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[] )
{
THD_3dim_dataset *xset=NULL , *cset ;
int nopt=1, datum=MRI_float, nvals, ii;
MRI_IMAGE *ysim=NULL ;
char *prefix = "Tcorr1D", *smethod="pearson";
char *xnam=NULL , *ynam=NULL ;
byte *mask=NULL ; int mask_nx,mask_ny,mask_nz , nmask=0 ;
int do_atanh = 0 ; /* 12 Jan 2018 */
/*----*/
AFNI_SETUP_OMP(0) ; /* 24 Jun 2013 */
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
printf("Usage: 3dTcorr1D [options] xset y1D\n"
"Computes the correlation coefficient between each voxel time series\n"
"in the input 3D+time dataset 'xset' and each column in the 1D time\n"
"series file 'y1D', and stores the output values in a new dataset.\n"
"\n"
"OPTIONS:\n"
" -pearson = Correlation is the normal Pearson (product moment)\n"
" correlation coefficient [this is the default method].\n"
" -spearman = Correlation is the Spearman (rank) correlation\n"
" coefficient.\n"
" -quadrant = Correlation is the quadrant correlation coefficient.\n"
" -ktaub = Correlation is Kendall's tau_b coefficient.\n"
" ++ For 'continuous' or finely-discretized data, tau_b and\n"
" rank correlation are nearly equivalent (but not equal).\n"
" -dot = Doesn't actually compute a correlation coefficient; just\n"
" calculates the dot product between the y1D vector(s)\n"
" and the dataset time series.\n"
"\n"
" -Fisher = Apply the 'Fisher' (inverse hyperbolic tangent) transformation\n"
" to the results.\n"
" ++ It does not make sense to use this with '-ktaub', but if\n"
" you want to do it, the program will not stop you.\n"
" ++ Cannot be used with '-dot'!\n"
"\n"
" -prefix p = Save output into dataset with prefix 'p'\n"
" [default prefix is 'Tcorr1D'].\n"
"\n"
" -mask mmm = Only process voxels from 'xset' that are nonzero\n"
" in the 3D mask dataset 'mmm'.\n"
" ++ Other voxels in the output will be set to zero.\n"
"\n"
" -float = Save results in float format [the default format].\n"
" -short = Save results in scaled short format [to save disk space].\n"
" ++ Cannot be used with '-dot'!\n"
"\n"
"NOTES:\n"
"* The output dataset is functional bucket type, with one sub-brick\n"
" per column of the input y1D file.\n"
"* No detrending, blurring, or other pre-processing options are available;\n"
" if you want these things, see 3dDetrend or 3dTproject or 3dcalc.\n"
" [In other words, this program presumes you know what you are doing!]\n"
"* Also see 3dTcorrelate to do voxel-by-voxel correlation of TWO\n"
" 3D+time datasets' time series, with similar options.\n"
"* You can extract the time series from a single voxel with given\n"
" spatial indexes using 3dmaskave, and then run it with 3dTcorr1D:\n"
" 3dmaskave -quiet -ibox 40 30 20 epi_r1+orig > r1_40_30_20.1D\n"
" 3dTcorr1D -pearson -Fisher -prefix c_40_30_20 epi_r1+orig r1_40_30_20.1D\n"
"* http://en.wikipedia.org/wiki/Correlation\n"
"* http://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient\n"
"* http://en.wikipedia.org/wiki/Spearman%%27s_rank_correlation_coefficient\n"
"* http://en.wikipedia.org/wiki/Kendall_tau_rank_correlation_coefficient\n"
"\n"
"-- RWCox - Apr 2010\n"
" - Jun 2010: Multiple y1D columns; OpenMP; -short; -mask.\n"
) ;
PRINT_AFNI_OMP_USAGE("3dTcorr1D",NULL) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
mainENTRY("3dTcorr1D main"); machdep(); AFNI_logger("3dTcorr1D",argc,argv);
PRINT_VERSION("3dTcorr1D") ; THD_check_AFNI_version("3dTcorr1D") ;
/*-- option processing --*/
while( nopt < argc && argv[nopt][0] == '-' ){
if( strcmp(argv[nopt],"-mask") == 0 ){ /* 28 Jun 2010 */
THD_3dim_dataset *mset ;
if( ++nopt >= argc ) ERROR_exit("Need argument after '-mask'") ;
if( mask != NULL ) 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 ) ;
INFO_message("Number of voxels in mask = %d",nmask) ;
if( nmask < 2 ) ERROR_exit("Mask is too small to process") ;
nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-float") == 0 ){ /* 27 Jun 2010 */
datum = MRI_float ; nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-short") == 0 ){
datum = MRI_short ; nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-pearson") == 0 ){
smethod = "pearson" ; nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-dot") == 0 ){
smethod = "dot" ; nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-spearman") == 0 || strcasecmp(argv[nopt],"-rank") == 0 ){
smethod = "spearman" ; nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-quadrant") == 0 ){
smethod = "quadrant" ; nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-ktaub") == 0 || strcasecmp(argv[nopt],"-taub") == 0 ){
smethod = "ktaub" ; nopt++ ; continue ;
}
if( strcasecmp(argv[nopt],"-fisher") == 0 ){ /* 12 Jan 2018 */
do_atanh = 1 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-prefix") == 0 ){
prefix = argv[++nopt] ;
if( !THD_filename_ok(prefix) ) ERROR_exit("Illegal value after -prefix!") ;
nopt++ ; continue ;
}
ERROR_exit("Unknown option: %s",argv[nopt]) ;
}
/*------------ open datasets, check for legality ------------*/
if( nopt+1 >= argc )
ERROR_exit("Need 2 non-option arguments on command line!?") ;
/* despite what the help says, if the 1D file is first, that's OK */
if( STRING_HAS_SUFFIX(argv[nopt],"1D") ){
ININFO_message("reading 1D file %s",argv[nopt]) ;
ysim = mri_read_1D( argv[nopt] ) ; ynam = argv[nopt] ;
if( ysim == NULL ) ERROR_exit("Can't read 1D file %s",argv[nopt]) ;
} else {
ININFO_message("reading dataset file %s",argv[nopt]) ;
xset = THD_open_dataset( argv[nopt] ) ; xnam = argv[nopt] ;
if( xset == NULL ) ERROR_exit("Can't open dataset %s",argv[nopt]) ;
}
/* read whatever type of file (3D or 1D) we don't already have */
nopt++ ;
if( xset != NULL ){
ININFO_message("reading 1D file %s",argv[nopt]) ;
ysim = mri_read_1D( argv[nopt] ) ; ynam = argv[nopt] ;
if( ysim == NULL ) ERROR_exit("Can't read 1D file %s",argv[nopt]) ;
} else {
ININFO_message("reading dataset file %s",argv[nopt]) ;
xset = THD_open_dataset( argv[nopt] ) ; xnam = argv[nopt] ;
if( xset == NULL ) ERROR_exit("Can't open dataset %s",argv[nopt]) ;
}
nvals = DSET_NVALS(xset) ; /* number of time points */
ii = (strcmp(smethod,"dot")==0) ? 2 : 3 ;
if( nvals < ii )
ERROR_exit("Input dataset %s length is less than ii?!",xnam,ii) ;
if( ysim->nx < nvals )
ERROR_exit("1D file %s has %d time points, but dataset has %d values",
ynam,ysim->nx,nvals) ;
else if( ysim->nx > nvals )
WARNING_message("1D file %s has %d time points, dataset has %d",
ynam,ysim->nx,nvals) ;
if( mri_allzero(ysim) )
ERROR_exit("1D file %s is all zero!",ynam) ;
if( ysim->ny > 1 )
INFO_message("1D file %s has %d columns: correlating with ALL of them!",
ynam,ysim->ny) ;
if( strcmp(smethod,"dot") == 0 && do_atanh ){
WARNING_message("'-dot' turns off '-Fisher'") ; do_atanh = 0 ;
}
if( strcmp(smethod,"dot") == 0 && datum == MRI_short ){
WARNING_message("'-dot' turns off '-short'") ; datum = MRI_float ;
}
cset = THD_Tcorr1D( xset, mask, nmask, ysim, smethod,
prefix, (datum==MRI_short) , do_atanh );
tross_Make_History( "3dTcorr1D" , argc,argv , cset ) ;
DSET_unload(xset) ; /* no longer needful */
/* finito */
DSET_write(cset) ;
INFO_message("Wrote dataset: %s\n",DSET_BRIKNAME(cset)) ;
exit(0) ;
}