Hello Freesurfer"s Developers,

I am trying to follow PetSurfer (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer) to apply PVC to Pet images.

Default pipeline is working however, whenever i try to use another atlas, Schaefer parcellation, mri_gtmpvc command I get following error:

WARNING: LTAconcat(): inverting LTA 1 to match geometry

Replacing 18

Pruning ctab

tissue type schema

Checking tissue type

ERROR: CheckSegTissueType() tissue type for seg 258 Head-ExtraCerebral not set

Failed tissue type check

I have searched to list several people who have issued similar errors but unfortunately i could not find any solution that works for me. Below you can find commands I used:

$ gtmseg --s subject --o gtmseg.mgz --ctx-annot Schaefer2018_400Parcels_7Networks_order.annot 1000 2000 --ctab Schaefer2018_400Parcels_7Networks_order_LUT.txt
$ mri_coreg --s subject  --mov  AbetaPre.nii.gz --reg AbetaPre.reg.lta
$ mri_gtmpvc --i AbetaPre.nii.gz --psf 8 --reg AbetaPre.reg.lta --regheader --seg gtmseg.mgz  --default-seg-merge --auto-mask PSF .01 --mgx .01 --km-ref 8 47 --o gtmpvc.output 

Also I checked the run of gtmseg via "tkmeditfv" where i can visualise 258 Head-ExtraCerebral, and additionally I checked gtmseg.ctab file also 258 Head-ExtraCerebral in the list.

I will be happy to hear from you. 
Kind regards.

Ph.D. Bahar Hazal Yalçınkaya