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Thank you Douglas, I tried quickly via correcting my gtmseg.ctab output with standardized for gtmseg only for tissue types, it runs without error, I will create a new look up table and try further.
Thanks again, Kind regards.
On Tue, Apr 6, 2021 at 3:53 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
gtmseg will not give an error, but the color table that gtmseg outputs will not be right and needs to be fixed.
On 4/6/2021 9:41 AM, Bahar Hazal Yalçınkaya wrote:
External Email - Use CautionThanks 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 CautionHello 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://secure-web.cisco.com/1B2HO1KM0jnhlHMvubnOYbXX6eMhgWiZ6pFbmY8cJ2rCR2z... 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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-- Ph.D. Bahar Hazal Yalçınkaya
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