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$FREESURFER/bin/gtmseg $FREESURFER_HOME/bin/gtmseg

The current list of files you can update in your 8.0.0 Freesurfer installation are as follows (including a brief comment about the change(s):

$FREESURFER_HOME/bin/csvprint
Script changed to use python3 - values for eTIV should no longer be misreported as 0.00 for data processed with the recon-all command

$FREESURFER_HOME/bin/recon-all
Fixes for options -autorecon1, -nonuintensitycor.  Add flag -no-fix-ga to turn off fixing of gyrus ambiens part of the cortex label.

$FREESURFER_HOME/bin/gtmseg
gtmseg now uses samseg by default

$FREESURFERR_HOME/bin/xhemireg
Modifications to make xhemireg work with 8.0.

$FREESURFER_HOME/bin/xcerebralseg
gtmseg now uses samseg by default

$FREESURFER_HOME/bin/post-recon-all
gtmseg now uses samseg by default

$FREESURFER_HOME/python/packages/gems/SamsegLongitudinal.py
fix parameters to surfa.image.transform()

$FREESURFER_HOME/etc/recon-config.yaml 
Added option -no-fix-ga to turn off fixing of gyrus ambiens part of the cortex label.


If these updates are of interest to you, then please go the 8.0.0 download URL,
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/8.0.0/
- and download the fs8_update.sh script.

Please note THESE UPDATES DO NOT CHANGE THE OUTPUT OF THE recon-all COMMAND.

On MacOS run the script as follows,
$ sudo FREESURFER_HOME=/Applications/freesurfer/8.0.0  bash  fs8_updates.sh

On CentOS and Rocky8 Linux run the script as follows,
$ sudo FREESURFER_HOME=/usr/local/freesurfer/8.0.0-1  bash  fs8_updates.sh

On Ubuntu Linux run the scripts as follows,
$ sudo FREESURFER_HOME=/usr/local/freesurfer/8.0.0  bash  fs8_updates.sh

You will be prompted on the command line as to whether or not you want to install each file, including displaying the description of the change(s) listed above.

rel7downloads/rel8updates (last edited 2025-04-11 20:22:54 by buildqa)