Try adding --replace 29 3 This just replaces the "undetermined" voxels with white matter
On 2/5/2021 1:45 PM, miracle ozzoude wrote:
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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
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