External Email - Use Caution Hello Freesurfer"s Developers,
I am trying to follow *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-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
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