Statistic Information about fastsurfer HOT 4 CLOSED

You can just run the mri_segstats command on the FastSurferCNN generated labels to get these numbers without running the full recon-surf pipeline. I think there are examples of a call in the recon-surf.sh script.

from fastsurfer.

An example command can be found here: https://github.com/Deep-MI/FastSurfer/blob/master/recon_surf/recon-surf.sh#L457
The FreeSurfer wiki also provides a short overview: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats

Best,
Leonie

from fastsurfer.

Thanks for the guidance. Can I just run mri_segstats command without freesurfer installed in the server? I'm not very familiar with the command line, do you mean I run
mri_segstat --xxx
in the terminal under recon-surf folder?

from fastsurfer.

This is a freesurfer command, so you either need freesurfer installed or at least need to copy the binary and maybe the freesurfer .license file, and set the $FREESURFER_HOME environment variable to where the .license file is and then put the binary into the bin folder below: $FREESURFER_HOME/bin/mri_segstats .
That may work, never tried it. Probably easier to have a local install of FreeSurfer in your space on the server.

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