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.
