You will need to create a new color table. This is not hard, but not easy either. First, there should be a color table already there. I'm not sure what that will be like; it might have your segments in it, it might not. It might be easier to run gtmseg with the standard options and look at the color table, then try to replicate it with your segmentation
On 4/5/2021 6:43 AM, Bahar Hazal Yalçınkaya wrote:
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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 https://secure-web.cisco.com/1oGyZvXtztP0MX30hKqio2fJStw1wQuIW11p5b1b0CkNwSGz7RCQalhqGZJFfIT2Ob3QQETtldwxv9y8xYVYGSkRdQ_GjplqWAGkIFRP1S40sf8UfJTbg-jdroEwAQvGW-9HmP1fatTZ8h3DhbPvM4MaRIdn-gicol4f85-JI5PjVoycwQ5z0q2oYvFmz9DuRwGJZg7EiKqmfCLYhXNUOPOwhpm1kKKikeaQrRAVCr4-WbYz4Z0GXBVuflZqXa84PEzxVj0uL51CZ_xoDuhu3DA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer) 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-annotSchaefer2018_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
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