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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: [ https://secure-web.cisco.com/1Ri4u8JcCgMmT8lkhPiOD8Jt189NZVInJMJiY327a8k4d2-...) ).
Thank you very much!
Miguel