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The final posteriors are used in two ways. To get the "hard" segmentation we
simply assign each voxel the label corresponding to the maximum posteriors in
that location.
To get our volume estimates we divide the volume of each voxel between the
labels proportionately to the posteriors. Essentially this is just multiplying
the posteriors by the volume of a voxel and summing across voxels.
If you are doing this with the output posteriors you may need check that the
posteriors sum to 1 in each voxel. i.e. they haven't been renormalised for
visualisation and you have the posteriors for labels outside of the thalamus
which are also modelled during the segmentation.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of zlseu2109
<zlseu2...@163.com>
Sent: 15 July 2023 13:05
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] some thalamic subregions are not shown in image of
ThalamicNuclei.v13.T1.mgz
External Email - Use Caution
Thanks for your answer!
I’ve output posterior probabilities and got 25 heat maps (.mgz files) for
thalamic nuclei. However, I do not know the standard you use to generate the
volume measurements of individual thalamic nuclei. Could you explain it? Can I
apply this standard to heat maps I’ve got and output .mgz/.nii file of each
nuclei for further analysis?
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---- Replied Message ----
From Tregidgo, Henry<h.tregi...@ucl.ac.uk> <mailto:h.tregi...@ucl.ac.uk>
Date 07/10/2023 21:41
To freesurfer@nmr.mgh.harvard.edu<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject Re: [Freesurfer] some thalamic subregions are not shown in
image of ThalamicNuclei.v13.T1.mgz
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of zlseu2109 <zlseu2...@163.com<mailto:zlseu2...@163.com>>
Sent: 10 July 2023 14:11
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: chm...@163.com<mailto:chm...@163.com>
<chm...@163.com<mailto:chm...@163.com>>
Subject: [Freesurfer] some thalamic subregions are not shown in image of
ThalamicNuclei.v13.T1.mgz
⚠ Caution: External sender
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TO: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
FROM: zlseu2...@163.com<mailto:zlseu2...@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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