Dear Freesurfers,
I am trying to apply partial volume correction to my PET images, following the steps explained in the PetSurfer wiki.
When I run the mri_gtmpvc command, it works fine for most of the subjects but for some of them I get the following error message:
/autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space Loading input /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space/SUVR.nii.gz done loading input 1 frames $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3 cd /autofs/space/alicudi_002/users/mscat/users/elena/scripts/PVC mri_gtmpvc --i /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space/SUVR.nii.gz --reg /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space/SUVR.reg.lta --psf 6 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/gtmpvc.output sysname Linux hostname alicudi.nmr.mgh.harvard.edu machine x86_64 user ehmuelas vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 40 avail.processors, using 1
Creating output directory /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/gtmpvc.output Loading seg for gtm /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/mri/gtmseg.mgz Loading seg ctab /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/mri/gtmseg.ctab Reading /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/mri/gtmseg.lta
Replacing 18 Pruning ctab Checking tissue type ERROR: CheckSegTissueType() tissue type for seg 64 Right-F3orb not set Failed tissue type check
And the command line that I ran:
mri_gtmpvc --i $path_to_suvr/SUVR.nii.gz --reg $path_to_suvr/SUVR.reg.lta --psf 6 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o $path_to_recon/$subj"_recon"/gtmpvc.output
Could you please help me out with this?
Many thanks in advance!
Elena