;
char *Fname_output = NULL;
char *Fname_outputBV = NULL;
char *Fname_bval = NULL;
int opt;
FILE *fin=NULL, *fout=NULL, *finbv=NULL, *foutBV=NULL;
int i,j,k;
int BZER=0,idx=0,idx2=0;
MRI_IMAGE *flim=NULL;
MRI_IMAGE *preREADIN=NULL;
MRI_IMAGE *preREADBVAL=NULL;
float *READIN=NULL;
float *READBVAL=NULL;
float OUT_MATR[MAXGRADS][7]; // b- or g-matrix
float OUT_GRAD[MAXGRADS][4]; // b- or g-matrix
int INV[3] = {1,1,1}; // if needing to switch
int FLAG[MAXGRADS];
float temp;
int YES_B = 0;
int EXTRA_ZEROS=0;
int HAVE_BVAL = 0;
int BVAL_OUT = 0;
int BVAL_OUT_SEP = 0;
float BMAX_REF = 1; // i.e., essentially zero
int IN_FORM = 0; // 0 for row, 1 for col
int OUT_FORM = 1; // 1 for col, 2 for bmatr
int HAVE_BMAX_REF=0 ; // referring to user input value
int count_in=0, count_out=0;
THD_3dim_dataset *dwset=NULL, *dwout=NULL;
int Nbrik = 0;
char *prefix=NULL ;
float **temp_arr=NULL, **temp_grad=NULL;
int Ndwi = 0, dwi=0, Ndwout = 0, Ndwi_final = 0, Ndwout_final = 0;
int Nvox = 0;
int DWI_COMP_FAC = 0;
int ct_dwi = 0;
float MaxDP = 0;
mainENTRY("1dDW_Grad_o_Mat"); machdep();
if (argc == 1) { usage_1dDW_Grad_o_Mat(1); exit(0); }
iarg = 1;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-help") == 0 ||
strcmp(argv[iarg],"-h") == 0 ) {
usage_1dDW_Grad_o_Mat(strlen(argv[iarg])>3 ? 2:1);
exit(0);
}
if( strcmp(argv[iarg],"-flip_x") == 0) {
INV[0] = -1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-flip_y") == 0) {
INV[1] = -1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-flip_z") == 0) {
INV[2] = -1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-keep_b0s") == 0) {
YES_B = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-put_zeros_top") == 0) {
EXTRA_ZEROS = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_grad_rows") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_grad_rows'\n") ;
Fname_input = argv[iarg];
count_in++;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_grad_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_grad_cols'\n") ;
Fname_input = argv[iarg];
count_in++;
IN_FORM = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_gmatT_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_matT_cols'\n") ;
Fname_input = argv[iarg];
count_in++;
IN_FORM = 2;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_gmatA_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_matA_cols'\n") ;
Fname_input = argv[iarg];
count_in++;
IN_FORM = 3;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_bmatT_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_matT_cols'\n") ;
Fname_input = argv[iarg];
count_in++;
IN_FORM = 4;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_bmatA_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_matA_cols'\n") ;
Fname_input = argv[iarg];
count_in++;
IN_FORM = 5;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_grad_rows") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_grad_cols'\n") ;
Fname_output = argv[iarg];
count_out++;
OUT_FORM = 0;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_grad_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_grad_cols'\n") ;
Fname_output = argv[iarg];
count_out++;
OUT_FORM = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_gmatT_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_gmatT_cols'\n") ;
Fname_output = argv[iarg];
count_out++;
OUT_FORM = 2;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_gmatA_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_gmatA_cols'\n") ;
Fname_output = argv[iarg];
count_out++;
OUT_FORM = 3;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_bmatT_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_bmatT_cols'\n") ;
Fname_output = argv[iarg];
count_out++;
OUT_FORM = 4;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_bmatA_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_bmatA_cols'\n") ;
Fname_output = argv[iarg];
count_out++;
OUT_FORM = 5;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_bvals") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_bvals'\n") ;
Fname_bval = argv[iarg];
HAVE_BVAL = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-bmax_ref") == 0) {
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-bmax_ref'\n");
BMAX_REF = atof(argv[iarg]);
HAVE_BMAX_REF = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_bval_col") == 0) {
BVAL_OUT = 1;
iarg++ ; continue ;
}
// May,2015
if( strcmp(argv[iarg],"-out_bval_row_sep") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_bval_row_sep'\n") ;
Fname_outputBV = argv[iarg];
BVAL_OUT_SEP = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-proc_dset") == 0 ){ // in DWIs
if( ++iarg >= argc )
ERROR_exit("Need argument after '-proc_dset'") ;
dwset = THD_open_dataset( argv[iarg] ) ;
if( dwset == NULL )
ERROR_exit("Can't open DWI dataset '%s'", argv[iarg]) ;
DSET_load(dwset) ; CHECK_LOAD_ERROR(dwset) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-pref_dset") == 0 ){ // will be output
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-pref_dset'");
prefix = strdup(argv[iarg]) ;
if( !THD_filename_ok(prefix) )
ERROR_exit("Illegal name after '-pref_dset'");
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-dwi_comp_fac") == 0) {
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-dwi_comp_fac'\n");
DWI_COMP_FAC = atoi(argv[iarg]);
if (DWI_COMP_FAC <=1)
ERROR_exit("The compression factor after '-dwi_comp_fac'"
"must be >1!");
iarg++ ; continue ;
}
ERROR_message("Bad option '%s'\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * *
if( (Fname_input == NULL) ) {
fprintf(stderr,
"\n\tBad Command-lining! Option '-in_*' requires argument.\n");
exit(1);
}
if( (Fname_output == NULL) ) {
fprintf(stderr,
"\n\tBad Command-lining! Option '-out_*' requires arg.\n");
exit(2);
}
if( count_in > 1 ) {
fprintf(stderr,
"\n\tBad Command-lining! Can't have >1 vec file input.\n");
exit(3);
}
if( count_out > 1 ) {
fprintf(stderr,
"\n\tBad Command-lining! Can't have >1 output file opt.\n");
exit(4);
}
if(YES_B && dwset) {
fprintf(stderr,
"\n** Bad Command-lining! "
"Can't have '-keep_b0s' and '-proc_dset' together.\n");
exit(5);
}
if( !prefix && dwset) {
fprintf(stderr,
"\n** Bad Command-lining! "
"Need an output '-pref_dset' when using '-proc_dset'.\n");
exit(6);
}
if(YES_B && DWI_COMP_FAC) {
fprintf(stderr,
"\n** Bad Command-lining! "
"Can't have '-keep_b0s' and '-dwi_comp_fac' together.\n");
exit(7);
}
if(!HAVE_BVAL && (BVAL_OUT || BVAL_OUT_SEP)) {
fprintf(stderr,
"\n** Bad Command-lining! "
"Can't have ask for outputting bvals with no '-in_bvals FILE'.\n");
exit(8);
}
// ********************************************************************
// ************************* start reading ****************************
// ********************************************************************
flim = mri_read_1D (Fname_input);
if (flim == NULL) {
ERROR_exit("Error reading gradient vector file");
}
if( IN_FORM )
preREADIN = mri_transpose(flim); // effectively *undoes* autotranspose
else
preREADIN = mri_copy(flim);
mri_free(flim);
idx = preREADIN->ny;
if( HAVE_BVAL ) {
flim = mri_read_1D (Fname_bval);
if (flim == NULL) {
ERROR_exit("Error reading b-value file");
}
if( flim->ny == 1)
preREADBVAL = mri_transpose(flim); // effectively *undoes* autotransp
else
preREADBVAL = mri_copy(flim);
mri_free(flim);
idx2 = preREADBVAL->ny;
}
if(idx>= MAXGRADS ) {
printf("Error, too many input grads.\n");
mri_free (preREADIN);
if( HAVE_BVAL ) mri_free (preREADBVAL);
exit(4);
}
if( ( (preREADIN->nx != 3 ) && (preREADIN->ny != 3 )) &&
(preREADIN->nx != 6 ) )
printf("Probably an error, "
"because there aren't 3 or 6 numbers in columns!\n");
if( HAVE_BVAL && ( idx != idx2 ) ) {
printf("Error, because the number of bvecs (%d)\n"
"and bvals (%d) don't appear to match!\n", idx, idx2);
mri_free (preREADIN);
mri_free (preREADBVAL);
exit(3);
}
if(dwset) {
Nbrik = DSET_NVALS(dwset);
if( idx != Nbrik ) {
fprintf(stderr,
"\n** ERROR: the number of bvecs (%d) does not match the "
"number of briks in '-proc_dset' (%d).\n", idx, Nbrik);
exit(4);
}
}
READIN = MRI_FLOAT_PTR( preREADIN );
if( HAVE_BVAL )
READBVAL = MRI_FLOAT_PTR( preREADBVAL );
// 0 is grad row;
// 1 is grad col;
// 2 is gmatrRow col T;
// 3 is gmatrDiag col A;
// 4 is bmatrRow col T;
// 5 is bmatrDiag col A;
//if( IN_FORM == 0 ) // grad rows, no binfo
// for( i=0; i<idx ; i++ )
// for ( j=0; j<3 ; j++ )
// OUT_GRAD[i][j+1] = *(READIN +j*idx +i) ;
//else
if ( IN_FORM <= 1 ) // grad cols, no binfo
for( i=0; i<idx ; i++ )
for ( j=0; j<3 ; j++ )
OUT_GRAD[i][j+1] = *(READIN + 3*i+j);
// A/row/3dDWItoDT: Bxx, Byy, Bzz, Bxy, Bxz, Byz
// T/diag/TORTOISE: b_xx 2b_xy 2b_xz b_yy 2b_yz b_zz
else if ( (IN_FORM == 3) || (IN_FORM ==5 ) ) { // diag matr
for( i=0; i<idx ; i++ ) {
for( j=0; j<3 ; j++ ) {
OUT_MATR[i][j+1] = *(READIN+6*i+j);
OUT_MATR[i][3+j+1] = *(READIN+6*i+3+j);
}
for( j=0; j<3 ; j++ )
if(OUT_MATR[i][j] < 0 )
CHECK++;
}
if(CHECK > 0)
INFO_message("Warning: you *said* you input a mat'T',"
" but the matr diagonals don't appear to be uniformly"
" positive. If input cols 0, 3 and 5 are positive,"
" then you might have meant mat'A'?");
}
else if ( (IN_FORM ==2 ) || (IN_FORM ==4 ) ) { // row matr
CHECK = 0;
for( i=0; i<idx ; i++ ) {
OUT_MATR[i][1] = *(READIN +6*i);
OUT_MATR[i][2] = *(READIN +6*i+3);
OUT_MATR[i][3] = *(READIN +6*i+5);
OUT_MATR[i][4] = *(READIN +6*i+1)/2.;
OUT_MATR[i][5] = *(READIN +6*i+2)/2.;
OUT_MATR[i][6] = *(READIN +6*i+4)/2.;
}
for( i=0; i<idx ; i++ )
for( j=0; j<3 ; j++ )
if(OUT_MATR[i][j] < 0 )
CHECK++;
if(CHECK > 0)
INFO_message("Warning: you *said* you input a mat'A',"
" but the matr diagonals don't appear to be uniformly"
" positive. If input cols 0, 1 and 2 are positive,"
" then you might have meant mat'T'?");
}
else{
fprintf(stderr, "Coding error with format number (%d), not allowed.\n",
IN_FORM);
exit(2);
}
// get bval info
if( ( (IN_FORM ==4 ) || (IN_FORM ==5 ) ) ) { //bval
for( i=0; i<idx ; i++ ) {
OUT_MATR[i][0] = OUT_GRAD[i][0] =
OUT_MATR[i][1] + OUT_MATR[i][2] + OUT_MATR[i][3];
if( OUT_MATR[i][0] > 0.000001)
for( j=1 ; j<7 ; j++ )
OUT_MATR[i][j]/= OUT_MATR[i][0];
}
}
else if ( HAVE_BVAL )
for( i=0; i<idx ; i++ ) {
OUT_MATR[i][0] = OUT_GRAD[i][0] = *(READBVAL + i);
}
else if ( OUT_FORM > 3 || BVAL_OUT || BVAL_OUT_SEP || HAVE_BMAX_REF ) {
fprintf(stderr, "ERROR: you asked for b-value dependent output, "
"but gave me no bvals to work with.\n");
exit(2);
}
// * * * ** * * * * * * * * ** ** * * ** * * ** * ** * ** * * *
// at this point, all IN_FORM >1 cases which need bval have led to:
// + grad[0] has bval
// + matr[0] has bval
// + matr file normalized and in diagonal form
// * * * ** * * * * * * * * ** ** * * ** * * ** * ** * ** * * *
for( i=0; i<idx ; i++ )
if( IN_FORM > 1)
j = GradConv_Gsign_from_BmatA( OUT_GRAD[i]+1, OUT_MATR[i]+1);
else
j = GradConv_BmatA_from_Gsign( OUT_MATR[i]+1, OUT_GRAD[i]+1);
// flip if necessary
for( i=0 ; i<idx ; i++) {
for( j=0 ; j<3 ; j++)
OUT_GRAD[i][j+1]*= INV[j];
OUT_MATR[i][4]*= INV[0]*INV[1];
OUT_MATR[i][5]*= INV[0]*INV[2];
OUT_MATR[i][6]*= INV[1]*INV[2];
}
BZER=0;
for( i=0 ; i<idx ; i++) {
if( HAVE_BVAL || (IN_FORM ==4) || (IN_FORM ==5) )
if( OUT_GRAD[i][0] >= BMAX_REF )
FLAG[i] = 1;
else{
if( YES_B )
FLAG[i] = 1;
BZER++;
}
else {
temp = 0.;
for( j=1 ; j<4 ; j++)
temp+= pow(OUT_GRAD[i][j],2);
if( temp > 0.1 )
FLAG[i] = 1;
else{
if( YES_B )
FLAG[i] = 1;
BZER++;
}
}
}
if(YES_B) {
printf("\tChose to *keep* %d b0s,\tas well as \t%d grads\n",
BZER,idx-BZER);
BZER=0;
}
else {
printf("\tGetting rid of %d b0s,\tleaving the %d grads\n",
BZER,idx-BZER);
Ndwi = idx-BZER;
}
Ndwi_final = idx-BZER; // default: all DWIs
if( DWI_COMP_FAC ) {
if( Ndwi % DWI_COMP_FAC != 0 ) {
fprintf(stderr, "\n** ERROR can't compress: "
"Ndwi=%d, and %d/%d has a nonzero remainder (=%d).\n",
Ndwi,Ndwi,DWI_COMP_FAC, Ndwi % DWI_COMP_FAC );
exit(1);
}
else {
Ndwi_final = Ndwi/DWI_COMP_FAC;
INFO_message("You have chosen a compression factor of %d, "
"with %d DWIs,\n"
"\tso that afterward there will be %d DWIs.",
DWI_COMP_FAC, Ndwi, Ndwi_final);
}
}
if(BVAL_OUT_SEP)
if( (foutBV = fopen(Fname_outputBV, "w")) == NULL) {
fprintf(stderr, "\n\nError opening file %s.\n",Fname_outputBV);
exit(1);
}
if( (fout = fopen(Fname_output, "w")) == NULL) {
fprintf(stderr, "\n\nError opening file %s.\n",Fname_output);
exit(1);
}
// 0 is grad row;
// 1 is grad col;
// 2 is gmatrRow col T;
// 3 is gmatrDiag col A;
// 4 is bmatrRow col T;
// 5 is bmatrDiag col A;
if( OUT_FORM>0) {
if( EXTRA_ZEROS ) {
if( BVAL_OUT )
fprintf(fout,"%8d ", 0);
if( BVAL_OUT_SEP )
fprintf(foutBV,"%8d ", 0);
if( OUT_FORM == 1 )
for( k=1 ; k<4 ; k++ )
fprintf(fout,"%11.5f ", 0.0);
else if ( OUT_FORM > 1 ) // bit superfluous at this point
for( k=1 ; k<7 ; k++ )
fprintf(fout,"%11.5f ", 0.0);
fprintf(fout,"\n");
}
ct_dwi = 0;
for(i=0 ; i<idx ; i++){
if(FLAG[i]) {
if( BVAL_OUT )
fprintf(fout,"%8d ", (int) OUT_GRAD[i][0]);
if( BVAL_OUT_SEP )
fprintf(foutBV,"%8d ", (int) OUT_GRAD[i][0]);
if( (OUT_FORM == 4) || (OUT_FORM ==5) )
for( k=1 ; k<7 ; k++ )
OUT_MATR[i][k]*= OUT_MATR[i][0];
if( OUT_FORM == 1 ) // grad col
for( k=1 ; k<4 ; k++ )
fprintf(fout,"%11.5f ", OUT_GRAD[i][k]);
else if( (OUT_FORM == 3) || (OUT_FORM == 5) ) { // gmat
for( k=1 ; k<6 ; k++ )
fprintf(fout,"%11.5f ", OUT_MATR[i][k]);
fprintf(fout,"%11.5f", OUT_MATR[i][k]);
}
else if ( (OUT_FORM == 2 ) || (OUT_FORM ==4)) { // bmat
fprintf(fout,"%11.5f ", OUT_MATR[i][1]);
fprintf(fout,"%11.5f ", 2*OUT_MATR[i][4]);
fprintf(fout,"%11.5f ", 2*OUT_MATR[i][5]);
fprintf(fout,"%11.5f ", OUT_MATR[i][2]);
fprintf(fout,"%11.5f ", 2*OUT_MATR[i][6]);
fprintf(fout,"%11.5f", OUT_MATR[i][3]);
}
fprintf(fout,"\n");
ct_dwi++;
}
if( (ct_dwi == Ndwi_final) && DWI_COMP_FAC ) {
INFO_message("Reached compression level: DWI number %d",
Ndwi_final);
break;
}
}
}
else if(OUT_FORM ==0) {
if(BVAL_OUT)
WARNING_message("Ignoring '-out_bval_col' option, since "
" you are outputting in rows.");
for( k=1 ; k<4 ; k++ ) {
if(EXTRA_ZEROS){
fprintf(fout,"% -11.5f ", 0.0);
if( (k==1) && BVAL_OUT_SEP ) // only output 1 zeroin bval file
fprintf(foutBV,"%8d ", 0);
}
ct_dwi = 0;
for(i=0 ; i<idx ; i++) {
if(FLAG[i]) {
fprintf(fout,"% -11.5f ", OUT_GRAD[i][k]);
if( (k==1) && BVAL_OUT_SEP )// only output 1 zeroin bval file
fprintf(foutBV,"%8d ", (int) OUT_GRAD[i][0]);
ct_dwi++;
}
if( (ct_dwi == Ndwi_final) && DWI_COMP_FAC ) {
INFO_message("Reached compression level: DWI number %d",
Ndwi_final);
break;
}
}
fprintf(fout,"\n");
}
}
fclose(fout);
if( BVAL_OUT_SEP ) {
fprintf(foutBV,"\n");
fclose(foutBV);
}
if(dwset) {
INFO_message("Processing the B0+DWI file now.");
if(!BZER) {
fprintf(stderr, "\n** Error in processing data set: "
"no b=0 values from bvecs/bval info!\n");
exit(5);
}
// FLAG marks where DWIs are if not using '-keep_b0s'!
Nvox = DSET_NVOX(dwset);
Ndwout = Ndwi+1;
temp_arr = calloc( Ndwout,sizeof(temp_arr));
for( i=0 ; i<Ndwout ; i++)
temp_arr[i] = calloc( Nvox,sizeof(float));
temp_grad = calloc( Ndwi,sizeof(temp_grad));
for( i=0 ; i<Ndwi ; i++)
temp_grad[i] = calloc( 3,sizeof(float));
if( (temp_arr == NULL) || (temp_grad == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(123);
}
dwi = 0; // keep track of DWI contraction
for( i=0 ; i<Nbrik ; i++)
if( !FLAG[i] ) // b=0
for( j=0 ; j<Nvox ; j++)
temp_arr[0][j]+= THD_get_voxel(dwset,j,i);
else {
for( j=0 ; j<3 ; j++)
temp_grad[dwi][j]= OUT_GRAD[i][j+1];
dwi++;
for( j=0 ; j<Nvox ; j++)
temp_arr[dwi][j]+= THD_get_voxel(dwset,j,i);
}
if( dwi != Ndwi ) {
fprintf(stderr, "\n** Mismatch in internal DWI counting!\n");
exit(6);
}
// average the values
for( j=0 ; j<Nvox ; j++)
temp_arr[0][j]/= BZER; // can't be zero here.
if( DWI_COMP_FAC ) {
INFO_message("Compressing DWI file");
for( k=1 ; k<DWI_COMP_FAC ; k++)
for( i=0 ; i<Ndwi_final ; i++)
for( j=0 ; j<Nvox ; j++)
temp_arr[1+i][j]+= temp_arr[1+k*Ndwi_final+i][j];
for( i=0 ; i<Ndwi_final ; i++)
for( j=0 ; j<Nvox ; j++)
temp_arr[1+i][j]/= DWI_COMP_FAC;
INFO_message("Checking closeness of compressed gradient values");
MaxDP = GradCloseness(temp_grad, Ndwi, DWI_COMP_FAC);
INFO_message("The max angular difference between matched/compressed\n"
"\tgradients is: %f", MaxDP);
if( MaxDP > 2)
WARNING_message("The max angular difference seem kinda big-- you\n"
" sure about the compression factor?");
}
Ndwout_final = Ndwi_final + 1;
INFO_message("Writing the processed data set.");
dwout = EDIT_empty_copy( dwset );
EDIT_dset_items(dwout,
ADN_nvals, Ndwout_final,
ADN_ntt, 0,
ADN_datum_all, MRI_float ,
ADN_prefix, prefix,
ADN_none );
for( i=0; i<Ndwout_final ; i++) {
EDIT_substitute_brick(dwout, i, MRI_float, temp_arr[i]);
temp_arr[i]=NULL;
}
// if necessary
for( i=Ndwout_final ; i<Ndwout ; i++)
temp_arr[i]=NULL;
THD_load_statistics( dwout );
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(dwout)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(dwout));
tross_Make_History("1dDW_Grad_o_Mat", argc, argv, dwout);
THD_write_3dim_dataset(NULL, NULL, dwout, True);
DSET_delete(dwout);
free(dwout);
DSET_delete(dwset);
free(dwset);
for( i=0 ; i<Ndwout_final ; i++)
free(temp_arr[i]);
free(temp_arr);
}
mri_free(preREADIN);
if( HAVE_BVAL )
mri_free(preREADBVAL);
if(prefix)
free(prefix);
printf("\n\tDone. Check output file '%s' for results",Fname_output);
if(dwset) {
printf("\n\t-> as well as the data_set '%s'",DSET_FILECODE(dwout));
}
if(BVAL_OUT_SEP)
printf("\n\t-> and even the b-value rows '%s'",Fname_outputBV);
printf("\n\n");
exit(0);
}
int main( int argc , char * argv[] )
{
int iv,nvals , nvec , ii,jj,kk , nvox ;
THD_3dim_dataset * new_dset=NULL ;
double * choleski ;
float ** refvec , * fv , * fc , * fit ;
MRI_IMAGE * flim ;
/*** read input options ***/
if( argc < 2 || strncmp(argv[1],"-help",4) == 0 ) DT_Syntax() ;
/*-- 20 Apr 2001: addto the arglist, if user wants to [RWCox] --*/
mainENTRY("3dDetrend main"); machdep() ; PRINT_VERSION("3dDetrend");
AFNI_logger("3dDetrend",argc,argv) ;
{ int new_argc ; char ** new_argv ;
addto_args( argc , argv , &new_argc , &new_argv ) ;
if( new_argv != NULL ){ argc = new_argc ; argv = new_argv ; }
}
DT_read_opts( argc , argv ) ;
/*** create new dataset (empty) ***/
new_dset = EDIT_empty_copy( DT_dset ) ; /* make a copy of its header */
/* modify its header */
tross_Copy_History( DT_dset , new_dset ) ;
tross_Make_History( "3dDetrend" , argc,argv , new_dset ) ;
EDIT_dset_items( new_dset ,
ADN_prefix , DT_output_prefix ,
ADN_directory_name, DT_session ,
ADN_none ) ;
/* can't re-write existing dataset */
if( THD_deathcon() && THD_is_file(DSET_HEADNAME(new_dset)) )
ERROR_exit("File %s already exists!\n",DSET_HEADNAME(new_dset) ) ;
/* read input in, and attach its bricks to the output dataset */
/* (not good in a plugin, but OK in a standalone program!) */
if( DT_verb ) INFO_message("Loading input dataset bricks\n") ;
DSET_mallocize( new_dset ) ;
DSET_mallocize( DT_dset ) ;
DSET_load( DT_dset ) ; CHECK_LOAD_ERROR(DT_dset) ;
nvals = DSET_NVALS(new_dset) ;
for( iv=0 ; iv < nvals ; iv++ )
EDIT_substitute_brick( new_dset , iv ,
DSET_BRICK_TYPE(DT_dset,iv) ,
DSET_ARRAY(DT_dset,iv) ) ;
if( DT_norm && DSET_BRICK_TYPE(new_dset,0) != MRI_float ){
INFO_message("Turning -normalize option off (input not in float format)");
DT_norm = 0 ;
}
/* load reference (detrending) vectors;
setup to do least squares fitting of each voxel */
nvec = 0 ;
for( ii=0 ; ii < IMARR_COUNT(DT_imar) ; ii++ ) /* number of detrending vectors */
nvec += IMARR_SUBIMAGE(DT_imar,ii)->ny ;
refvec = (float **) malloc( sizeof(float *)*nvec ) ;
for( kk=ii=0 ; ii < IMARR_COUNT(DT_imar) ; ii++ ){
fv = MRI_FLOAT_PTR( IMARR_SUBIMAGE(DT_imar,ii) ) ;
for( jj=0 ; jj < IMARR_SUBIMAGE(DT_imar,ii)->ny ; jj++ ) /* compute ptr */
refvec[kk++] = fv + ( jj * IMARR_SUBIMAGE(DT_imar,ii)->nx ) ; /* to vectors */
}
fit = (float *) malloc( sizeof(float) * nvals ) ; /* will get fit to voxel data */
/*--- do the all-voxels-together case ---*/
if( !DT_byslice ){
choleski = startup_lsqfit( nvals , NULL , nvec , refvec ) ;
if( choleski == NULL )
ERROR_exit("Choleski factorization fails: linearly dependent vectors!\n") ;
/* loop over voxels, fitting and detrending (or replacing) */
nvox = DSET_NVOX(new_dset) ;
if( DT_verb ) INFO_message("Computing voxel fits\n") ;
for( kk=0 ; kk < nvox ; kk++ ){
flim = THD_extract_series( kk , new_dset , 0 ) ; /* data */
fv = MRI_FLOAT_PTR(flim) ;
fc = delayed_lsqfit( nvals, fv, nvec, refvec, choleski ) ; /* coef */
for( ii=0 ; ii < nvals ; ii++ ) fit[ii] = 0.0 ;
for( jj=0 ; jj < nvec ; jj++ )
for( ii=0 ; ii < nvals ; ii++ )
fit[ii] += fc[jj] * refvec[jj][ii] ; /* fit */
if( !DT_replace ) /* remove */
for( ii=0 ; ii < nvals ; ii++ ) fit[ii] = fv[ii] - fit[ii] ;
if( DT_norm ) THD_normalize( nvals , fit ) ; /* 23 Nov 1999 */
THD_insert_series( kk, new_dset, nvals, MRI_float, fit, 0 ) ;
free(fc) ; mri_free(flim) ;
}
free(choleski) ;
/*- end of all-voxels-together case -*/
}
#ifdef ALLOW_BYSLICE
else { /*- start of slice case [08 Dec 1999] -*/
int ksl , nslice , tt , nx,ny , nxy , kxy ;
MRI_IMAGE * vim ;
/* make separate space for the slice-wise detrending vectors */
for( kk=ii=0 ; ii < DT_nvector ; ii++ ){
for( jj=0 ; jj < IMARR_SUBIMAGE(DT_imar,ii)->ny ; jj++ ) /* replace ptrs */
refvec[kk++] = (float *) malloc( sizeof(float) * nvals ) ; /* to vectors */
}
nslice = DSET_NZ(new_dset) ;
nxy = DSET_NX(new_dset) * DSET_NY(new_dset) ;
/* loop over slices */
for( ksl=0 ; ksl < nslice ; ksl++ ){
if( DT_verb ) INFO_message("Computing voxel fits for slice %d\n",ksl) ;
/* extract slice vectors from input interlaced vectors */
for( kk=ii=0 ; ii < DT_nvector ; ii++ ){ /* loop over vectors */
vim = IMARR_SUBIMAGE(DT_imar,ii) ; /* ii-th vector image */
nx = vim->nx ; ny = vim->ny ; /* dimensions */
for( jj=0 ; jj < ny ; jj++ ){ /* loop over columns */
fv = MRI_FLOAT_PTR(vim) + (jj*nx) ; /* ptr to column */
for( tt=0 ; tt < nvals ; tt++ ) /* loop over time */
refvec[kk][tt] = fv[ksl+tt*nslice] ; /* data point */
}
}
/* initialize fitting for this slice */
choleski = startup_lsqfit( nvals , NULL , nvec , refvec ) ;
if( choleski == NULL )
ERROR_exit("Choleski fails: linearly dependent vectors at slice %d\n",ksl) ;
/* loop over voxels in this slice */
for( kxy=0 ; kxy < nxy ; kxy++ ){
kk = kxy + ksl*nxy ; /* 3D index */
flim = THD_extract_series( kk , new_dset , 0 ) ; /* data */
fv = MRI_FLOAT_PTR(flim) ;
fc = delayed_lsqfit( nvals, fv, nvec, refvec, choleski ) ; /* coef */
for( ii=0 ; ii < nvals ; ii++ ) fit[ii] = 0.0 ;
for( jj=0 ; jj < nvec ; jj++ )
for( ii=0 ; ii < nvals ; ii++ )
fit[ii] += fc[jj] * refvec[jj][ii] ; /* fit */
if( !DT_replace ) /* remove */
for( ii=0 ; ii < nvals ; ii++ ) fit[ii] = fv[ii] - fit[ii] ;
if( DT_norm ) THD_normalize( nvals , fit ) ; /* 23 Nov 1999 */
THD_insert_series( kk, new_dset, nvals, MRI_float, fit, 0 ) ;
free(fc) ; mri_free(flim) ;
}
free(choleski) ;
} /* end of loop over slices */
} /*- end of -byslice case -*/
#endif
/*-- done done done done --*/
DSET_write(new_dset) ;
if( DT_verb ) WROTE_DSET(new_dset) ;
exit(0) ;
}
int main( int argc , char * argv[] )
{
int iarg ;
THD_3dim_dataset *inset , *outset ;
int add_I=0 , add_S=0 , add_A=0 , add_P=0 , add_L=0 , add_R=0 ;
int RLsiz=0, APsiz=0, ISsiz=0 ; /* 23 Mar 2004 */
char * prefix="zeropad" ;
int add_z=0 ; /* 07 Feb 2001 */
int mm_flag=0 ; /* 13 Feb 2001 */
int flag ;
THD_3dim_dataset *mset=NULL ; /* 14 May 2002 */
/*-- help? --*/
mainENTRY("3dZeropad main"); machdep(); AFNI_logger("3dZeropad",argc,argv);
PRINT_VERSION("3dZeropad") ;
/*-- read command line options --*/
if( argc == 1){ usage_3dZeropad(1); exit(0); } /* Bob's help shortcut */
iarg = 1 ;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-help") == 0 || strcmp(argv[iarg],"-h") == 0){
usage_3dZeropad(strlen(argv[iarg])>3 ? 2:1);
exit(0);
}
/*- -I, -S, etc. -*/
if( strlen(argv[iarg]) == 2 ){
switch( argv[iarg][1] ){
case 'I': add_I = (int) strtod(argv[++iarg],NULL) ; break ;
case 'S': add_S = (int) strtod(argv[++iarg],NULL) ; break ;
case 'A': add_A = (int) strtod(argv[++iarg],NULL) ; break ;
case 'P': add_P = (int) strtod(argv[++iarg],NULL) ; break ;
case 'L': add_L = (int) strtod(argv[++iarg],NULL) ; break ;
case 'R': add_R = (int) strtod(argv[++iarg],NULL) ; break ;
/* 07 Feb 2001: slice-direction is special */
case 'z':
case 'Z': add_z = (int) strtod(argv[++iarg],NULL) ; break ;
default:
fprintf(stderr,"** 3dZeropad: Illegal option: %s\n",argv[iarg]) ; exit(1) ;
}
if( mset != NULL ){
fprintf(stderr,"** 3dZeropad: Can't use %s with -master!\n",argv[iarg-1]) ;
exit(1) ;
}
iarg++ ; continue ; /* skip to next argument */
}
/*- -RL, -AP, -IS [23 Mar 2004] -*/
if( strcmp(argv[iarg],"-RL") == 0 || strcmp(argv[iarg],"-LR") == 0 ){
if( add_R || add_L || mset != NULL ){
fprintf(stderr,"** 3dZeropad: Can't use -RL with -R, -L, or -master!\n");
exit(1) ;
}
RLsiz = (int) strtod(argv[++iarg],NULL) ;
if( RLsiz < 1 ){
fprintf(stderr,"** 3dZeropad: value after -RL is illegal!\n") ;
exit(1) ;
}
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-AP") == 0 || strcmp(argv[iarg],"-PA") == 0 ){
if( add_A || add_P || mset != NULL ){
fprintf(stderr,"** 3dZeropad: Can't use -AP with -A, -P, or -master!\n");
exit(1) ;
}
APsiz = (int) strtod(argv[++iarg],NULL) ;
if( APsiz < 1 ){
fprintf(stderr,"** 3dZeropad: value after -AP is illegal!\n") ;
exit(1) ;
}
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-IS") == 0 || strcmp(argv[iarg],"-SI") == 0 ){
if( add_S || add_I || mset != NULL ){
fprintf(stderr,"** 3dZeropad: Can't use -IS with -I, -S, or -master!\n");
exit(1) ;
}
ISsiz = (int) strtod(argv[++iarg],NULL) ;
if( ISsiz < 1 ){
fprintf(stderr,"** 3dZeropad: value after -IS is illegal!\n") ;
exit(1) ;
}
iarg++ ; continue ;
}
/*- -mm -*/
if( strcmp(argv[iarg],"-mm") == 0 ){
if( mset != NULL ){
fprintf(stderr,"** 3dZeropad: Can't use %s with -master!\n",argv[iarg]) ;
exit(1) ;
}
mm_flag = 1 ;
iarg++ ; continue ;
}
/*- -prefix -*/
if( strcmp(argv[iarg],"-prefix") == 0 ){
prefix = argv[++iarg] ;
if( !THD_filename_ok(prefix) ){
fprintf(stderr,"** 3dZeropad: Illegal string after -prefix!\n"); exit(1) ;
}
iarg++ ; continue ;
}
/*-- -master [14 May 2002] --*/
if( strcmp(argv[iarg],"-master") == 0 ){
if( add_I || add_S || add_A || mm_flag ||
add_P || add_R || add_L || add_z ||
RLsiz || APsiz || ISsiz ){
fprintf(stderr,"** 3dZeropad: Can't use -master with -I,-S,-A,-P,-R,-L, or -mm!\n");
exit(1) ;
}
if( mset != NULL ){
fprintf(stderr,"** 3dZeropad: Can't use -master twice!\n"); exit(1);
}
mset = THD_open_dataset( argv[++iarg] ) ;
if( !ISVALID_DSET(mset) ){
fprintf(stderr,"** 3dZeropad: Can't open -master %s\n",argv[iarg]); exit(1);
}
THD_make_cardinal(mset); /* deoblique 21 Oct, 2011 [rickr] */
iarg++ ; continue ;
}
/*- what the hell? -*/
fprintf(stderr,"** 3dZeropad: Illegal option: %s\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1) ;
}
if (iarg < 2) {
ERROR_message("Too few options, try %s -help for details\n",argv[0]);
exit(1);
}
/*- check to see if the user asked for something, anything -*/
if( mset == NULL ){
if( add_I==0 && add_S==0 && add_P==0 &&
add_A==0 && add_L==0 && add_R==0 && add_z==0 &&
RLsiz==0 && APsiz==0 && ISsiz==0 ){
fprintf(stderr,"++ 3dZeropad: All inputs are zero? Making a copy!\n") ;
}
}
/* check for conflicts [23 Mar 2004] */
if( RLsiz > 0 && (add_R || add_L || add_z) ){
fprintf(stderr,"** 3dZeropad: Can't use -R or -L or -z with -RL!\n"); exit(1);
}
if( APsiz > 0 && (add_A || add_P || add_z) ){
fprintf(stderr,"** 3dZeropad: Can't use -A or -P or -z with -AP!\n"); exit(1);
}
if( ISsiz > 0 && (add_I || add_S || add_z) ){
fprintf(stderr,"** 3dZeropad: Can't use -I or -S or -z with -IS!\n"); exit(1);
}
/*-- read the input dataset --*/
if( iarg >= argc ){
fprintf(stderr,"** 3dZeropad: No input dataset on command line!\n"); exit(1);
}
#if 0
if( strncmp(argv[iarg],"3dcalc(",7) == 0 ){
fprintf(stderr,"** 3dZeropad: Can't use '3dcalc()' input datasets here!\n"); exit(1);
}
#endif
inset = THD_open_dataset( argv[iarg] ) ;
if( inset == NULL ){
fprintf(stderr,"** 3dZeropad: Can't open dataset %s\n",argv[iarg]); exit(1);
}
THD_make_cardinal(inset); /* deoblique 21 Oct, 2011 [rickr] */
#if 0
if( DSET_IS_MASTERED(inset) ){
fprintf(stderr,"** 3dZeropad: Can't use partial datasets!\n"); exit(1);
}
#endif
/*-- 14 May 2002: use master dataset now? --*/
if( mset != NULL ){
THD_dataxes *max=mset->daxes, *iax=inset->daxes ;
int nerr=0 ;
float mxbot,mybot,mzbot , mxtop,mytop,mztop , mdx,mdy,mdz ;
float ixbot,iybot,izbot , ixtop,iytop,iztop , idx,idy,idz ;
int mnx,mny,mnz , inx,iny,inz ;
int add_xb,add_xt , add_yb,add_yt , add_zb,add_zt ;
/* check if datasets are oriented the same */
if( max->xxorient != iax->xxorient ||
max->yyorient != iax->yyorient ||
max->zzorient != iax->zzorient ){
fprintf(stderr,
"** 3dZeropad: Master (%s) and Input (%s) dataset not oriented the same!\n",
DSET_PREFIX(mset), DSET_PREFIX(inset));
nerr++ ;
}
/* check if datasets have same voxel dimensions */
mdx = max->xxdel ; mdy = max->yydel ; mdz = max->zzdel ;
idx = iax->xxdel ; idy = iax->yydel ; idz = iax->zzdel ;
mnx = max->nxx ; mny = max->nyy ; mnz = max->nzz ;
inx = iax->nxx ; iny = iax->nyy ; inz = iax->nzz ;
if( fabs(mdx-idx) > 0.01*fabs(mdx) ||
fabs(mdy-idy) > 0.01*fabs(mdy) ||
fabs(mdz-idz) > 0.01*fabs(mdz) ){
fprintf(stderr,"** 3dZeropad: Master and Input datasets don't have same voxel size!\n");
nerr++ ;
}
if( nerr ) exit(1) ;
/* calculate coords at top and bottom of each dataset */
mxbot = max->xxorg ; mxtop = mxbot + mnx*mdx ;
mybot = max->yyorg ; mytop = mybot + mny*mdy ;
mzbot = max->zzorg ; mztop = mzbot + mnz*mdz ;
ixbot = iax->xxorg ; ixtop = ixbot + inx*idx ;
iybot = iax->yyorg ; iytop = iybot + iny*idy ;
izbot = iax->zzorg ; iztop = izbot + inz*idz ;
/* calculate amount to add/trim at each face */
add_xb = (int) rint((ixbot-mxbot)/idx) ;
add_xt = (int) rint((mxtop-ixtop)/idx) ;
add_yb = (int) rint((iybot-mybot)/idy) ;
add_yt = (int) rint((mytop-iytop)/idy) ;
add_zb = (int) rint((izbot-mzbot)/idz) ;
add_zt = (int) rint((mztop-iztop)/idz) ;
/* map trims from x,y,z to RL,AP,IS coords */
switch( iax->xxorient ){
case ORI_R2L_TYPE: add_R = add_xb ; add_L = add_xt ; break ;
case ORI_L2R_TYPE: add_L = add_xb ; add_R = add_xt ; break ;
case ORI_I2S_TYPE: add_I = add_xb ; add_S = add_xt ; break ;
case ORI_S2I_TYPE: add_S = add_xb ; add_I = add_xt ; break ;
case ORI_A2P_TYPE: add_A = add_xb ; add_P = add_xt ; break ;
case ORI_P2A_TYPE: add_P = add_xb ; add_A = add_xt ; break ;
}
switch( iax->yyorient ){
case ORI_R2L_TYPE: add_R = add_yb ; add_L = add_yt ; break ;
case ORI_L2R_TYPE: add_L = add_yb ; add_R = add_yt ; break ;
case ORI_I2S_TYPE: add_I = add_yb ; add_S = add_yt ; break ;
case ORI_S2I_TYPE: add_S = add_yb ; add_I = add_yt ; break ;
case ORI_A2P_TYPE: add_A = add_yb ; add_P = add_yt ; break ;
case ORI_P2A_TYPE: add_P = add_yb ; add_A = add_yt ; break ;
}
switch( iax->zzorient ){
case ORI_R2L_TYPE: add_R = add_zb ; add_L = add_zt ; break ;
case ORI_L2R_TYPE: add_L = add_zb ; add_R = add_zt ; break ;
case ORI_I2S_TYPE: add_I = add_zb ; add_S = add_zt ; break ;
case ORI_S2I_TYPE: add_S = add_zb ; add_I = add_zt ; break ;
case ORI_A2P_TYPE: add_A = add_zb ; add_P = add_zt ; break ;
case ORI_P2A_TYPE: add_P = add_zb ; add_A = add_zt ; break ;
}
fprintf(stderr,"++ 3dZeropad -master => -I %d -S %d -A %d -P %d -R %d -L %d\n",
add_I,add_S,add_A,add_P,add_R,add_L ) ;
DSET_delete(mset) ;
}
/*-- 07 Feb 2001: if -z was used, fix that now --*/
if( add_z != 0 ){
switch( inset->daxes->zzorient ){
case ORI_R2L_TYPE:
case ORI_L2R_TYPE:
if( add_R != 0 && add_R != add_z ) fprintf(stderr,"++ 3dZeropad: -z overrides -R\n");
if( add_L != 0 && add_L != add_z ) fprintf(stderr,"++ 3dZeropad: -z overrides -L\n");
add_R = add_L = add_z ;
break ;
case ORI_P2A_TYPE:
case ORI_A2P_TYPE:
if( add_P != 0 && add_P != add_z ) fprintf(stderr,"++ 3dZeropad: -z overrides -P\n");
if( add_A != 0 && add_A != add_z ) fprintf(stderr,"++ 3dZeropad: -z overrides -A\n");
add_P = add_A = add_z ;
break ;
case ORI_I2S_TYPE:
case ORI_S2I_TYPE:
if( add_I != 0 && add_I != add_z ) fprintf(stderr,"++ 3dZeropad: -z overrides -I\n");
if( add_I != 0 && add_S != add_z ) fprintf(stderr,"++ 3dZeropad: -z overrides -S\n");
add_I = add_S = add_z ;
break ;
}
}
/*-- 23 Mar 2004: expand/contract if ordered --*/
if( RLsiz > 0 ){
int nold=0 ;
if( inset->daxes->xxorient == ORI_R2L_TYPE || inset->daxes->xxorient == ORI_L2R_TYPE )
nold = inset->daxes->nxx ;
else if( inset->daxes->yyorient == ORI_R2L_TYPE || inset->daxes->yyorient == ORI_L2R_TYPE )
nold = inset->daxes->nyy ;
else if( inset->daxes->zzorient == ORI_R2L_TYPE || inset->daxes->zzorient == ORI_L2R_TYPE )
nold = inset->daxes->nzz ;
if( nold > 0 ){
add_R = (RLsiz-nold) / 2 ;
add_L = RLsiz-(nold+add_R) ;
}
}
if( APsiz > 0 ){
int nold=0 ;
if( inset->daxes->xxorient == ORI_A2P_TYPE || inset->daxes->xxorient == ORI_P2A_TYPE )
nold = inset->daxes->nxx ;
else if( inset->daxes->yyorient == ORI_A2P_TYPE || inset->daxes->yyorient == ORI_P2A_TYPE )
nold = inset->daxes->nyy ;
else if( inset->daxes->zzorient == ORI_A2P_TYPE || inset->daxes->zzorient == ORI_P2A_TYPE )
nold = inset->daxes->nzz ;
if( nold > 0 ){
add_A = (APsiz-nold) / 2 ;
add_P = APsiz-(nold+add_A) ;
}
}
if( ISsiz > 0 ){
int nold=0 ;
if( inset->daxes->xxorient == ORI_I2S_TYPE || inset->daxes->xxorient == ORI_S2I_TYPE )
nold = inset->daxes->nxx ;
else if( inset->daxes->yyorient == ORI_I2S_TYPE || inset->daxes->yyorient == ORI_S2I_TYPE )
nold = inset->daxes->nyy ;
else if( inset->daxes->zzorient == ORI_I2S_TYPE || inset->daxes->zzorient == ORI_S2I_TYPE )
nold = inset->daxes->nzz ;
if( nold > 0 ){
add_I = (ISsiz-nold) / 2 ;
add_S = ISsiz-(nold+add_I) ;
}
}
/*-- 04 Oct 2000: all the real work is now in thd_zeropad.c --*/
flag = ZPAD_PURGE ;
if( mm_flag ) flag |= ZPAD_MM ;
outset = THD_zeropad( inset ,
add_I, add_S, add_A, add_P, add_L, add_R,
prefix , flag ) ;
if( THD_deathcon() && THD_is_file(DSET_HEADNAME(outset)) ){
fprintf(stderr,
"** 3dZeropad: output file %s already exists - FATAL ERROR!\n",
DSET_HEADNAME(outset) ) ;
exit(1) ;
}
if( outset == NULL ){
fprintf(stderr,"** 3dZeropad: Some error occurred in processing!\n") ;
exit(1) ;
}
tross_Copy_History( inset , outset ) ; /* 31 Jan 2001 - RWCox */
tross_Make_History( "3dZeropad" , argc,argv , outset ) ;
if (DSET_write(outset) != False) {
fprintf(stderr,"++ output dataset: %s\n",DSET_BRIKNAME(outset)) ;
exit(0) ;
} else {
fprintf(stderr,
"** 3dZeropad: Failed to write output!\n" ) ;
exit(1) ;
}
}
MRI_IMARR * THD_extract_many_series( int ns, int *ind, THD_3dim_dataset *dset )
{
MRI_IMARR *imar ; /* output */
MRI_IMAGE *im ;
int nv , ival , kk ;
char *iar ; /* brick in the input */
float **far ; /* 27 Feb 2003: ptrs to output */
ENTRY("THD_extract_many_series") ;
if( ns <= 0 || ind == NULL | dset == NULL ) RETURN( NULL );
/* try to load dataset */
nv = dset->dblk->nvals ;
iar = DSET_ARRAY(dset,0) ;
if( iar == NULL ){ /* if data needs to be loaded from disk */
(void) THD_load_datablock( dset->dblk ) ;
iar = DSET_ARRAY(dset,0) ;
if( iar == NULL ){
static int nerr=0 ;
if( nerr < 2 ){ ERROR_message("Can't load dataset %s",DSET_HEADNAME(dset)); nerr++; }
RETURN( NULL );
}
}
/* create output */
far = (float **) malloc(sizeof(float *)*ns) ; /* 27 Feb 2003 */
NULL_CHECK(far) ;
INIT_IMARR(imar) ;
for( kk=0 ; kk < ns ; kk++ ){
im = mri_new( nv , 1 , MRI_float ) ; /* N.B.: now does 0 fill */
far[kk] = MRI_FLOAT_PTR(im) ; /* ptr to kk-th output series */
ADDTO_IMARR(imar,im) ;
}
/* fill the output */
switch( DSET_BRICK_TYPE(dset,0) ){
default: /* don't know what to do --> return nada */
DESTROY_IMARR(imar) ; free(far) ;
RETURN( NULL );
case MRI_byte:{
byte * bar ;
for( ival=0 ; ival < nv ; ival++ ){
bar = (byte *) DSET_ARRAY(dset,ival) ;
if( bar != NULL ){
for( kk=0 ; kk < ns ; kk++ ){
far[kk][ival] = (float)bar[ind[kk]] ;
}
}
}
}
break ;
case MRI_short:{
short * bar ;
for( ival=0 ; ival < nv ; ival++ ){
bar = (short *) DSET_ARRAY(dset,ival) ;
if( bar != NULL ){
for( kk=0 ; kk < ns ; kk++ ){
far[kk][ival] = (float)bar[ind[kk]] ;
}
}
}
}
break ;
case MRI_float:{
float * bar ;
for( ival=0 ; ival < nv ; ival++ ){
bar = (float *) DSET_ARRAY(dset,ival) ;
if( bar != NULL ){
for( kk=0 ; kk < ns ; kk++ ){
far[kk][ival] = bar[ind[kk]] ;
}
}
}
}
break ;
#if 0
case MRI_int:{
int * bar ;
for( ival=0 ; ival < nv ; ival++ ){
bar = (int *) DSET_ARRAY(dset,ival) ;
if( bar != NULL ){
for( kk=0 ; kk < ns ; kk++ ){
far[kk][ival] = bar[ind[kk]] ;
}
}
}
}
break ;
case MRI_double:{
double * bar ;
for( ival=0 ; ival < nv ; ival++ ){
bar = (double *) DSET_ARRAY(dset,ival) ;
if( bar != NULL ){
for( kk=0 ; kk < ns ; kk++ ){
far[kk][ival] = (float)bar[ind[kk]] ;
}
}
}
}
break ;
#endif
case MRI_complex:{
complex * bar ;
for( ival=0 ; ival < nv ; ival++ ){
bar = (complex *) DSET_ARRAY(dset,ival) ;
if( bar != NULL ){
for( kk=0 ; kk < ns ; kk++ ){
far[kk][ival] = bar[ind[kk]].r ;
}
}
}
}
break ;
}
/* scale outputs, if needed */
if( THD_need_brick_factor(dset) ){
MRI_IMAGE *qim ;
for( kk=0 ; kk < ns ; kk++ ){
im = IMARR_SUBIMAGE(imar,kk) ;
qim = mri_mult_to_float( dset->dblk->brick_fac , im ) ;
mri_free(im) ;
IMARR_SUBIMAGE(imar,kk) = qim ;
}
}
#if 0 /* 27 Feb 2003 */
/* convert to floats, if needed */
if( IMARR_SUBIMAGE(imar,0)->kind != MRI_float ){
MRI_IMAGE * qim ;
for( kk=0 ; kk < ns ; kk++ ){
im = IMARR_SUBIMAGE(imar,kk) ;
qim = mri_to_float( im ) ;
mri_free(im) ;
IMARR_SUBIMAGE(imar,kk) = qim ;
}
}
#endif
/* add time axis stuff to output images, if present */
if( dset->taxis != NULL ){
float zz , tt ;
int kz ;
for( kk=0 ; kk < ns ; kk++ ){
kz = ind[kk] / ( dset->daxes->nxx * dset->daxes->nyy ) ;
zz = dset->daxes->zzorg + kz * dset->daxes->zzdel ;
tt = THD_timeof( 0 , zz , dset->taxis ) ;
im = IMARR_SUBIMAGE(imar,kk) ;
im->xo = tt ; im->dx = dset->taxis->ttdel ; /* origin and delta */
if( dset->taxis->units_type == UNITS_MSEC_TYPE ){ /* convert to sec */
im->xo *= 0.001 ; im->dx *= 0.001 ;
}
}
} else {
for( kk=0 ; kk < ns ; kk++ ){
im = IMARR_SUBIMAGE(imar,kk) ;
im->xo = 0.0 ; im->dx = 1.0 ;
}
}
free(far) ; RETURN(imar);
}
int main( int argc , char * argv[] )
{
int ninp , ids , nv , iv,jv,kv , ivout , new_nvals ;
THD_3dim_dataset * new_dset=NULL , * dset ;
char buf[256] ;
/*----- 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
/*** read input options ***/
if( argc < 2 || strncmp(argv[1],"-help",4) == 0 ) B2F_Syntax() ;
mainENTRY("3dbuc2fim main"); machdep(); AFNI_logger(PROGRAM_NAME,argc,argv);
PRINT_VERSION("3dbuc2fim") ; AUTHOR(PROGRAM_AUTHOR);
B2F_read_opts( argc , argv ) ;
/*** create new dataset (empty) ***/
ninp = B2F_dsar->num ;
if( ninp < 1 ){
fprintf(stderr,"*** No input datasets?\n") ; exit(1) ;
}
new_nvals = 0 ;
for( ids=0 ; ids < ninp ; ids++ ) new_nvals += NSUBV(ids) ;
/*----- Check for acceptable number of sub-bricks -----*/
if (new_nvals < 1)
{ fprintf(stderr,"*** Less than 1 sub-brick specified\n") ; exit(1) ; }
if (new_nvals > 2)
{ fprintf(stderr,"*** More than 2 sub-bricks specified\n") ; exit(1) ; }
if( B2F_verb ) printf("-verb: output will have %d sub-bricks\n",new_nvals) ;
new_dset = EDIT_empty_copy( DSUB(0) ) ;
if( ninp == 1 ) tross_Copy_History( DSUB(0) , new_dset ) ;
tross_Make_History( "3dbuc2fim" , argc,argv , new_dset ) ;
/*----- Set default value for function type. This will be changed later,
if the second sub-brick has a statistic type. -----*/
if (new_nvals == 1)
B2F_func_type = FUNC_FIM_TYPE;
else
B2F_func_type = FUNC_THR_TYPE;
EDIT_dset_items (new_dset ,
ADN_prefix , B2F_output_prefix ,
ADN_directory_name, B2F_session ,
ADN_type , HEAD_FUNC_TYPE,
ADN_func_type , B2F_func_type,
ADN_ntt , 0 ,
ADN_nvals , new_nvals ,
ADN_none ) ;
if( THD_deathcon() && THD_is_file(DSET_HEADNAME(new_dset)) ){
fprintf(stderr,"*** Fatal error: file %s already exists!\n",
DSET_HEADNAME(new_dset) ) ;
exit(1) ;
}
THD_force_malloc_type( new_dset->dblk , DATABLOCK_MEM_MALLOC ) ;
/*** loop over input datasets ***/
if( ninp > 1 ) myXtFree( new_dset->keywords ) ;
ivout = 0 ;
for( ids=0 ; ids < ninp ; ids++ ){
dset = DSUB(ids) ;
nv = NSUBV(ids) ;
DSET_load(dset) ; CHECK_LOAD_ERROR(dset) ;
/** loop over sub-bricks to output **/
for( iv=0 ; iv < nv ; iv++ ){
jv = SUBV(ids,iv) ; /* which sub-brick to use */
EDIT_substitute_brick( new_dset , ivout ,
DSET_BRICK_TYPE(dset,jv) , DSET_ARRAY(dset,jv) ) ;
/*----- If this sub-brick is from a bucket dataset,
preserve the label for this sub-brick -----*/
if (dset->func_type == FUNC_BUCK_TYPE)
sprintf (buf, "%s", DSET_BRICK_LABEL(dset,jv));
else
sprintf(buf,"%.12s[%d]",DSET_PREFIX(dset),jv) ;
EDIT_dset_items( new_dset , ADN_brick_label_one+ivout, buf , ADN_none ) ;
#if 0
sprintf(buf,"%s[%d]",DSET_FILECODE(dset),jv) ;
EDIT_dset_items(
new_dset, ADN_brick_keywords_replace_one+ivout, buf, ADN_none ) ;
#endif
EDIT_dset_items(
new_dset ,
ADN_brick_fac_one +ivout, DSET_BRICK_FACTOR(dset,jv),
#if 0
ADN_brick_keywords_append_one+ivout, DSET_BRICK_KEYWORDS(dset,jv) ,
#endif
ADN_none ) ;
/** possibly write statistical parameters for this sub-brick **/
kv = DSET_BRICK_STATCODE(dset,jv) ;
if( FUNC_IS_STAT(kv) ){ /* input sub-brick has stat params */
int npar = MAX_STAT_AUX , lv ;
float * par = (float *) malloc( sizeof(float) * (npar) ) ;
float * sax = DSET_BRICK_STATAUX(dset,jv) ;
for( lv=0 ; lv < npar ; lv++ )
par[lv] = (sax != NULL && lv < FUNC_need_stat_aux[kv]) ? sax[lv] : 0.0;
if (ivout == 1)
{
EDIT_dset_items(new_dset ,
ADN_func_type , kv,
ADN_stat_aux, par ,
ADN_none ) ;
}
free(par) ;
/* 2: if the input dataset has statistical parameters */
} else if( ISFUNC(dset) && /* dset has stat */
FUNC_IS_STAT(dset->func_type) && /* params */
jv == FUNC_ival_thr[dset->func_type] ){ /* thr sub-brick */
int npar , lv ;
float * par , * sax ;
kv = dset->func_type ;
npar = MAX_STAT_AUX ;
par = (float *) malloc( sizeof(float) * (npar+2) ) ;
sax = dset->stat_aux ;
for( lv=0 ; lv < npar ; lv++ )
par[lv] = (sax != NULL) ? sax[lv] : 0.0 ;
if (ivout == 1)
{
for( lv=0 ; lv < npar+2 ; lv++ )
printf ("par[%d] = %f \n", lv, par[lv]);
EDIT_dset_items(new_dset ,
ADN_func_type , kv,
ADN_stat_aux, par ,
ADN_none ) ;
}
free(par) ;
}
/** print a message? **/
if( B2F_verb ) printf("-verb: copied %s[%d] into %s[%d]\n" ,
DSET_FILECODE(dset) , jv ,
DSET_FILECODE(new_dset) , ivout ) ;
ivout++ ;
}
/** loop over all bricks in input dataset and
unload them if they aren't going into the output
(not required, but is done to economize on memory) **/
if( nv < DSET_NVALS(dset) ){
for( kv=0 ; kv < DSET_NVALS(dset) ; kv++ ){ /* all input sub-bricks */
for( iv=0 ; iv < nv ; iv++ ){ /* all output sub-bricks */
jv = SUBV(ids,iv) ;
if( jv == kv ) break ; /* input matches output */
}
if( iv == nv ){
mri_free( DSET_BRICK(dset,kv) ) ;
#if 0
if( B2F_verb ) printf("-verb: unloaded unused %s[%d]\n" ,
DSET_FILECODE(dset) , kv ) ;
#endif
}
}
}
} /* end of loop over input datasets */
if( B2F_verb ) fprintf(stderr,"-verb: loading statistics\n") ;
THD_load_statistics( new_dset ) ;
THD_write_3dim_dataset( NULL,NULL , new_dset , True ) ;
if( B2F_verb ) fprintf(stderr,"-verb: wrote output: %s\n",DSET_BRIKNAME(new_dset)) ;
exit(0) ;
}
int main( int argc , char *argv[] )
{
int force=0 ; /* KRH loudly deprecating usage 04/13/05/ */
int iarg=1 ;
THD_3dim_dataset *dset ; /* output dataset */
int nvals , ii , jj , kk ;
MRI_IMARR *anar ; /* stuff from ANALYZE headers */
MRI_IMAGE *anim ;
int nxan=0,nyan=0,nzan=0 , an_datum=0 , an_swapped=0 ;
float dxan=-1.0,dyan=0.0,dzan=0.0 ;
char anor[8] = "\0" ;
THD_ivec3 nxyz , orixyz ;
THD_fvec3 dxyz , orgxyz ;
float TR=1.0 ; int tunits=UNITS_SEC_TYPE ;
int is_fbuc=0 , is_abuc=0 , is_3dtime=0 ;
int view_type=VIEW_ORIGINAL_TYPE ;
char *prefix="a2a" ;
int xorient=-1, yorient=-1, zorient=-1 ;
int use_zoff=0,use_xoff=0,use_yoff=0 ; float zoff=0.0,xoff=0.0,yoff=0.0 ;
THD_3dim_dataset *gset=NULL ; /* geometry parent */
float *fac ;
char **flab , *fatr ;
/*-- help the poor user? --*/
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){ A2A_help(); exit(0); }
mainENTRY("3dANALYZEtoAFNI main"); machdep(); PRINT_VERSION("3dANALYZEtoAFNI");
/*-- parse options --*/
while( iarg < argc && argv[iarg][0] == '-' ){
/* -prefix */
if( strcmp(argv[iarg],"-prefix") == 0 ){
if( ++iarg >= argc ){
fprintf(stderr,"** -prefix needs an argument!\n"); exit(1);
}
prefix = argv[iarg] ;
if( !THD_filename_ok(prefix) ){
fprintf(stderr,"** Illegal prefix!\n"); exit(1);
}
if( strstr(prefix,"/") != NULL ){
fprintf(stderr,"** Can't use directory names in the prefix!\n"); exit(1);
}
iarg++ ; continue ;
}
/* -view */
if( strcmp(argv[iarg],"-view") == 0 ){
char *str ;
if( ++iarg >= argc ){
fprintf(stderr,"** -view needs an argument!\n"); exit(1);
}
str = argv[iarg] ; if( str[0] == '+' ) str++ ;
for( ii=FIRST_VIEW_TYPE ; ii <= LAST_VIEW_TYPE ; ii++ )
if( strcmp(str,VIEW_codestr[ii]) == 0 ) break ;
if( ii <= LAST_VIEW_TYPE ){
view_type = ii ;
} else {
fprintf(stderr,"** Illegal -view code!\n"); exit(1);
}
iarg++ ; continue ;
}
/* -zorigin */
if( strcmp(argv[iarg],"-zorigin") == 0 ){
if( ++iarg >= argc ){
fprintf(stderr,"** -zorigin needs an argument!\n"); exit(1);
}
zoff = strtod( argv[iarg] , NULL ) ;
use_zoff = 1 ;
iarg++ ; continue ;
}
/* -orient */
#define ORCODE(aa) \
( (aa)=='R' ? ORI_R2L_TYPE : (aa)=='L' ? ORI_L2R_TYPE : \
(aa)=='P' ? ORI_P2A_TYPE : (aa)=='A' ? ORI_A2P_TYPE : \
(aa)=='I' ? ORI_I2S_TYPE : (aa)=='S' ? ORI_S2I_TYPE : ILLEGAL_TYPE )
#define OR3OK(x,y,z) ( ((x)&6) + ((y)&6) + ((z)&6) == 6 )
if( strcmp(argv[iarg],"-orient") == 0 ){
char acod ;
if( ++iarg >= argc ){
fprintf(stderr,"** -orient needs an argument!\n"); exit(1);
}
if( strlen(argv[iarg]) != 3 ){
fprintf(stderr,"** Illegal -orient code!\n"); exit(1);
}
acod = toupper(argv[iarg][0]) ; xorient = ORCODE(acod) ;
acod = toupper(argv[iarg][1]) ; yorient = ORCODE(acod) ;
acod = toupper(argv[iarg][2]) ; zorient = ORCODE(acod) ;
if( xorient<0 || yorient<0 || zorient<0 ||
! OR3OK(xorient,yorient,zorient) ){
fprintf(stderr,"** Unusable -orient code!\n"); exit(1);
}
iarg++ ; continue ;
}
/* -geomparent */
if( strcmp(argv[iarg],"-geomparent") == 0 ){
if( ++iarg >= argc ){
fprintf(stderr,"** -geomparent needs an argument!\n"); exit(1);
}
gset = THD_open_dataset( argv[iarg] ); CHECK_OPEN_ERROR(gset,argv[iarg]);
iarg++ ; continue ;
}
/* -TR */
if( strcmp(argv[iarg],"-TR") == 0 ){
char *eptr ;
if( ++iarg >= argc ){
fprintf(stderr,"** -geomparent needs an argument!\n"); exit(1);
}
TR = strtod( argv[iarg] , &eptr ) ;
if( TR <= 0.0 ){
fprintf(stderr,"** -TR needs a positive value after it!\n"); exit(1);
}
if( strcmp(eptr,"ms")==0 || strcmp(eptr,"msec")==0 ){
tunits = UNITS_MSEC_TYPE ;
WARNING_message("TR in millisecond units is deprecated.") ;
} else if( strcmp(eptr,"s")==0 || strcmp(eptr,"sec")==0 ){
tunits = UNITS_SEC_TYPE ;
} else if( strcmp(eptr,"Hz")==0 || strcmp(eptr,"Hertz")==0 ){
tunits = UNITS_HZ_TYPE ;
}
is_3dtime = 1 ; is_abuc = is_fbuc = 0 ;
iarg++ ; continue ;
}
/* -fbuc */
if( strcmp(argv[iarg],"-fbuc") == 0 ){
is_fbuc = 1 ; is_abuc = is_3dtime = 0 ;
iarg++ ; continue ;
}
/* -abuc */
if( strcmp(argv[iarg],"-abuc") == 0 ){
is_abuc = 1 ; is_fbuc = is_3dtime = 0 ;
iarg++ ; continue ;
}
/* -OK */
if( strcmp(argv[iarg],"-OK") == 0 ){
force = 1 ;
iarg++ ; continue ;
}
/** don't know this one **/
fprintf(stderr,"** Illegal option %s\n",argv[iarg]); exit(1);
}
if (!force) { A2A_help(); exit(0);
}
/*-- check number of remaining args --*/
nvals = argc - iarg ;
if( nvals <= 0 ){
fprintf(stderr,"** No ANALYZE files on command line!?\n"); exit(1);
}
/*-- try to read each ANALYZE file and glean info from it --*/
CLEAR_MRILIB_globals ; /* setup */
fac = (float *) malloc(sizeof(float)*nvals) ;
for( ii=iarg ; ii < argc ; ii++ ){
if( strstr(argv[ii],"/") != NULL ){
fprintf(stderr,"** ANALYZE files must all be in current directory!\n") ;
exit(1) ;
}
anar = mri_read_analyze75( argv[ii] ) ; /* read it */
if( anar == NULL || IMARR_COUNT(anar) == 0 ){
fprintf(stderr,"** Can't read %s as ANALYZE-75 format .hdr file!\n",argv[ii]);
exit(1) ;
}
anim = IMARR_SUBIM(anar,0) ; /* first 2D image */
fac[ii-iarg] = anim->dv ; /* save scale factor, if any */
if( ii == iarg ){ /* first time in: store header values */
nxan = anim->nx ; nyan = anim->ny ; nzan = IMARR_COUNT(anar) ;
if( MRILIB_orients[0] != '\0' ) strcpy(anor,MRILIB_orients) ;
an_datum = anim->kind ;
if( anim->dw > 0.0 ){ dxan = anim->dx; dyan = anim->dy; dzan = anim->dz; }
an_swapped = anim->was_swapped ;
} else { /* check later sub-bricks */
if( nxan != anim->nx || nyan != anim->ny || nzan != IMARR_COUNT(anar) ){
fprintf(stderr,"** File %s has different dimensions than %s\n",
argv[ii] , argv[iarg] ) ;
exit(1) ;
}
if( an_datum != anim->kind ){
fprintf(stderr,"** File %s has different kind of data than %s\n",
argv[ii] , argv[iarg] ) ;
exit(1) ;
}
if( an_swapped != anim->was_swapped ){
fprintf(stderr,"** File %s %s byte-swapped, but %s %s\n",
argv[ii] , (anim->was_swapped) ? "is" : "isn't" ,
argv[iarg] , (an_swapped) ? "is" : "isn't" ) ;
exit(1) ;
}
if( anim->dw > 0.0 ){
if( dxan < 0.0 ){
dxan = anim->dx; dyan = anim->dy; dzan = anim->dz;
} else {
if( dxan != anim->dx || dyan != anim->dy || dzan != anim->dz ){
fprintf(stderr,"++ WARNING: File %s has variant voxel sizes!\n",
argv[ii]) ;
}
}
}
if( anor[0] == '\0' && MRILIB_orients[0] != '\0' )
strcpy(anor,MRILIB_orients) ;
} /* end of checking later volumes for compatibility */
/* destroy this data (we've sucked it dry) */
DESTROY_IMARR(anar) ;
} /* end of loop over ANALYZE files */
/*-- check geomparent, if present --*/
if( gset != NULL ){
if( DSET_NX(gset)!=nxan || DSET_NY(gset)!=nyan || DSET_NZ(gset)!=nzan ){
fprintf(stderr,"** geomparent and ANALYZE files have different dimensions!\n");
exit(1) ;
}
if( xorient >= 0 ){
fprintf(stderr,"++ WARNING: geomparent overrides -orient!\n") ;
}
xorient = gset->daxes->xxorient ;
yorient = gset->daxes->yyorient ;
zorient = gset->daxes->zzorient ;
if( use_zoff ){
fprintf(stderr,"++ WARNING: geomparent overrides -zorigin!\n") ;
}
use_xoff = use_yoff = use_zoff = 1 ;
xoff = gset->daxes->xxorg ;
yoff = gset->daxes->yyorg ;
zoff = gset->daxes->zzorg ;
dxan = gset->daxes->xxdel ;
dyan = gset->daxes->yydel ;
dzan = gset->daxes->zzdel ;
if( gset->taxis != NULL ){
TR = gset->taxis->ttdel ;
tunits = gset->taxis->units_type ;
}
DSET_delete(gset) ; /* delete to save memory */
} else { /* don't have geomparent, so check if other data is OK */
if( xorient < 0 ){
xorient = ORI_R2L_TYPE ;
yorient = ORI_A2P_TYPE ;
zorient = ORI_I2S_TYPE ;
fprintf(stderr,"++ WARNING: orientation defaults to RAI\n") ;
}
if( dxan <= 0.0 ){
dxan = dyan = dzan = 1.0 ;
fprintf(stderr,"++ WARNING: voxel size defaults to 1 mm\n") ;
}
if( ORIENT_sign[xorient] == '-' ) dxan = -dxan ;
if( ORIENT_sign[yorient] == '-' ) dyan = -dyan ;
if( ORIENT_sign[zorient] == '-' ) dzan = -dzan ;
} /* end of setup for new dataset parameters */
/*-- At last: create empty output dataset --*/
dset = EDIT_empty_copy(NULL) ;
nxyz.ijk[0] = nxan ; dxyz.xyz[0] = dxan ;
nxyz.ijk[1] = nyan ; dxyz.xyz[1] = dyan ;
nxyz.ijk[2] = nzan ; dxyz.xyz[2] = dzan ;
orixyz.ijk[0] = xorient ;
orixyz.ijk[1] = yorient ;
orixyz.ijk[2] = zorient ;
orgxyz.xyz[0] = (use_xoff) ? xoff : -0.5*(nxan-1)*dxan ;
orgxyz.xyz[1] = (use_yoff) ? yoff : -0.5*(nyan-1)*dyan ;
orgxyz.xyz[2] = (use_zoff) ? zoff : -0.5*(nzan-1)*dzan ;
EDIT_dset_items( dset ,
ADN_prefix , prefix ,
ADN_datum_all , an_datum ,
ADN_nxyz , nxyz ,
ADN_xyzdel , dxyz ,
ADN_xyzorg , orgxyz ,
ADN_xyzorient , orixyz ,
ADN_nvals , nvals ,
ADN_view_type , view_type ,
ADN_brick_fac , fac ,
ADN_none ) ;
/*-- select dataset type (3D+time or bucket) --*/
if( nvals == 1 && is_3dtime ){
is_3dtime = 0; is_abuc = 1;
fprintf(stderr,"++ WARNING: can't make a 3D+time dataset from 1 volume!\n") ;
}
if( !is_3dtime && !is_abuc && !is_fbuc ){
if( nvals > 1 ) is_3dtime = 1 ;
else is_abuc = 1 ;
}
if( is_3dtime ){
EDIT_dset_items( dset ,
ADN_ntt , nvals ,
ADN_ttorg , 0.0 ,
ADN_ttdel , TR ,
ADN_ttdur , 0.0 ,
ADN_tunits , tunits ,
ADN_type , HEAD_ANAT_TYPE ,
ADN_func_type, ANAT_EPI_TYPE ,
ADN_none ) ;
} else if( is_abuc ){
EDIT_dset_items( dset ,
ADN_type , HEAD_ANAT_TYPE ,
ADN_func_type, ANAT_BUCK_TYPE ,
ADN_none ) ;
} else if( is_fbuc ){
EDIT_dset_items( dset ,
ADN_type , HEAD_FUNC_TYPE ,
ADN_func_type, FUNC_BUCK_TYPE ,
ADN_none ) ;
}
/*-- make filename array and store it in dataset header --*/
flab = (char **) malloc(sizeof(char *)*nvals) ;
kk = 0 ;
for( ii=0 ; ii < nvals ; ii++ ){
jj = strlen( argv[iarg+ii] ) ; /* convert .hdr */
flab[ii] = strdup( argv[iarg+ii] ) ; /* filename to */
strcpy( flab[ii]+jj-3 , "img" ) ; /* .img name */
kk += (jj+2) ;
THD_store_datablock_label( dset->dblk , ii , flab[ii] ) ;
}
fatr = malloc(kk) ; fatr[0] = '\0' ; /* all filenames */
for( ii=0 ; ii < nvals ; ii++ ){ /* into one big */
strcat(fatr,flab[ii] ); strcat(fatr," "); /* string */
free(flab[ii]) ;
}
/*-- setting this attribute marks the dataset as being
stored by volumes, rather than all data in one .BRIK file --*/
THD_set_string_atr( dset->dblk , "VOLUME_FILENAMES" , fatr ) ;
free(fatr) ; free(flab) ;
/*-- set byte ordering flag --*/
jj = mri_short_order() ; /* order of this CPU */
if( an_swapped )
dset->dblk->diskptr->byte_order = REVERSE_ORDER(jj) ;
else
dset->dblk->diskptr->byte_order = jj ;
/*-- set history attribute --*/
tross_Make_History( "3dANALYZEtoAFNI" , argc,argv , dset ) ;
/*-- write dataset header --*/
THD_write_3dim_dataset( NULL,NULL , dset , False ) ;
fprintf(stderr,"++ Wrote dataset header %s\n",DSET_HEADNAME(dset)) ;
exit(0) ;
}
int main(int argc, char **argv)
{
static char FuncName[]={"3dSeg"};
SEG_OPTS *Opt=NULL;
char *atr=NULL;
float *mixfrac= NULL;
int i=0;
double ff;
SUMA_SEND_2AFNI SS2A;
SUMA_Boolean LocalHead = NOPE;
SUMA_STANDALONE_INIT;
SUMA_mainENTRY;
SUMAg_DOv = SUMA_Alloc_DisplayObject_Struct (SUMA_MAX_DISPLAYABLE_OBJECTS);
Opt = Seg_Default(argv, argc);
Opt = Seg_ParseInput (Opt,argv, argc);
Opt->hist = tross_commandline( FuncName , argc , argv ) ;
/* load the input data */
if (!(Opt->aset = Seg_load_dset( Opt->aset_name ))) {
SUMA_RETURN(1);
}
if (!Seg_CheckOpts(Opt)) {
SUMA_S_Err("Failed on option check");
SUMA_RETURN(1);
}
/* Load mask dataset */
if (Opt->mset_name) {
if (!strncasecmp(Opt->mset_name,"auto", 4)) {
byte *mm=NULL;
int j;
short *sb=NULL;
if (!(mm = THD_automask(Opt->aset))) {
SUMA_RETURN(1);
}
NEW_SHORTY(Opt->aset, DSET_NVALS(Opt->aset),
"automask.cp", Opt->mset);
sb = (short *)DSET_ARRAY(Opt->mset,0);
for (j=0; j<DSET_NVOX(Opt->mset); ++j) {
sb[j] = (short)mm[j];
}
free(mm); mm=NULL;
} else if (!(Opt->mset = Seg_load_dset( Opt->mset_name ))) {
SUMA_RETURN(1);
}
}
/* reference classes */
if (Opt->gold_name) {
if (!(Opt->gold = Seg_load_dset( Opt->gold_name ))) {
SUMA_RETURN(1);
}
}
if (Opt->gold_bias_name) {
if (!(Opt->gold_bias = Seg_load_dset( Opt->gold_bias_name ))) {
SUMA_RETURN(1);
}
}
if (!Opt->clss) {
SUMA_S_Err("Need -classes option");
SUMA_RETURN(1);
}
/* Talk ? */
if (Opt->ps->cs->talk_suma) {
Opt->ps->cs->istream = SUMA_BRAINWRAP_LINE;
Opt->ps->cs->afni_istream = SUMA_AFNI_STREAM_INDEX2;
if (!SUMA_SendToAfni (Opt->ps->cs, NULL, 0)) {
SUMA_SL_Err("Failed to initialize SUMA_SendToAfni");
Opt->ps->cs->afni_Send = NOPE;
Opt->ps->cs->Send = NOPE;
} else {
/* send in_vol to afni */
SUMA_SL_Note("Sending anat volume to AFNI");
SS2A.dset = Opt->aset; SS2A.at_sb=-1;
if (!SUMA_SendToAfni(Opt->ps->cs, &SS2A, 1)) {
SUMA_SL_Err("Failed to send volume to AFNI");
Opt->ps->cs->afni_Send = NOPE;
}
}
}
/* classified set ? */
if (Opt->this_cset_name) { /* user supplied initializer */
if (!(Opt->cset = Seg_load_dset( Opt->this_cset_name ))) {
SUMA_RETURN(1);
}
}
/* labeltable? */
if (Opt->labeltable_name) {
Dtable *vl_dtable=NULL;
char *labeltable_str=NULL;
int kk=0;
/* read the table */
if (!(labeltable_str = AFNI_suck_file( Opt->labeltable_name))) {
ERROR_exit("Failed to read %s", Opt->labeltable_name);
}
if (!(vl_dtable = Dtable_from_nimlstring(labeltable_str))) {
ERROR_exit("Could not parse labeltable");
}
CLASS_KEYS_FROM_LT(vl_dtable);
destroy_Dtable(vl_dtable); vl_dtable=NULL;
}
if (!Opt->keys) {
Dtable *vl_dtable=NULL;
if (Opt->cset && (vl_dtable = DSET_Label_Dtable(Opt->cset))) {
if (Opt->debug) SUMA_S_Note("Getting keys from -cset dataset");
/* try getting keys from cset */
CLASS_KEYS_FROM_LT(vl_dtable);
/* Do not delete vl_dtable, it is the same pointer in Opt->cset */
} else {
/* add default keys */
if (Opt->debug) SUMA_S_Note("Keys not available, assuming defaults");
Opt->keys = (int *)calloc(Opt->clss->num, sizeof(int));
for (i=0; i<Opt->clss->num; ++i) {
Opt->keys[i] = i+1;
}
}
}
/* Make sure you have no negative values and requesting bias field correction.
The implementation uses log() for this so the negative values would be
ill advised */
{
float amin, amax;
THD_subbrick_minmax(Opt->aset, 0, 1,&amin, &amax);
if (amin < 0 && Opt->bias_param > 0) {
SUMA_S_Err("Cannot use field bias correction on volumes with negative\n"
"values. Either turn off bias field estimation with -bias_fwhm 0.0\n"
"or shift the values of the input by something like:\n"
" 3dcalc -a %s -expr 'a+bool(a)*%d' -prefix SHIFTED\n"
"and rerun the segmentation on SHIFTED. Note the suggested shift\n"
"leaves zero values unchanged.",
DSET_HEADNAME(Opt->aset), (int)ceil(-amin+1.0));
exit(1);
}
}
/* Show the match between keys and classes */
if (Opt->debug > 1) {
SUMA_S_Note("Class-->key map");
SUMA_ShowClssKeys(Opt->clss->str, Opt->clss->num, Opt->keys);
}
if (Opt->clss->num < 2) {
if (Opt->debug <= 1) {
SUMA_S_Note("Class-->key map");
SUMA_ShowClssKeys(Opt->clss->str, Opt->clss->num, Opt->keys);
}
SUMA_S_Err("Less than 2 classes? I am out of here");
SUMA_RETURN(0);
}
/* Mask setup */
if (Opt->debug > 1) {
SUMA_S_Note("MaskSetup");
}
Opt->cmask = MaskSetup(Opt, Opt->aset, 1,
&(Opt->mset), &(Opt->cmask), Opt->dimcmask,
Opt->mask_bot, Opt->mask_top, &(Opt->cmask_count));
if (Opt->VoxDbg >= 0) {
SUMA_S_Note("DBG setup");
fprintf(Opt->VoxDbgOut, "Command:");
for (i=0; i<argc; ++i) {
fprintf(Opt->VoxDbgOut, "%s ", argv[i]);
}
fprintf(Opt->VoxDbgOut, "\nDebug info for voxel %d\n", Opt->VoxDbg);
}
Opt->cs = SUMA_New_Class_Stat(Opt->clss->str, Opt->clss->num,
Opt->keys, 3, NULL);
/* Load prob. of class given features */
if (Opt->priCgAname && strcmp(Opt->priCgAname, "INIT_MIXFRAC")) {
if (!(Opt->priCgA = Seg_load_dset(Opt->priCgAname))) {
SUMA_S_Errv("Failed to read priCgA %s\n", Opt->priCgAname);
SUMA_RETURN(1);
}
if (GRID_MISMATCH(Opt->priCgA, Opt->aset)) {
SUMA_S_Err("All input data must have same grid (-priCgA != -aset)");
SUMA_RETURN(1);
}
/* Make sure dset is properly formatted */
if (!SUMA_ShortizeProbDset(&Opt->priCgA,
Opt->cs,
Opt->cmask, Opt->cmask_count,
Opt, &Opt->priCgA)) {
SUMA_S_Errv("Failed to shortize priCgA %s\n", Opt->priCgAname);
SUMA_RETURN(1);
}
/* set the floor of the input dset */
if (0) {
SUMA_S_Note("Setting probability floor, USEFULNESS NOT TESTED...");
if (!set_p_floor(Opt->priCgA, 0.1, Opt->cmask)) {
SUMA_S_Errv("Failed to set p floor for priCgA %s\n",
Opt->priCgAname);
SUMA_RETURN(1);
}
}
} else {
/* uniform probability */
}
/* Load prob. of class given location */
if (Opt->priCgLname && strcmp(Opt->priCgLname, "INIT_MIXFRAC")) {
if (!(Opt->priCgL = Seg_load_dset(Opt->priCgLname))) {
SUMA_S_Errv("Failed to read priCgL %s\n", Opt->priCgLname);
SUMA_RETURN(1);
}
if (GRID_MISMATCH(Opt->priCgL, Opt->aset)) {
SUMA_S_Err("All input data must have same grid (-priCgL != -aset)");
SUMA_RETURN(1);
}
/* Make sure dset is properly formatted */
if (!SUMA_ShortizeProbDset(&Opt->priCgL,
Opt->cs,
Opt->cmask, Opt->cmask_count,
Opt, &Opt->priCgL)) {
SUMA_S_Errv("Failed to shortize priCgL %s\n", Opt->priCgLname);
SUMA_RETURN(1);
}
} else {
/* uniform probability */
}
/* check on weights of priors */
if (Opt->wA >= 0.0 && Opt->wL < 0.0) {
Opt->wL = 1.0 - Opt->wA;
} else if (Opt->wL >= 0.0 && Opt->wA < 0.0) {
Opt->wA = 1.0 - Opt->wL;
} else if (Opt->wA < 0.0 && Opt->wL < 0.0) { /* defaults */
Opt->wA = 0.5; Opt->wL = 0.5;
}
ff = Opt->wA+Opt->wL;
Opt->wA = Opt->wA/ff; Opt->wL = Opt->wL/ff;
if (!Opt->cset) {
if (!SUMA_SegInitCset(Opt->aset,
&Opt->cset,
Opt->cmask, Opt->cmask_count,
Opt->mixopt,
Opt->cs,
Opt)) {
SUMA_S_Err("Failed to get initializer");
SUMA_RETURN(1);
}
}
if (Opt->debug > 1) {
SUMA_Seg_Write_Dset(Opt->proot, "classes_init", Opt->cset,
-1, Opt->hist);
}
/* Now add the 'OTHER' class if needed */
if (Opt->Other) {
if (!SUMA_AddOther( Opt->clss, &Opt->keys,
Opt->cmask, Opt->cmask_count,
Opt->cset, Opt->pstCgALL,
Opt->priCgA, Opt->priCgL,
Opt->cs)) {
SUMA_S_Err("Failed to add other");
SUMA_RETURN(0);
}
}
/* store mixfrac in class stats */
for (i=0;i<Opt->cs->N_label; ++i) {
if ((ff = SUMA_mixopt_2_mixfrac(Opt->mixopt, Opt->cs->label[i],
Opt->cs->keys[i], Opt->cs->N_label,
Opt->cmask, Opt->cset))<0.0) {
SUMA_S_Errv("Can't get mixfrac for %s\n", Opt->mixopt);
SUMA_RETURN(1);
}
SUMA_set_Stat(Opt->cs, Opt->cs->label[i], "init.mix", ff);
SUMA_set_Stat(Opt->cs, Opt->cs->label[i], "mix", ff);
}
/* Now call the workhorse */
if (!SUMA_SegEngine(Opt)) {
SUMA_S_Err("Failed in SUMA_SegEngine");
exit(1);
}
/* write output */
if (Opt->Bset && !Opt->this_fset_name) {
tross_Append_History(Opt->Bset, Opt->hist);
SUMA_Seg_Write_Dset(Opt->proot, "BiasField", /* DSET_PREFIX(Opt->Bset) */
Opt->Bset, -1, Opt->hist);
}
if (Opt->xset && !Opt->this_xset_name) {
AFNI_FEED(Opt->ps->cs, "BiasCorrect", -1, Opt->xset);
SUMA_Seg_Write_Dset(Opt->proot, "AnatUB", /* DSET_PREFIX(Opt->xset)*/
Opt->xset, -1, Opt->hist);
}
if (Opt->cset) {
SUMA_Seg_Write_Dset(Opt->proot, "Classes", /* Opt->crefix */
Opt->cset, -1, Opt->hist);
AFNI_FEED(Opt->ps->cs, "FinalClasses", -1, Opt->cset);
}
if (Opt->pstCgALL) {
SUMA_Seg_Write_Dset(Opt->proot, "Posterior", /* Opt->prefix */
Opt->pstCgALL, -1, Opt->hist);
AFNI_FEED(Opt->ps->cs, "pstCgALL-final", -1, Opt->pstCgALL);
}
if (Opt->aset) {
SUMA_Seg_Write_Dset(Opt->proot, "Anat",
Opt->aset, -1, Opt->hist);
}
if (Opt->debug) SUMA_S_Note("Writing Unmodulated output");
if (!(SUMA_pst_C_giv_ALL(Opt->xset,
Opt->cmask, Opt->cmask_count,
Opt->cs,
NULL, NULL,
Opt->B, Opt->T, 0,
&Opt->pstCgALL))) {
SUMA_S_Err("Failed in SUMA_pst_C_giv_ALL unmodulated");
SUMA_RETURN(1);
}
SUMA_Seg_Write_Dset(Opt->proot, "Unmodulated.p",
Opt->pstCgALL, -1, Opt->hist);
if (!(SUMA_assign_classes( Opt->pstCgALL, Opt->cs,
Opt->cmask, &Opt->cset))) {
SUMA_S_Err("Failed in assign_classes");
SUMA_RETURN(1);
}
SUMA_Seg_Write_Dset(Opt->proot, "Unmodulated.c",
Opt->cset, -1, Opt->hist);
/* all done, free */
Opt = free_SegOpts(Opt);
PRINT_COMPILE_DATE ;
SUMA_RETURN(0);
}
int main( int argc , char * argv[] )
{
int ninp , ids , nv , iv,jv,kv , ivout , new_nvals , have_fdr = 0, nfdr = 0 ;
THD_3dim_dataset * new_dset=NULL , * dset ;
char buf[256] ;
double angle;
/*----- identify program -----*/
#if 0
printf ("\n\nProgram %s \n", PROGRAM_NAME);
printf ("Last revision: %s \n\n", LAST_MOD_DATE);
#endif
/*** read input options ***/
mainENTRY("3dbucket main"); machdep(); PRINT_VERSION("3dbucket") ;
set_obliquity_report(0); /* silence obliquity */
/*-- 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 ; }
}
AFNI_logger("3dbucket",argc,argv) ;
BUCK_read_opts( argc , argv ) ;
/*** create new dataset (empty) ***/
ninp = BUCK_dsar->num ;
if( ninp < 1 ){
fprintf(stderr,"*** No input datasets?\n") ; exit(1) ;
}
new_nvals = 0 ;
for( ids=0 ; ids < ninp ; ids++ ) new_nvals += NSUBV(ids) ;
if( BUCK_verb ) printf("-verb: output will have %d sub-bricks\n",new_nvals) ;
new_dset = EDIT_empty_copy( DSUB(0) ) ;
/* 23 May 2005: check for axis consistency */
/* 06 Feb 2008: and see if there are fdrcurves to perpetuate */
if( DSUB(0)->dblk->brick_fdrcurve ) have_fdr = 1 ;
for( iv=1 ; iv < ninp ; iv++ ){
if( !EQUIV_DATAXES(new_dset->daxes,DSUB(iv)->daxes) )
fprintf(stderr,"++ WARNING: %s grid mismatch with %s\n",
DSET_BRIKNAME(DSUB(0)) , DSET_BRIKNAME(DSUB(iv)) ) ;
if( DSUB(iv)->dblk->brick_fdrcurve ) have_fdr = 1 ;
angle = dset_obliquity_angle_diff(new_dset, DSUB(iv), -1.0);
if (angle > 0.0) {
WARNING_message(
"dataset %s has an obliquity difference of %f degress with %s\n",
new_dset ,
angle, DSUB(iv) );
}
}
/* if( ninp == 1 ) */ tross_Copy_History( DSUB(0) , new_dset ) ;
tross_Make_History( "3dbucket" , argc,argv , new_dset ) ;
EDIT_dset_items( new_dset ,
ADN_prefix , BUCK_output_prefix ,
ADN_directory_name, BUCK_session ,
ADN_type , BUCK_type ,
ADN_func_type , ISANATTYPE(BUCK_type) ? ANAT_BUCK_TYPE
: FUNC_BUCK_TYPE,
ADN_ntt , 0 ,
ADN_nvals , new_nvals ,
ADN_none ) ;
/* can't re-write existing dataset, unless glueing is used */
if (! BUCK_glue){
if( THD_deathcon() && THD_is_file(DSET_HEADNAME(new_dset)) ){
fprintf(stderr,"*** Fatal error: file %s already exists!\n",
DSET_HEADNAME(new_dset) ) ;
exit(1) ;
}
} else { /* if glueing is used, make the 'new'
dataset have the same idcode as the old one */
new_dset->idcode = DSUB(0) -> idcode ; /* copy the struct */
}
THD_force_malloc_type( new_dset->dblk , DATABLOCK_MEM_MALLOC ) ;
/* if there are fdr curves, allocate space 06 Feb 2008 [rickr] */
if( have_fdr ){
new_dset->dblk->brick_fdrcurve = (floatvec **)calloc(sizeof(floatvec *),
new_nvals) ;
if( !new_dset->dblk->brick_fdrcurve ){
fprintf(stderr,"** failed to alloc %d fdrcurves\n",new_nvals);
exit(1);
}
if( BUCK_verb ) printf("-verb: adding fdrcurve list\n");
new_dset->dblk->brick_mdfcurve = (floatvec **)calloc(sizeof(floatvec *),
/* 22 Oct 2008 */ new_nvals) ;
}
/*** loop over input datasets ***/
if( ninp > 1 ) myXtFree( new_dset->keywords ) ;
ivout = 0 ;
for( ids=0 ; ids < ninp ; ids++ ){
dset = DSUB(ids) ;
nv = NSUBV(ids) ;
if( ! BUCK_dry ){
DSET_load(dset) ; CHECK_LOAD_ERROR(dset) ;
}
/** loop over sub-bricks to output **/
for( iv=0 ; iv < nv ; iv++ ){
jv = SUBV(ids,iv) ; /* which sub-brick to use */
if( ! BUCK_dry ){
EDIT_substitute_brick( new_dset , ivout ,
DSET_BRICK_TYPE(dset,jv) , DSET_ARRAY(dset,jv) ) ;
/*----- preserve label when one exists --- Modified March 2010 ZSS*/
if (DSET_HAS_LABEL(dset, jv) )
sprintf (buf, "%s", DSET_BRICK_LABEL(dset,jv));
else
sprintf(buf,"%.12s[%d]",DSET_PREFIX(dset),jv) ;
EDIT_dset_items( new_dset , ADN_brick_label_one+ivout, buf , ADN_none ) ;
#if 0
sprintf(buf,"%s[%d]",DSET_FILECODE(dset),jv) ;
EDIT_dset_items(
new_dset, ADN_brick_keywords_replace_one+ivout, buf, ADN_none ) ;
#endif
EDIT_dset_items(
new_dset ,
ADN_brick_fac_one +ivout, DSET_BRICK_FACTOR(dset,jv),
#if 0
ADN_brick_keywords_append_one+ivout, DSET_BRICK_KEYWORDS(dset,jv) ,
#endif
ADN_none ) ;
/** possibly write statistical parameters for this sub-brick **/
kv = DSET_BRICK_STATCODE(dset,jv) ;
if( FUNC_IS_STAT(kv) ){ /* input sub-brick has stat params */
int npar = FUNC_need_stat_aux[kv] , lv ;
float * par = (float *) malloc( sizeof(float) * (npar+2) ) ;
float * sax = DSET_BRICK_STATAUX(dset,jv) ;
par[0] = kv ;
par[1] = npar ;
for( lv=0 ; lv < npar ; lv++ )
par[lv+2] = (sax != NULL) ? sax[lv] : 0.0 ;
EDIT_dset_items(new_dset ,
ADN_brick_stataux_one+ivout , par ,
ADN_none ) ;
free(par) ;
/* 2: if the input dataset has statistical parameters */
} else if( ISFUNC(dset) && /* dset has stat */
FUNC_IS_STAT(dset->func_type) && /* params */
jv == FUNC_ival_thr[dset->func_type] ){ /* thr sub-brick */
int npar , lv ;
float * par , * sax ;
kv = dset->func_type ;
npar = FUNC_need_stat_aux[kv] ;
par = (float *) malloc( sizeof(float) * (npar+2) ) ;
sax = dset->stat_aux ;
par[0] = kv ;
par[1] = npar ;
for( lv=0 ; lv < npar ; lv++ )
par[lv+2] = (sax != NULL) ? sax[lv] : 0.0 ;
EDIT_dset_items(new_dset ,
ADN_brick_stataux_one+ivout , par ,
ADN_none ) ;
free(par) ;
}
/** append any fdrcurve **/
if( have_fdr ){
/* fixed iv->jv (ick!), noticed by dglen 16 Mar 2010 [rickr] */
if(dset->dblk->brick_fdrcurve && dset->dblk->brick_fdrcurve[jv]){
COPY_floatvec(new_dset->dblk->brick_fdrcurve[ivout],
dset->dblk->brick_fdrcurve[jv]) ;
nfdr++;
}
else new_dset->dblk->brick_fdrcurve[ivout] = NULL ;
if(dset->dblk->brick_mdfcurve && dset->dblk->brick_mdfcurve[jv]){
COPY_floatvec(new_dset->dblk->brick_mdfcurve[ivout],
dset->dblk->brick_mdfcurve[jv]) ;
}
else new_dset->dblk->brick_mdfcurve[ivout] = NULL ;
}
/** print a message? **/
if( BUCK_verb ) printf("-verb: copied %s[%d] into %s[%d]\n" ,
DSET_FILECODE(dset) , jv ,
DSET_FILECODE(new_dset) , ivout ) ;
} else {
printf("-dry: would copy %s[%d] into %s[%d]\n" ,
DSET_FILECODE(dset) , jv ,
DSET_FILECODE(new_dset) , ivout ) ;
}
ivout++ ;
}
/** loop over all bricks in input dataset and
unload them if they aren't going into the output
(not required, but is done to economize on memory) **/
if( ! BUCK_dry && nv < DSET_NVALS(dset) ){
for( kv=0 ; kv < DSET_NVALS(dset) ; kv++ ){ /* all input sub-bricks */
for( iv=0 ; iv < nv ; iv++ ){ /* all output sub-bricks */
jv = SUBV(ids,iv) ;
if( jv == kv ) break ; /* input matches output */
}
if( iv == nv ){
mri_free( DSET_BRICK(dset,kv) ) ;
#if 0
if( BUCK_verb ) printf("-verb: unloaded unused %s[%d]\n" ,
DSET_FILECODE(dset) , kv ) ;
#endif
}
}
}
} /* end of loop over input datasets */
if( ! BUCK_dry ){
if( BUCK_verb ){
if( have_fdr ) fprintf(stderr,"-verb: added %d of %d fdr curves\n",
nfdr, new_nvals);
fprintf(stderr,"-verb: loading statistics\n") ;
}
THD_load_statistics( new_dset ) ;
if( BUCK_glue ) putenv("AFNI_DECONFLICT=OVERWRITE") ;
if( BUCK_glue && BUCK_ccode >= 0 )
THD_set_write_compression(BUCK_ccode) ; /* 16 Mar 2010 */
THD_write_3dim_dataset( NULL,NULL , new_dset , True ) ;
if( BUCK_verb ) fprintf(stderr,"-verb: wrote output: %s\n",DSET_BRIKNAME(new_dset)) ;
}
exit(0) ;
}
int main( int argc , char *argv[] )
{
THD_3dim_dataset *dset , *oset=NULL , *tset=NULL ;
int nvals , iv , nxyz , ii,jj,kk , iarg , kz,kzold ;
float cut1=2.5,cut2=4.0 , sq2p,sfac , fq ;
MRI_IMAGE *flim ;
char *prefix="despike" , *tprefix=NULL ;
int corder=-1 , nref , ignore=0 , polort=2 , nuse , nomask=0 ;
int nspike, nbig, nproc ;
float **ref ;
float c21,ic21 , pspike,pbig ;
short *sar , *qar ;
byte *tar , *mask=NULL ;
float *zar , *yar ;
int datum ;
int localedit=0 ; /* 04 Apr 2007 */
int verb=1 ;
int do_NEW = 0 ; /* 29 Nov 2013 */
MRI_IMAGE *NEW_psinv=NULL ;
int dilate = 4 ; /* 04 Dec 2013 */
int ctim = 0 ;
/*----- Read command line -----*/
AFNI_SETUP_OMP(0) ; /* 24 Jun 2013 */
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
printf("Usage: 3dDespike [options] dataset\n"
"Removes 'spikes' from the 3D+time input dataset and writes\n"
"a new dataset with the spike values replaced by something\n"
"more pleasing to the eye.\n"
"\n"
"Method:\n"
" * L1 fit a smooth-ish curve to each voxel time series\n"
" [see -corder option for description of the curve]\n"
" [see -NEW option for a different & faster fitting method]\n"
" * Compute the MAD of the difference between the curve and\n"
" the data time series (the residuals).\n"
" * Estimate the standard deviation 'sigma' of the residuals\n"
" as sqrt(PI/2)*MAD.\n"
" * For each voxel value, define s = (value-curve)/sigma.\n"
" * Values with s > c1 are replaced with a value that yields\n"
" a modified s' = c1+(c2-c1)*tanh((s-c1)/(c2-c1)).\n"
" * c1 is the threshold value of s for a 'spike' [default c1=2.5].\n"
" * c2 is the upper range of the allowed deviation from the curve:\n"
" s=[c1..infinity) is mapped to s'=[c1..c2) [default c2=4].\n"
"\n"
"Options:\n"
" -ignore I = Ignore the first I points in the time series:\n"
" these values will just be copied to the\n"
" output dataset [default I=0].\n"
" -corder L = Set the curve fit order to L:\n"
" the curve that is fit to voxel data v(t) is\n"
"\n"
" k=L [ (2*PI*k*t) (2*PI*k*t) ]\n"
" f(t) = a+b*t+c*t*t + SUM [ d * sin(--------) + e * cos(--------) ]\n"
" k=1 [ k ( T ) k ( T ) ]\n"
"\n"
" where T = duration of time series;\n"
" the a,b,c,d,e parameters are chosen to minimize\n"
" the sum over t of |v(t)-f(t)| (L1 regression);\n"
" this type of fitting is is insensitive to large\n"
" spikes in the data. The default value of L is\n"
" NT/30, where NT = number of time points.\n"
"\n"
" -cut c1 c2 = Alter default values for the spike cut values\n"
" [default c1=2.5, c2=4.0].\n"
" -prefix pp = Save de-spiked dataset with prefix 'pp'\n"
" [default pp='despike']\n"
" -ssave ttt = Save 'spikiness' measure s for each voxel into a\n"
" 3D+time dataset with prefix 'ttt' [default=no save]\n"
" -nomask = Process all voxels\n"
" [default=use a mask of high-intensity voxels, ]\n"
" [as created via '3dAutomask -dilate 4 dataset'].\n"
" -dilate nd = Dilate 'nd' times (as in 3dAutomask). The default\n"
" value of 'nd' is 4.\n"
" -q[uiet] = Don't print '++' informational messages.\n"
"\n"
" -localedit = Change the editing process to the following:\n"
" If a voxel |s| value is >= c2, then replace\n"
" the voxel value with the average of the two\n"
" nearest non-spike (|s| < c2) values; the first\n"
" one previous and the first one after.\n"
" Note that the c1 cut value is not used here.\n"
"\n"
" -NEW = Use the 'new' method for computing the fit, which\n"
" should be faster than the L1 method for long time\n"
" series (200+ time points); however, the results\n"
" are similar but NOT identical. [29 Nov 2013]\n"
" * You can also make the program use the 'new'\n"
" method by setting the environment variable\n"
" AFNI_3dDespike_NEW\n"
" to the value YES; as in\n"
" setenv AFNI_3dDespike_NEW YES (csh)\n"
" export AFNI_3dDespike_NEW=YES (bash)\n"
" * If this variable is set to YES, you can turn off\n"
" the '-NEW' processing by using the '-OLD' option.\n"
" -->>* For time series more than 500 points long, the\n"
" '-OLD' algorithm is tremendously slow. You should\n"
" use the '-NEW' algorith in such cases.\n"
" ** At some indeterminate point in the future, the '-NEW'\n"
" method will become the default!\n"
" -->>* As of 29 Sep 2016, '-NEW' is the default if there\n"
" is more than 500 points in the time series dataset.\n"
"\n"
" -NEW25 = A slightly more aggressive despiking approach than\n"
" the '-NEW' method.\n"
"\n"
"Caveats:\n"
"* Despiking may interfere with image registration, since head\n"
" movement may produce 'spikes' at the edge of the brain, and\n"
" this information would be used in the registration process.\n"
" This possibility has not been explored or calibrated.\n"
"* [LATER] Actually, it seems like the registration problem\n"
" does NOT happen, and in fact, despiking seems to help!\n"
"* Check your data visually before and after despiking and\n"
" registration!\n"
" [Hint: open 2 AFNI controllers, and turn Time Lock on.]\n"
) ;
PRINT_AFNI_OMP_USAGE("3dDespike",NULL) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
/** AFNI package setup and logging **/
mainENTRY("3dDespike main"); machdep(); AFNI_logger("3dDespike",argc,argv);
PRINT_VERSION("3dDespike") ; AUTHOR("RW Cox") ;
/** parse options **/
if( AFNI_yesenv("AFNI_3dDespike_NEW") ) do_NEW = 1 ; /* 29 Nov 2013 */
iarg = 1 ;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strncmp(argv[iarg],"-q",2) == 0 ){ /* 04 Apr 2007 */
verb = 0 ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-v",2) == 0 ){
verb++ ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-NEW") == 0 ){ /* 29 Nov 2013 */
do_NEW = 1 ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-NEW25") == 0 ){ /* 29 Sep 2016 */
do_NEW = 1 ; use_des25 = 1 ; cut1 = 2.5f ; cut2 = 3.2f ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-OLD") == 0 ){
do_NEW = 0 ; iarg++ ; continue ;
}
/** -localedit **/
if( strcmp(argv[iarg],"-localedit") == 0 ){ /* 04 Apr 2007 */
localedit = 1 ; iarg++ ; continue ;
}
/** don't use masking **/
if( strcmp(argv[iarg],"-nomask") == 0 ){
nomask = 1 ; iarg++ ; continue ;
}
/** dilation count [04 Dec 2013] **/
if( strcmp(argv[iarg],"-dilate") == 0 ){
dilate = (int)strtod(argv[++iarg],NULL) ;
if( dilate <= 0 ) dilate = 1 ;
else if( dilate > 99 ) dilate = 99 ;
iarg++ ; continue ;
}
/** output dataset prefix **/
if( strcmp(argv[iarg],"-prefix") == 0 ){
prefix = argv[++iarg] ;
if( !THD_filename_ok(prefix) ) ERROR_exit("-prefix is not good");
iarg++ ; continue ;
}
/** ratio dataset prefix **/
if( strcmp(argv[iarg],"-ssave") == 0 ){
tprefix = argv[++iarg] ;
if( !THD_filename_ok(tprefix) ) ERROR_exit("-ssave prefix is not good");
iarg++ ; continue ;
}
/** trigonometric polynomial order **/
if( strcmp(argv[iarg],"-corder") == 0 ){
corder = strtol( argv[++iarg] , NULL , 10 ) ;
if( corder < 0 ) ERROR_exit("Illegal value of -corder");
iarg++ ; continue ;
}
/** how much to ignore at start **/
if( strcmp(argv[iarg],"-ignore") == 0 ){
ignore = strtol( argv[++iarg] , NULL , 10 ) ;
if( ignore < 0 ) ERROR_exit("Illegal value of -ignore");
iarg++ ; continue ;
}
/** thresholds for s ratio **/
if( strcmp(argv[iarg],"-cut") == 0 ){
cut1 = strtod( argv[++iarg] , NULL ) ;
cut2 = strtod( argv[++iarg] , NULL ) ;
if( cut1 < 1.0 || cut2 < cut1+0.5 )
ERROR_exit("Illegal values after -cut");
iarg++ ; continue ;
}
ERROR_exit("Unknown option: %s",argv[iarg]) ;
}
c21 = cut2-cut1 ; ic21 = 1.0/c21 ;
/*----- read input dataset -----*/
if( iarg >= argc ) ERROR_exit("No input dataset!!??");
dset = THD_open_dataset( argv[iarg] ) ;
CHECK_OPEN_ERROR(dset,argv[iarg]) ;
datum = DSET_BRICK_TYPE(dset,0) ;
if( (datum != MRI_short && datum != MRI_float) || !DSET_datum_constant(dset) )
ERROR_exit("Can't process non-short, non-float dataset!") ;
if( verb ) INFO_message("Input data type = %s\n",MRI_TYPE_name[datum]) ;
nvals = DSET_NUM_TIMES(dset) ; nuse = nvals - ignore ;
if( nuse < 15 )
ERROR_exit("Can't use dataset with < 15 time points per voxel!") ;
if( nuse > 500 && !do_NEW ){
INFO_message("Switching to '-NEW' method since number of time points = %d > 500",nuse) ;
do_NEW = 1 ;
}
if( use_des25 && nuse < 99 ) use_des25 = 0 ;
if( verb ) INFO_message("ignoring first %d time points, using last %d",ignore,nuse);
if( corder > 0 && 4*corder+2 > nuse ){
ERROR_exit("-corder %d is too big for NT=%d",corder,nvals) ;
} else if( corder < 0 ){
corder = rint(nuse/30.0) ; if( corder > 50 && !do_NEW ) corder = 50 ;
if( verb ) INFO_message("using %d time points => -corder %d",nuse,corder) ;
} else {
if( verb ) INFO_message("-corder %d set from command line",corder) ;
}
nxyz = DSET_NVOX(dset) ;
if( verb ) INFO_message("Loading dataset %s",argv[iarg]) ;
DSET_load(dset) ; CHECK_LOAD_ERROR(dset) ;
/*-- create automask --*/
if( !nomask ){
mask = THD_automask( dset ) ;
if( verb ){
ii = THD_countmask( DSET_NVOX(dset) , mask ) ;
INFO_message("%d voxels in the automask [out of %d in dataset]",ii,DSET_NVOX(dset)) ;
}
for( ii=0 ; ii < dilate ; ii++ )
THD_mask_dilate( DSET_NX(dset), DSET_NY(dset), DSET_NZ(dset), mask, 3 ) ;
if( verb ){
ii = THD_countmask( DSET_NVOX(dset) , mask ) ;
INFO_message("%d voxels in the dilated automask [out of %d in dataset]",ii,DSET_NVOX(dset)) ;
}
} else {
if( verb ) INFO_message("processing all %d voxels in dataset",DSET_NVOX(dset)) ;
}
/*-- create empty despiked dataset --*/
oset = EDIT_empty_copy( dset ) ;
EDIT_dset_items( oset ,
ADN_prefix , prefix ,
ADN_brick_fac , NULL ,
ADN_datum_all , datum ,
ADN_none ) ;
if( THD_deathcon() && THD_is_file(DSET_HEADNAME(oset)) )
ERROR_exit("output dataset already exists: %s",DSET_HEADNAME(oset));
tross_Copy_History( oset , dset ) ;
tross_Make_History( "3dDespike" , argc , argv , oset ) ;
/* create bricks (will be filled with zeros) */
for( iv=0 ; iv < nvals ; iv++ )
EDIT_substitute_brick( oset , iv , datum , NULL ) ;
/* copy the ignored bricks */
switch( datum ){
case MRI_short:
for( iv=0 ; iv < ignore ; iv++ ){
sar = DSET_ARRAY(oset,iv) ;
qar = DSET_ARRAY(dset,iv) ;
memcpy( sar , qar , DSET_BRICK_BYTES(dset,iv) ) ;
DSET_unload_one(dset,iv) ;
}
break ;
case MRI_float:
for( iv=0 ; iv < ignore ; iv++ ){
zar = DSET_ARRAY(oset,iv) ;
yar = DSET_ARRAY(dset,iv) ;
memcpy( zar , yar , DSET_BRICK_BYTES(dset,iv) ) ;
DSET_unload_one(dset,iv) ;
}
break ;
}
/*-- setup to save a threshold statistic dataset, if desired --*/
if( tprefix != NULL ){
float *fac ;
tset = EDIT_empty_copy( dset ) ;
fac = (float *) malloc( sizeof(float) * nvals ) ;
for( ii=0 ; ii < nvals ; ii++ ) fac[ii] = TFAC ;
EDIT_dset_items( tset ,
ADN_prefix , tprefix ,
ADN_brick_fac , fac ,
ADN_datum_all , MRI_byte ,
ADN_func_type , FUNC_FIM_TYPE ,
ADN_none ) ;
free(fac) ;
tross_Copy_History( tset , dset ) ;
tross_Make_History( "3dDespike" , argc , argv , tset ) ;
#if 0
if( THD_is_file(DSET_HEADNAME(tset)) )
ERROR_exit("-ssave dataset already exists");
#endif
tross_Copy_History( tset , dset ) ;
tross_Make_History( "3dDespike" , argc , argv , tset ) ;
for( iv=0 ; iv < nvals ; iv++ )
EDIT_substitute_brick( tset , iv , MRI_byte , NULL ) ;
}
/*-- setup to find spikes --*/
sq2p = sqrt(0.5*PI) ;
sfac = sq2p / 1.4826f ;
/* make ref functions */
nref = 2*corder+3 ;
ref = (float **) malloc( sizeof(float *) * nref ) ;
for( jj=0 ; jj < nref ; jj++ )
ref[jj] = (float *) malloc( sizeof(float) * nuse ) ;
/* r(t) = 1 */
for( iv=0 ; iv < nuse ; iv++ ) ref[0][iv] = 1.0 ;
jj = 1 ;
/* r(t) = t - tmid */
{ float tm = 0.5 * (nuse-1.0) ; float fac = 2.0 / nuse ;
for( iv=0 ; iv < nuse ; iv++ ) ref[1][iv] = (iv-tm)*fac ;
jj = 2 ;
/* r(t) = (t-tmid)**jj */
for( ; jj <= polort ; jj++ )
for( iv=0 ; iv < nuse ; iv++ )
ref[jj][iv] = pow( (iv-tm)*fac , (double)jj ) ;
}
for( kk=1 ; kk <= corder ; kk++ ){
fq = (2.0*PI*kk)/nuse ;
/* r(t) = sin(2*PI*k*t/N) */
for( iv=0 ; iv < nuse ; iv++ )
ref[jj][iv] = sin(fq*iv) ;
jj++ ;
/* r(t) = cos(2*PI*k*t/N) */
for( iv=0 ; iv < nuse ; iv++ )
ref[jj][iv] = cos(fq*iv) ;
jj++ ;
}
/****** setup for the NEW solution method [29 Nov 2013] ******/
if( do_NEW ){
NEW_psinv = DES_get_psinv(nuse,nref,ref) ;
INFO_message("Procesing time series with NEW model fit algorithm") ;
} else {
INFO_message("Procesing time series with OLD model fit algorithm") ;
}
/*--- loop over voxels and do work ---*/
#define Laplace_t2p(val) ( 1.0 - nifti_stat2cdf( (val), 15, 0.0, 1.4427 , 0.0 ) )
if( verb ){
if( !localedit ){
INFO_message("smash edit thresholds: %.1f .. %.1f MADs",cut1*sq2p,cut2*sq2p) ;
ININFO_message(" [ %.3f%% .. %.3f%% of normal distribution]",
200.0*qg(cut1*sfac) , 200.0*qg(cut2*sfac) ) ;
ININFO_message(" [ %.3f%% .. %.3f%% of Laplace distribution]" ,
100.0*Laplace_t2p(cut1) , 100.0*Laplace_t2p(cut2) ) ;
} else {
INFO_message("local edit threshold: %.1f MADS",cut2*sq2p) ;
ININFO_message(" [ %.3f%% of normal distribution]",
200.0*qg(cut2*sfac) ) ;
ININFO_message(" [ %.3f%% of Laplace distribution]",
100.0*Laplace_t2p(cut1) ) ;
}
INFO_message("%d slices to process",DSET_NZ(dset)) ;
}
kzold = -1 ;
nspike = 0 ; nbig = 0 ; nproc = 0 ; ctim = NI_clock_time() ;
AFNI_OMP_START ;
#pragma omp parallel if( nxyz > 6666 )
{ int ii , iv , iu , id , jj ;
float *far , *dar , *var , *fitar , *ssp , *fit , *zar ;
short *sar , *qar ; byte *tar ;
float fsig , fq , cls , snew , val ;
float *NEW_wks=NULL ;
#pragma omp critical (DESPIKE_malloc)
{ far = (float *) malloc( sizeof(float) * nvals ) ;
dar = (float *) malloc( sizeof(float) * nvals ) ;
var = (float *) malloc( sizeof(float) * nvals ) ;
fitar = (float *) malloc( sizeof(float) * nvals ) ;
ssp = (float *) malloc( sizeof(float) * nvals ) ;
fit = (float *) malloc( sizeof(float) * nref ) ;
if( do_NEW ) NEW_wks = (float *)malloc(sizeof(float)*DES_workspace_size(nuse,nref)) ;
}
#ifdef USE_OMP
INFO_message("start OpenMP thread #%d",omp_get_thread_num()) ;
#endif
#pragma omp for
for( ii=0 ; ii < nxyz ; ii++ ){ /* ii = voxel index */
if( mask != NULL && mask[ii] == 0 ) continue ; /* skip this voxel */
#ifndef USE_OMP
kz = DSET_index_to_kz(dset,ii) ; /* starting a new slice */
if( kz != kzold ){
if( verb ){
fprintf(stderr, "++ start slice %2d",kz ) ;
if( nproc > 0 ){
pspike = (100.0*nspike)/nproc ;
pbig = (100.0*nbig )/nproc ;
fprintf(stderr,
"; so far %d data points, %d edits [%.3f%%], %d big edits [%.3f%%]",
nproc,nspike,pspike,nbig,pbig ) ;
}
fprintf(stderr,"\n") ;
}
kzold = kz ;
}
#else
if( verb && ii % 2345 == 1234 ) fprintf(stderr,".") ;
#endif
/*** extract ii-th time series into far[] ***/
switch( datum ){
case MRI_short:
for( iv=0 ; iv < nuse ; iv++ ){
qar = DSET_ARRAY(dset,iv+ignore) ; /* skip ignored data */
far[iv] = (float)qar[ii] ;
}
break ;
case MRI_float:
for( iv=0 ; iv < nuse ; iv++ ){
zar = DSET_ARRAY(dset,iv+ignore) ;
far[iv] = zar[ii] ;
}
break ;
}
AAmemcpy(dar,far,sizeof(float)*nuse) ; /* copy time series into dar[] */
/*** solve for L1 fit ***/
if( do_NEW )
cls = DES_solve( NEW_psinv , far , fit , NEW_wks ) ; /* 29 Nov 2013 */
else
cls = cl1_solve( nuse , nref , far , ref , fit,0 ) ; /* the slow part */
if( cls < 0.0f ){ /* fit failed! */
#if 0
fprintf(stderr,"curve fit fails at voxel %d %d %d\n",
DSET_index_to_ix(dset,ii) ,
DSET_index_to_jy(dset,ii) ,
DSET_index_to_kz(dset,ii) ) ;
#endif
continue ; /* skip this voxel */
}
for( iv=0 ; iv < nuse ; iv++ ){ /* detrend */
val = fit[0]
+ fit[1]*ref[1][iv] /* quadratic part of curve fit */
+ fit[2]*ref[2][iv] ;
for( jj=3 ; jj < nref ; jj++ ) /* rest of curve fit */
val += fit[jj] * ref[jj][iv] ;
fitar[iv] = val ; /* save curve fit value */
var[iv] = dar[iv]-val ; /* remove fitted value = resid */
far[iv] = fabsf(var[iv]) ; /* abs value of resid */
}
/*** compute estimate standard deviation of detrended data ***/
fsig = sq2p * qmed_float(nuse,far) ; /* also mangles far array */
/*** process time series for spikes, editing data in dar[] ***/
if( fsig > 0.0f ){ /* data wasn't fit perfectly */
/* find spikiness for each point in time */
fq = 1.0f / fsig ;
for( iv=0 ; iv < nuse ; iv++ ){
ssp[iv] = fq * var[iv] ; /* spikiness s = how many sigma out */
}
/* save spikiness in -ssave datset */
if( tset != NULL ){
for( iv=0 ; iv < nuse ; iv++ ){
tar = DSET_ARRAY(tset,iv+ignore) ;
snew = ITFAC*fabsf(ssp[iv]) ; /* scale for byte storage */
tar[ii] = BYTEIZE(snew) ; /* cf. mrilib.h */
}
}
/* process values of |s| > cut1, editing dar[] */
for( iv=0 ; iv < nuse ; iv++ ){ /* loop over time points */
if( !localedit ){ /** classic 'smash' edit **/
if( ssp[iv] > cut1 ){
snew = cut1 + c21*mytanh((ssp[iv]-cut1)*ic21) ; /* edit s down */
dar[iv] = fitar[iv] + snew*fsig ;
#pragma omp critical (DESPIKE_counter)
{ nspike++ ; if( ssp[iv] > cut2 ) nbig++ ; }
} else if( ssp[iv] < -cut1 ){
snew = -cut1 + c21*mytanh((ssp[iv]+cut1)*ic21) ; /* edit s up */
dar[iv] = fitar[iv] + snew*fsig ;
#pragma omp critical (DESPIKE_counter)
{ nspike++ ; if( ssp[iv] < -cut2 ) nbig++ ; }
}
} else { /** local edit: 04 Apr 2007 **/
if( ssp[iv] >= cut2 || ssp[iv] <= -cut2 ){
for( iu=iv+1 ; iu < nuse ; iu++ ) /* find non-spike above */
if( ssp[iu] < cut2 && ssp[iu] > -cut2 ) break ;
for( id=iv-1 ; id >= 0 ; id-- ) /* find non-spike below */
if( ssp[id] < cut2 && ssp[id] > -cut2 ) break ;
switch( (id>=0) + 2*(iu<nuse) ){ /* compute replacement val */
case 3: val = 0.5*(dar[iu]+dar[id]); break; /* iu and id OK */
case 2: val = dar[iu] ; break; /* only iu OK */
case 1: val = dar[id] ; break; /* only id OK */
default: val = fitar[iv] ; break; /* shouldn't be */
}
dar[iv] = val ;
#pragma omp critical (DESPIKE_counter)
{ nspike++ ; nbig++ ; }
}
}
} /* end of loop over time points */
#pragma omp atomic
nproc += nuse ; /* number data points processed */
} /* end of processing time series when fsig is positive */
/* put dar[] time series (possibly edited above) into output bricks */
switch( datum ){
case MRI_short:
for( iv=0 ; iv < nuse ; iv++ ){
sar = DSET_ARRAY(oset,iv+ignore) ; /* output brick */
sar[ii] = (short)dar[iv] ; /* original or mutated data */
}
break ;
case MRI_float:
for( iv=0 ; iv < nuse ; iv++ ){
zar = DSET_ARRAY(oset,iv+ignore) ; /* output brick */
zar[ii] = dar[iv] ; /* original or mutated data */
}
break ;
}
} /* end of loop over voxels #ii */
#pragma omp critical (DESPIKE_malloc)
{ free(fit); free(ssp); free(fitar); free(var); free(dar); free(far);
if( do_NEW ) free(NEW_wks) ; }
} /* end OpenMP */
AFNI_OMP_END ;
#ifdef USE_OMP
if( verb ) fprintf(stderr,"\n") ;
#endif
ctim = NI_clock_time() - ctim ;
INFO_message( "Elapsed despike time = %s" , nice_time_string(ctim) ) ;
if( ctim > 345678 && !do_NEW )
ININFO_message("That was SLOW -- try the '-NEW' option for a speedup") ;
#ifdef USE_OMP
if( verb ) fprintf(stderr,"\n") ;
#endif
/*--- finish up ---*/
if( do_NEW ) mri_free(NEW_psinv) ;
DSET_delete(dset) ; /* delete input dataset */
if( verb ){
if( nproc > 0 ){
pspike = (100.0*nspike)/nproc ;
pbig = (100.0*nbig )/nproc ;
INFO_message("FINAL: %d data points, %d edits [%.3f%%], %d big edits [%.3f%%]",
nproc,nspike,pspike,nbig,pbig ) ;
} else {
INFO_message("FINAL: no good voxels found to process!!??") ;
}
}
/* write results */
DSET_write(oset) ;
if( verb ) WROTE_DSET(oset) ;
DSET_delete(oset) ;
if( tset != NULL ){
DSET_write(tset) ;
if( verb ) WROTE_DSET(tset) ;
DSET_delete(tset) ;
}
exit( THD_get_write_error_count() ) ;
}
void THD_check_idcodes( THD_sessionlist *ssl )
{
int iss , idd,jdd , ivv , dsnum , nd ;
THD_session *sess ;
THD_3dim_dataset * dset , **dsl ;
ENTRY("THD_check_idcodes") ;
/*-- sanity check --*/
if( ! ISVALID_SESSIONLIST(ssl) || ssl->num_sess <= 0 ) EXRETURN ;
/*-- count number of datasets --*/
for( dsnum=iss=0 ; iss < ssl->num_sess ; iss++ ){
sess = ssl->ssar[iss] ; if( !ISVALID_SESSION(sess) ) continue ;
for( idd=0 ; idd < sess->num_dsset ; idd++ ){
for( ivv=FIRST_VIEW_TYPE ; ivv <= LAST_VIEW_TYPE ; ivv++ ){
dset = GET_SESSION_DSET(sess, idd, ivv);
/* dset = sess->dsset_xform_table[idd][ivv] ;*/
if( ISVALID_DSET(dset) ) dsnum++ ;
}
}
}
STATUS("counted datasets") ;
if( dsnum < 2 ) EXRETURN ; /* 21 Feb 2007 */
/*-- make list of datasets --*/
dsl = (THD_3dim_dataset **) malloc( sizeof(THD_3dim_dataset *) * dsnum ) ;
for( nd=iss=0 ; iss < ssl->num_sess ; iss++ ){
sess = ssl->ssar[iss] ; if( !ISVALID_SESSION(sess) ) continue ;
for( idd=0 ; idd < sess->num_dsset ; idd++ ){
for( ivv=FIRST_VIEW_TYPE ; ivv <= LAST_VIEW_TYPE ; ivv++ ){
dset = GET_SESSION_DSET(sess, idd, ivv);
/* dset = sess->dsset_xform_table[idd][ivv] ;*/
if( ISVALID_DSET(dset) ) dsl[nd++] = dset ;
}
}
}
STATUS("collected datasets") ;
/*-- check list for duplicates --*/
for( iss=idd=0 ; idd < dsnum-1 ; idd++ ){
nd = 0 ;
for( jdd=idd+1 ; jdd < dsnum ; jdd++ ){
if( DUPLICATE_DSETS(dsl[idd],dsl[jdd]) ){ /* 20 Dec 2001: change EQUIV_IDCODES() to DUPLICATE_DSETS() */
fprintf(stderr,
"\n*** WARNING: Identical ID codes in %s and %s",
DSET_HEADNAME(dsl[idd]) , DSET_HEADNAME(dsl[jdd]) ) ;
iss++ ;
}
}
}
if( iss > 0 ) fprintf(stderr,"\n") ;
free(dsl) ; EXRETURN ;
}
int main( int argc , char * argv[] )
{
THD_3dim_dataset *dset, *outset=NULL;
int iarg=1, npad = 0, extent=0;
char *prefix=NULL, *iname=NULL;
char *oijkext = NULL;
FILE *fout_ijkext=NULL;
int extent_ijk=0;
int extent_ijk_midslice=0;
int imid=0, jmid=0, kmid=0;
int extent_xyz_midslice=0;
float xmid=0, ymid=0, zmid=0;
/*-- startup bureaucracy --*/
mainENTRY("3dAutobox main"); machdep(); AFNI_logger("3dAutobox",argc,argv);
PRINT_VERSION("3dAutobox") ;
/*-- read command line options --*/
iarg = 1 ;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-help") == 0 || strcmp(argv[iarg],"-h") == 0){
help_autobox();
exit(0) ;
}
if( strcmp(argv[iarg],"-prefix") == 0 ){
prefix = argv[++iarg] ;
if( !THD_filename_ok(prefix) ){
fprintf(stderr,"** 3dAutobox: Illegal string after -prefix!\n");
exit(1) ;
}
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-input") == 0 ){
iname = argv[++iarg] ;
// This is a bad check, because it doesn't permit subbrick
// selection! Will do check later.
/*if( !THD_filename_ok(iname) ){
fprintf(stderr,"** 3dAutobox: Illegal string after -input!\n");
exit(1) ;
}*/
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-noclust") == 0 ){
MRI_autobbox_clust(0) ; /* turn of clustering and clipping */
THD_autobbox_clip(0) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-npad") == 0 ){
npad = (int)strtod(argv[++iarg],NULL) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-extent_ijk") == 0 ){
extent_ijk = 1 ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-extent_ijk_to_file") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-extent_ijk_to_file'\n") ;
oijkext = argv[iarg];
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-extent_ijk_midslice") == 0 ){
extent_ijk_midslice = 1 ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-extent_xyz_midslice") == 0 ){
extent_xyz_midslice = 1 ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-extent") == 0 ){
extent = 1 ;
iarg++ ; continue ;
}
/*- washappenin, dood? -*/
ERROR_message("** 3dAutobox: %s makes no sense here.\n",
argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
if( argc < 2){ help_autobox(); exit(0); }
/* got input ? */
if( iarg == argc-1 )
iname = argv[iarg] ;
else if (iarg != argc)
ERROR_exit("** 3dAutobox: %s is nonsense on the line \n"
" I know you're John; stop pretending you have an accent!",
argv[iarg]) ;
if( !iname )
ERROR_exit("** 3dAutobox: Where is my input?") ;
/*-- read data --*/
dset = THD_open_dataset(iname);
// Check here instead of after -input.
if( dset == NULL )
ERROR_exit("Can't open time series dataset '%s'.",iname);
CHECK_OPEN_ERROR(dset,iname);
if( DSET_BRICK_TYPE(dset,0) != MRI_short &&
DSET_BRICK_TYPE(dset,0) != MRI_byte &&
DSET_BRICK_TYPE(dset,0) != MRI_float )
ERROR_exit("** ILLEGAL dataset type: %s :-(",
MRI_type_name[DSET_BRICK_TYPE(dset,0)]) ;
DSET_load(dset) ; CHECK_LOAD_ERROR(dset) ;
{
int nx=DSET_NX(dset), ny=DSET_NY(dset), nz=DSET_NZ(dset), nxy=nx*ny ;
int xm=-1,xp=-1,ym=-1,yp=-1,zm=-1,zp=-1;
THD_autobbox( dset , &xm,&xp , &ym,&yp , &zm,&zp, NULL ) ;
xm -= npad; ym -= npad; zm -= npad; /* for LRF */
xp += npad; yp += npad; zp += npad;
INFO_message("Auto bbox: x=%d..%d y=%d..%d z=%d..%d\n",
xm,xp,ym,yp,zm,zp ) ;
// [PT: Oct 18, 2018] New output text file, if desired
if( oijkext ) {
if( (fout_ijkext = fopen(oijkext, "w")) == NULL ) {
fprintf(stderr, "\n\nError opening file %s.\n", oijkext);
exit(1);
}
fprintf( fout_ijkext, "%8d %8d %8d %8d %8d %8d\n",
xm, xp, ym, yp, zm, zp );
fclose(fout_ijkext);
INFO_message("Wrote ijk extents file: %s", oijkext);
}
if( extent_ijk )
printf( "%8d %8d %8d %8d %8d %8d\n",
xm, xp, ym, yp, zm, zp );
if( extent_ijk_midslice ) {
imid = (xm + xp) / 2; // integer division fine, b/c we need ints
jmid = (ym + yp) / 2;
kmid = (zm + zp) / 2;
printf( "%8d %8d %8d\n", imid, jmid, kmid );
}
if ( (extent && !prefix) || (extent_xyz_midslice && !prefix) )
prefix = "EXTENT_ONLY";
if( prefix ){
outset = THD_zeropad( dset ,
-xm, xp-nx+1,
-ym, yp-ny+1,
-zm, zp-nz+1,
prefix , ZPAD_IJK ) ;
if( THD_deathcon() && THD_is_file(DSET_HEADNAME(outset)) )
ERROR_exit("3dAutobox: output file %s already exists :-(",
DSET_HEADNAME(outset) ) ;
if( outset == NULL )
ERROR_exit("3dAutobox: Some error occurred in processing :-(") ;
tross_Copy_History( dset , outset ) ; /* 31 Jan 2001 - RWCox */
tross_Make_History( "3dAutobox" , argc,argv , outset ) ;
if (!strstr(prefix,"EXTENT_ONLY")) {
DSET_write(outset) ;
INFO_message("3dAutobox: output dataset = %s",
DSET_BRIKNAME(outset)) ;
}
if (extent) {
float RL_AP_IS[6];
THD_dset_extent(outset, '-', RL_AP_IS);
printf("Extent auto bbox: R=%f L=%f A=%f P=%f I=%f S=%f\n",
RL_AP_IS[0],RL_AP_IS[1],
RL_AP_IS[2],RL_AP_IS[3],
RL_AP_IS[4],RL_AP_IS[5] ) ;
}
if( extent_xyz_midslice ) {
INFO_message("aaa" );
float RL_AP_IS2[6];
THD_dset_extent(outset, '-', RL_AP_IS2);
xmid = (RL_AP_IS2[0] + RL_AP_IS2[1]) / 2.;
ymid = (RL_AP_IS2[2] + RL_AP_IS2[3]) / 2.;
zmid = (RL_AP_IS2[4] + RL_AP_IS2[5]) / 2.;
printf( "%10.5f %10.5f %10.5f\n", xmid, ymid, zmid );
}
}
}
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) ;
}
int THD_conformist( int ndset, THD_3dim_dataset **dset, int flags , int *ijkpad )
{
int iset , xpad_m,xpad_p , ypad_m,ypad_p , zpad_m,zpad_p , nwrit ;
THD_dataxes *cx , *dx ;
THD_3dim_dataset *qset ;
int_pair pm ;
int do_norefit = (flags & CONFORM_NOREFIT) ;
int do_rewrite = (flags & CONFORM_REWRITE) && !do_norefit ;
int do_ijkpad = (ijkpad != NULL) ;
ENTRY("THD_conformist") ;
/* check for good inputs */
if( ndset <= 0 || dset == NULL ) RETURN(-1) ;
for( iset=0 ; iset < ndset ; iset++ )
if( !ISVALID_DSET(dset[iset]) ) RETURN(-2) ;
/* check if all inputs are on the same grid (i.e., no work to do) */
for( iset=1 ; iset < ndset ; iset++ ){
if( ! EQUIV_DATAXES(dset[0]->daxes,dset[iset]->daxes) ) break ;
}
if( iset == ndset ){
if( do_ijkpad ){
for( iset=0 ; iset < 6*ndset ; iset++ ) ijkpad[iset] = 0 ;
}
RETURN(0) ;
}
/* construct the dataxes that encloses all the input datasets */
cx = THD_superset_dataxes( dset[0]->daxes , dset[1]->daxes ) ;
if( cx == NULL ){
ERROR_message("3dConformist: '%s' and '%s' aren't compatible",
DSET_HEADNAME(dset[0]) , DSET_HEADNAME(dset[1]) ) ;
RETURN(-3) ;
}
for( iset=2 ; iset < ndset ; iset++ ){
dx = THD_superset_dataxes( cx , dset[iset]->daxes ) ;
if( dx == NULL ){
ERROR_message("3dConformist: '%s' is not compatible with others",
DSET_HEADNAME(dset[iset]) ) ;
myXtFree(cx) ; RETURN(-3) ;
}
myXtFree(cx) ; cx = dx ; dx = NULL ;
}
/* now, re-create and re-write all datasets */
if( do_rewrite )
fprintf(stderr," + thd_conformist re-write loop: ") ;
for( nwrit=iset=0 ; iset < ndset ; iset++ ){
if( EQUIV_DATAXES(cx,dset[iset]->daxes) ){ /* already OK */
if( do_rewrite ) fprintf(stderr,"-") ;
if( do_ijkpad )
ijkpad[6*iset+0] = ijkpad[6*iset+1] = ijkpad[6*iset+2]
= ijkpad[6*iset+3] = ijkpad[6*iset+4] = ijkpad[6*iset+5] = 0 ;
continue ;
}
pm = zpadax_pm( cx->nxx , cx->xxorg ,
dset[iset]->daxes->nxx , dset[iset]->daxes->xxorg ,
cx->xxdel ) ;
xpad_m = pm.i ; xpad_p = pm.j ;
pm = zpadax_pm( cx->nyy , cx->yyorg ,
dset[iset]->daxes->nyy , dset[iset]->daxes->yyorg ,
cx->yydel ) ;
ypad_m = pm.i ; ypad_p = pm.j ;
pm = zpadax_pm( cx->nzz , cx->zzorg ,
dset[iset]->daxes->nzz , dset[iset]->daxes->zzorg ,
cx->zzdel ) ;
zpad_m = pm.i ; zpad_p = pm.j ;
if( do_ijkpad ){
ijkpad[6*iset+0] = xpad_m; ijkpad[6*iset+1] = xpad_p;
ijkpad[6*iset+2] = ypad_m; ijkpad[6*iset+3] = ypad_p;
ijkpad[6*iset+4] = zpad_m; ijkpad[6*iset+5] = zpad_p;
}
if( do_norefit ) continue ; /* just wanted ijkpad, I guess */
qset = THD_zeropad( dset[iset] ,
xpad_m,xpad_p , ypad_m,ypad_p , zpad_m,zpad_p ,
"BertieWooster" , ZPAD_PURGE | ZPAD_IJK ) ;
if( qset == NULL ){ /* this should never happen */
if( do_rewrite ) fprintf(stderr,"\n") ;
ERROR_message("thd_conformist: skipping dataset %s",
DSET_HEADNAME(dset[iset])) ;
continue ;
}
qset->idcode = dset[iset]->idcode ;
EDIT_dset_items( qset , ADN_prefix , DSET_PREFIX(dset[iset]) , ADN_none ) ;
if( do_rewrite ){
THD_delete_3dim_dataset( dset[iset] , True ) ;
DSET_overwrite(qset) ; DSET_unload(qset) ;
fprintf(stderr,"+") ;
} else {
THD_delete_3dim_dataset( dset[iset] , False ) ;
}
dset[iset] = qset ; nwrit++ ;
}
if( do_rewrite ) fprintf(stderr,"\n") ;
RETURN(nwrit) ;
}
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[]) {
int i,j,k,l,m,n,mm,ii;
int idx;
int iarg;
THD_3dim_dataset *insetTIME = NULL;
// THD_3dim_dataset *inset0 = NULL;
THD_3dim_dataset *MASK=NULL;
char *prefix="REHO" ;
char in_name[300];
char in_mask[300];
THD_3dim_dataset *outset=NULL;
char outname[300];
int NIFTI_OUT=0;
int DTYPE=0;
int HAVE_MASK = 0;
int ***mskd; // define mask of where time series are nonzero
double temp_sum;
// FILE *fout0, *fout1;
int Nvox=-1; // tot number vox
int Dim[4]={0,0,0,0};
float fbot = -1., ftop = -1;
float delF = -1;
float *allF=NULL;
float **allPar=NULL;
int Npar=NRSFC; // currently... see list below
char *namePar[NRSFC]={"ALFF", "MALFF", "FALFF",
"RSFA", "MRSFA", "FRSFA"};
int MIN_full=0, MAX_full=-1; // indices of full spect
int MIN_bp=0, MAX_bp = -1; // indices of lff/bp region
mainENTRY("3dAmpToRSFC"); machdep();
// ****************************************************************
// ****************************************************************
// load AFNI stuff
// ****************************************************************
// ****************************************************************
// INFO_message("version: NU");
/** scan args **/
if (argc == 1) { usage_AmpToRSFC(1); exit(0); }
iarg = 1;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-help") == 0 ||
strcmp(argv[iarg],"-h") == 0 ) {
usage_AmpToRSFC(strlen(argv[iarg])>3 ? 2:1);
exit(0);
}
if( strncmp(argv[iarg],"-band",5) == 0 ){
if( ++iarg >= argc-1 ) ERROR_exit("need 2 arguments after -band!") ;
fbot = strtod(argv[iarg++],NULL) ;
ftop = strtod(argv[iarg++],NULL) ;
continue ;
}
if( strcmp(argv[iarg],"-mask") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-mask'");
HAVE_MASK=1;
sprintf(in_mask,"%s", argv[iarg]);
MASK = THD_open_dataset(in_mask) ;
if( (MASK == NULL ))
ERROR_exit("Can't open time series dataset '%s'.",in_mask);
DSET_load(MASK); CHECK_LOAD_ERROR(MASK);
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],"-in_amp") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-in_amp'");
sprintf(in_name,"%s", argv[iarg]);
DTYPE = 1; // for amps
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_pow") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-in_pow'");
sprintf(in_name,"%s", argv[iarg]);
DTYPE = 2; // for pow
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-mask") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-mask'");
HAVE_MASK=1;
sprintf(in_mask,"%s", argv[iarg]);
MASK = THD_open_dataset(in_mask) ;
if( (MASK == NULL ))
ERROR_exit("Can't open time series dataset '%s'.",in_mask);
DSET_load(MASK); CHECK_LOAD_ERROR(MASK);
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-nifti") == 0) {
NIFTI_OUT=1;
iarg++ ; continue ;
}
ERROR_message("Bad option '%s'\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
// ---------------------------------------------------------------
// TEST BASIC INPUT PROPERTIES
if (iarg < 3) {
ERROR_message("Too few options. Try -help for details.\n");
exit(1);
}
if( !DTYPE ) {
ERROR_message("Think somebody forgot to specify an input file"
" using '-in_amp ...' or '-in_pow ...'.");
exit(12);
}
else{
insetTIME = THD_open_dataset(in_name) ;
if( (insetTIME == NULL ))
ERROR_exit("Can't open time series dataset '%s'.",in_name);
DSET_load(insetTIME); CHECK_LOAD_ERROR(insetTIME);
Nvox = DSET_NVOX(insetTIME) ;
Dim[0] = DSET_NX(insetTIME); Dim[1] = DSET_NY(insetTIME);
Dim[2] = DSET_NZ(insetTIME); Dim[3]= DSET_NVALS(insetTIME);
delF = DSET_TR(insetTIME);
}
if( (fbot<0) || (ftop<0) ) {
ERROR_message("Think somebody forgot to specify upper and lower"
" frequency bounds using '-band ... ...'.");
exit(11);
}
if( fbot > ftop )
ERROR_exit("Can't have ftop < fbot! Try entering frequency"
"band limits again");
if( MASK )
if ( Dim[0] != DSET_NX(MASK) || Dim[1] != DSET_NY(MASK) ||
Dim[2] != DSET_NZ(MASK) ) {
ERROR_message("Mask and inset don't appear to have the same "
"dimensions.\n");
exit(1);
}
// ****************************************************************
// ****************************************************************
// pre-stuff, make storage
// ****************************************************************
// ****************************************************************
// array of freqs-- starts at delta F, not zero, as the current
// input data sets must!
allF = (float *)calloc(Dim[3], sizeof(float));
// will be the output
allPar = calloc(Npar,sizeof(allPar));
for(i=0 ; i<Npar ; i++)
allPar[i] = calloc(Nvox,sizeof(float));
// MASK
mskd = (int ***) calloc( Dim[0], sizeof(int **) );
for ( i = 0 ; i < Dim[0] ; i++ )
mskd[i] = (int **) calloc( Dim[1], sizeof(int *) );
for ( i = 0 ; i < Dim[0] ; i++ )
for ( j = 0 ; j < Dim[1] ; j++ )
mskd[i][j] = (int *) calloc( Dim[2], sizeof(int) );
if( (mskd == NULL) || (allF == NULL) || (allPar == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure (mask).\n\n");
exit(33);
}
// *************************************************************
// *************************************************************
// Beginning of main loops
// *************************************************************
// *************************************************************
// Populate freq bands. For now, delF is constant. Later.... who
// knows, so make flexible
allF[0] = DSET_TIMEORIGIN(insetTIME);
if( allF[0] < EPS_V )
ERROR_exit("The t-axis (here, frequency) origin is 0!"
"\n\t-> but you shouldn't have a baseline 0-frequency!");
for( i=1 ; i<Dim[3] ; i++ )
allF[i] = allF[i-1] + delF;
// fill in rest of freq ranges; MIN_full=0 already
MAX_full = Dim[3]-1;
// these should be in order, so we can pass through like this.
for( i=0 ; i<Dim[3] ; i++ ) {
ii = Dim[3] - 1 - i;
if( allF[ii] >= fbot )
MIN_bp = ii;
if( allF[i] <= ftop )
MAX_bp = i;
}
if(MAX_bp < MIN_bp) // shouldn't happen...
ERROR_exit("Something went horribly wrong with reading in the "
"bandpass limits! bot:%f, top:%f",MIN_bp, MAX_bp);
INFO_message("Actual BP range: indices [%d, %d] -> "
"freqs [%.4f, %.4f]", MIN_bp, MAX_bp,
allF[MIN_bp], allF[MAX_bp]);
INFO_message("Full freq range: indices [%d, %d] -> "
"freqs [%.4f, %.4f]", MIN_full, MAX_full,
allF[MIN_full], allF[MAX_full]);
// go through once: define data vox
idx = 0;
for( k=0 ; k<Dim[2] ; k++ )
for( j=0 ; j<Dim[1] ; j++ )
for( i=0 ; i<Dim[0] ; i++ ) {
if( HAVE_MASK ) {
if( THD_get_voxel(MASK,idx,0)>0 )
mskd[i][j][k] = 1;
}
else {
temp_sum = 0.;
for ( l=0 ; l<Dim[3] ; l++ )
temp_sum+= abs(THD_get_voxel(insetTIME,idx,l));
if ( temp_sum > EPS_V )
mskd[i][j][k] = 1;
}
idx++;
}
INFO_message("Done masking.");
Spect_to_RSFC( insetTIME,
DTYPE,
Dim,
mskd,
MIN_bp, MAX_bp,
MIN_full, MAX_full,
allPar,
Npar
);
INFO_message("Done calculating parameters.");
// **************************************************************
// **************************************************************
// Store and output
// **************************************************************
// **************************************************************
for( m=0; m<Npar ; m++) {
outset = EDIT_empty_copy(insetTIME) ;
if(NIFTI_OUT)
sprintf(outname,"%s_%s.nii.gz",prefix, namePar[m]);
else
sprintf(outname,"%s_%s",prefix, namePar[m]);
INFO_message(" writing: %s %s", prefix, outname);
EDIT_dset_items( outset,
ADN_nvals , 1 ,
ADN_datum_all , MRI_float ,
ADN_prefix , outname ,
ADN_none ) ;
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outset)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(outset));
EDIT_substitute_brick(outset, 0, MRI_float, allPar[m]);
allPar[m]=NULL;
THD_load_statistics(outset);
tross_Make_History("3dAmpToRSFC", argc, argv, outset);
THD_write_3dim_dataset(NULL, NULL, outset, True);
if(outset) {
DSET_delete(outset);
free(outset);
}
}
// ************************************************************
// ************************************************************
// Freeing
// ************************************************************
// ************************************************************
if(allF)
free(allF);
if(MASK) {
DSET_delete(MASK);
free(MASK);
}
if(insetTIME) {
DSET_delete(insetTIME);
free(insetTIME);
}
if(mskd) {
for( i=0 ; i<Dim[0] ; i++)
for( j=0 ; j<Dim[1] ; j++)
free(mskd[i][j]);
for( i=0 ; i<Dim[0] ; i++)
free(mskd[i]);
free(mskd);
}
if(allPar) { // have freed other parts of this above
free(allPar);
}
return 0;
}
