Dear zlseu,
We currently do not have an “official” release of the probabilistic atlas in a reference space. It is try that some of the smallest nuclei may not appear in the hard (discrete) segmentation, but you can always use the option to write down
the posteriors. Then you can open the file corresponding to eg the Pt and see the soft probability map. The instructions can be found in the FAQ section of the wiki:
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Cheers,
/E
--
Juan Eugenio Iglesias
http://www.jeiglesias.com
From:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of zlseu2109 <zlseu2109@163.com>
Date: Monday, July 10, 2023 at 9:11 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: chmxie@163.com <chmxie@163.com>
Subject: [Freesurfer] some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz
External Email - Use Caution
TO: freesurfer@nmr.mgh.harvard.edu
FROM: zlseu2109@163.com
SUBJECT: segmentation of thalamic nuclei error: some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz
Hello FreeSurfer Developers,
I’ve segmented thalamic nuclei via thalamic nuclei atlas and gained volume result of 25 subregions of each thalamus, but some subregions (eg. Right Pt) cannot be shown by load ThalamicNuclei.v13.T1.mgz in freeview. I'm attempting to use this thalamic nuclei atlas for functional ROIs analysis, using other softwares (eg.SPM). Could you provide .nii file of this atlas? Or can you help me show this missed thalamic subregions? Or how can I transform the file of thalamic nuclei atlas in FreeSurfer pipeline to .nii file.
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one?
1) FreeSurfer version: freesurfer-Linux-ubuntu20_x86_64-7.3.2
2) Platform: Ubuntu Release 20.04.6 (focal)
