Thanks for response, color table and annotations are there "--ctx-annot Schaefer2018_400Parcels_7Networks_order.annot 1000 2000 --ctab Schaefer2018_400Parcels_7Networks_order_LUT.txt", gtmseg did not gave an error, you can see at attachments. (Also I can see 258 Head segmentation in gtmseg.ctab file) also mri_coreg is working well (see also attachments). The problem is the "mri_gtmpvc" command where it fails while checking tissue types more precisely it complains about Head segmentation.

I run with standard options. I checked everything I can think of, each file and image seems to be similar but still could not find a proper solution. Is there anything specific I need to check?

Thanks in advance,

Kind regards

On Tue, Apr 6, 2021 at 3:26 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

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:
External Email - Use Caution

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
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