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The Pt is one of a few nuclei that can sometimes not make it into the final visualisation (others being the Pc and Vm). For these very small nuclei, their posterior probabilities (soft segmentation) generated by the Bayesian segmentation algorithm sometimes don't "win" any voxels so they don't show up in the "hard" segmentation (ThalamicNuclei.v13.T1.mgz) where we display the labels with the voxelwise maximum posterior. However, we generate the volume measurements from the posteriors rather than the hard segmentation so we can give volume estimates for these nuclei.
If you would like to visualise the likely locations of these nuclei you can output the posterior probabilities to get a heat map by running the segmentation after setting the WRITE_POSTERIORS environmental variable. (eg. in bash > export WRITE_POSTERIORS=1)
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of zlseu2109 zlseu2109@163.com Sent: 10 July 2023 14:11 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
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TO: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu FROM: zlseu2109@163.commailto: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)
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