As of FreeSurfer 7+, the kvl* executables were removed, and most of the functionality has been rolled into the samseg pipeline. If you want to run an older version of FS, you can find them here:
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/
You can also build older versions from the source code on our github:
https://github.com/freesurfer/freesurfer
Samseg has not been optimized for exvivo data sets yet, but can be used to generate segmentations on exvivo scans with varying success. Documentation on samseg can be found here:
https://freesurfer.net/fswiki/Samseg
For the best segmentations, I'd recommend using volumes with the background masked out. Also, it is worth mentioning, if you are attempting to segment a hemisphere, samseg will likely place labels for both hemispheres (eg both lh-wm and rh-wm will show up as
labels the white matter of a single hemi), and you will probably want to combine the labels after they are generated by samseg.
External Email - Use Caution
Hello Dear Developers,
I am trying to segment ex vivo hemisphere brains following instructions here “https://freesurfer.net/fswiki/ExvivoRecon”. I was just proceeding to the Segment White Matter section and found that none of the kvl commands can be found in my installation. They
are also not found in the freesurfer/bin folder.
I searched the archive and found that there was one case that’s very similar to mine, but it occurred back in 2012 and on a Mac distribution. (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg24547.html)
Freesurfer version: freesurfer_ubuntu20-7-dev_amd64.deb
Platform: WSL-Ubuntu on Windows.