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/HippocampalSubfieldsAndNucleiOfAmy... (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/FreeSurferCol...
Kind regards,
/Eugenio
-- Juan Eugenio Iglesias 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: - *CA.FSvoxelSpace* - *FS60.FSvoxelSpace* - *FSvoxelSpace.mgz* - *HBT.FSvoxelSpace.mgz*
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*?
Another question arises, not only for the hippocampus segmentation but also for other segmentations. Is there a list on the FreeSurfer wiki that shows which region corresponds to each value in the segmentations? For example, in the file *lh.hippoAmygLabels-T1.v22.FSvoxelSpace.mgz*, the value 2000 corresponds to structure X. I am also interested in this labeling for the thalamus and brainstem segmentations (for the hypothalamus, I see that they are listed in a table on the website: [MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/HypothalamicSubunits%5D(https://su...)https://secure-web.cisco.com/1jAPRbUdDLiBJrm686owHhAmUnvRnT72oi9D4Bw3WHcn09MvGcPOz3Dq1Q9a4cVLScMfnUvOIU7GGWEvVuXjv6vcEkUwjtaI38NDc9gNet0f8NxT2G0WY_lNpw4UOxcrc0W2lQDskL4CZmDP-9p9xpEx3trrdV_WvJ-eGAw9ucHoMu_KaqcyRf-4iCpAs4Z9yo4yKuc4oFctggdKuibJdkvJtgeHzRM2O6aourNBQCpZrsvEwonu_2ZgZrv1RWENAmivKTCJVQvmbA1xrBiB2JvpU5c_ggBU8Cg66MsU-zP_y0gQxi5bUv-xQ5B9s8I08tlRSpZ5ByLV1tzv3gsHWCw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHypothalamicSubunits%5D%28https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHypothalamicSubunits%29).
Thank you very much!
Miguel