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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