diff --git a/mri_gtmpvc/mri_gtmpvc.cpp b/mri_gtmpvc/mri_gtmpvc.cpp index 7eaf93bebe0..422edbed64d 100644 --- a/mri_gtmpvc/mri_gtmpvc.cpp +++ b/mri_gtmpvc/mri_gtmpvc.cpp @@ -453,7 +453,7 @@ int main(int argc, char *argv[]) if(gtm->reduce_fov && gtm->mask){ LTA *seg2bbpet,*anat2bbpet,*lta; MRI *masktmp,*yvoltmp; - printf("Automask, reducing FOV\n"); + printf("Automask, reducing FOV %d\n",gtm->reduce_fov); if(gtm->reduce_fov == 1) gtm->automaskRegion = REGIONgetBoundingBox(gtm->mask,1); if(gtm->reduce_fov == 2) @@ -606,7 +606,7 @@ int main(int argc, char *argv[]) fprintf(logfp,"Turning VoxFracCor ON for simulation. It will be turned OFF for anlaysis.\n"); gtm->DoVoxFracCor = 1; } - printf("Building GTM DoVoxFracCor=%d\n",gtm->DoVoxFracCor);fflush(stdout); + printf("Building GTM DoVoxFracCor=%d (TFE)\n",gtm->DoVoxFracCor);fflush(stdout); if(Gdiag_no > 0) PrintMemUsage(stdout); PrintMemUsage(logfp); mytimer.reset(); @@ -1226,6 +1226,13 @@ static int parse_commandline(int argc, char **argv) { else if(!strcasecmp(option, "--sim-anat-seg")) DoSimAnatSeg=1; else if (!strcasecmp(option, "--chunk")) setenv("FS_USE_MRI_CHUNK","1",1); else if (!strcasecmp(option, "--no-chunk") ) unsetenv("FS_USE_MRI_CHUNK"); + else if(!strcasecmp(option, "--no-pvc")){ + // Turn off all pvc + gtm->cFWHM = 0; + gtm->rFWHM = 0; + gtm->sFWHM = 0; + gtm->DoVoxFracCor=0; + } else if(!strcasecmp(option, "--auto-mask")){ if(nargc < 2) CMDargNErr(option,2); sscanf(pargv[0],"%lf",>m->automask_fwhm); @@ -1678,7 +1685,7 @@ static void print_usage(void) { printf("\n"); printf(" --i inputvol : source data to PVC\n"); printf(" --frame F : only process 0-based frame F from inputvol\n"); - printf(" --psf psfmm : scanner PSF FWHM in mm\n"); + printf(" --psf psfmm : scanner PSF FWHM in mm (see also --no-tfe and --no-pvc)\n"); printf(" --seg segfile : anatomical segmentation to define regions for GTM\n"); printf(" --reg reg.lta : LTA registration file that maps PET to anatomical\n"); printf(" --regheader : assume input and seg share scanner space\n"); @@ -1709,7 +1716,8 @@ static void print_usage(void) { printf(" Note: tissue type lateralization will sligthly affect results since \n"); printf(" the tissue type is used to resolve ties.\n"); printf("\n"); - printf(" --no-tfe : do not correction for tissue fraction effect (with --psf 0 turns off PVC entirely)\n"); + printf(" --no-tfe : do not correction for tissue fraction effect (corrects by default)\n"); + printf(" --no-pvc : turns off PVC entirely (both PSF and TFE)\n"); printf(" --segpvfres resmm : set the tissue fraction resolution parameter (def is %g)\n",segpvfresmm); printf(" if a negative number is used, then it is treated as an upsampling factor (eg, -3)\n"); printf(" The TF is computed by dividing the PET voxel into subvoxels of size segpvfres\n");