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