Thanks Doug for your answer.

However, I got the same error when I tried replacing 29 with 3. I also tried --replace 29 2 but gave a similar error.

I've attached the gtmseg.ctab and seg.replace.list

Replacing 19
Pruning ctab
ERROR: CTABpruneCTab(): ctab does not have segid 3
Checking tissue type
/users/surface-based_analyses/pet_base_SUVR_fromcoregstep_nopvc.sh: line 98: 16610 Segmentation fault mri_gtmpvc --i ${pet} --reg ${reg_lta} --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask ${var_automask} ${mgx} --mgx ${mgx} --o ${gtm_out_nopvc} --rescale ${nr} --replace 29 3

On Fri, Feb 5, 2021 at 1:45 PM miracle ozzoude <miracooloz@gmail.com> wrote:

Hi Doug,

I followed the processing workflow as described on the PETSurfer wiki and gtmseg.mgz was created, but included a warning for only one of my subjects:

WARNING: segid 29 Left-undetermined tissue type is not set
Writing output file to /ID/mri/gtmseg.mgz
Writing colortable to /ID/mri/gtmseg.ctab
Writing lta file to /ID/mri/gtmseg.lta

Next, I ran both pvc and non-pvc. However, the non-pvc failed, whereas the pvc did not. These are the commands I ran and the error I got for non-pvc:

mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask PSF 0.01 --mgx 0.01 --o /gtmnopvc.output.ref --rescale 8 47
vgthresh 0.001000
nReplace 18
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
24 avail.processors, using 1
Creating output directory /gtmnopvc.output.ref
Loading seg for gtm /ID/mri/gtmseg.mgz
Loading seg ctab /ID/mri/gtmseg.ctab
Reading /ID/mri/gtmseg.lta
Replacing 18
Pruning ctab
Checking tissue type
ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set
Failed tissue type check

Also , in the aux folder of non-pvc, only limited amount of files were created, including:
Mask.nii, seg.ctab, seg.nii, seg.replace.list, seg.vol.nii
Any idea why only the non-pvc failed ? Any help would be greatly appreciated!

Many thanks