Dear Miguel,
Thank you very much for the interest in our work!
Your are right about *FSvoxelSpace*.mgz; these are resampled to the voxel space of the other 1mm isotropic volumes in the mri directory, and don’t look as pretty as the higher resolution counterparts.
The CA/FS60/HBT versions are simply different groupings of the labels, provided for convenience. This is explained in
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala (please see tables in Section 1 of that page). If you want all possible labels, then simply use the files without CA/FS60/HBT ;-)
The label map can be found in the file: $FREESURFER_HOME/FreeSurferColorLUT.txt
Or online here:
https://github.com/freesurfer/freesurfer/blob/dev/distribution/FreeSurferColorLUT.txt
Kind regards,
/Eugenio
http://www.jeiglesias.com
From:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas Fernández <miguelrivasfdez@gmail.com>
Date: Friday, February 21, 2025 at 1:18 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampus and amygdala segmentation
External Email - Use Caution
Dear Eugenio,
My name is Miguel. I am currently processing data of the ABCD Study using FreeSurfer. In our pipeline, we also include the specific FreeSurfer segmentations for the hippocampus and amygdala. As an additional
step, we would like to use these segmentations as masks. However, I see that FreeSurfer exports several files, and I am not entirely sure which one I should use.
From what I read on the wiki, the files with the suffix *FSvoxelSpace.mgz* are the segmentations that are in the same voxel space as the other FreeSurfer volumes, although it is noted that these segmentations
are somewhat rougher.
However, I see that there are several files with that name. For example, for the hippocampus segmentation in both hemispheres, we have:
I would like to have an image that contains all hippocampus and amygdala segmentations in a single image. In that case, which file should I use? Perhaps *FSvoxelSpace.mgz*?