External Email - Use Caution
Hi,
I am getting the following error on a Mac running MacOS Ventura 13.7.6, when
trying to run
>> sudo FREESURFER_HOME=/Applications/freesurfer/8.0.0 bash fs8_updates.sh
Password:
Machine context is darwin_arm64
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 196 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
curl: (22) The requested URL returned error: 404
*** Error: download of default config failed - if this error persists please
notify the Freesurfer team.
Any help in updating the URL would be greatly appreciated.
Thank you,
Mira
_______________________________________________
Mira Michelle Raman
Senior Neuroimaging Data Analyst
BrIDGe Lab, Division of Interdisciplinary Brain Sciences
Stanford University
1520 Page Mill Rd, 160.12
Palo Alto, CA 94304
________________________________
From: [email protected]
<[email protected]> on behalf of fsbuild
<[email protected]>
Sent: Friday, April 11, 2025 5:24 PM
To: [email protected] <[email protected]>
Subject: [Freesurfer] Updates/bug fixes available for the 8.0.0 release
External Email - Use Caution
Some updates/bug fixes are available for an existing installation of the
Freesurfer 8.0.0 release. The list of files you can update along with a brief
comment about the change(s) are:
$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.
Please note THESE UPDATES DO NOT CHANGE THE OUTPUT OF THE recon-all COMMAND.
If these updates are of interest to you, then please go the 8.0.0 download URL,
https://secure-web.cisco.com/1rUuA4kpgnJCa4nJf5wZq_2h1D18JWat2BgRrdJuw9kQRZlIpphuEbQXS94PsfOyopKRX44CaWGYJNAeeEbxLp3TLPEQbH3oOHOeN1Dgu5nSJ_ma-KcofKjCqYBf_QVD4e_y072Efiox_10OaERytgQgdn2ONoSMB3Hirbj5ltq0aI8SJ4qKyoWfkydHxOZu55_n9dgpsCcC8yw3_rmG5fLmX6kvn0cLiGAICkB966HcXGWh99dAhijpoTeYc6KcLTNiXu7391Op-B83S_Kk-IR59caB8LiZBzsqEWOeyGLVyl22VPRisY98U6UNOhUvur77PzdvonlgvQGyuo4Z0OQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F8.0.0%2F
- and download the fs8_update.sh script.
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.
_______________________________________________
Freesurfer mailing list -- [email protected]
To unsubscribe send an email to [email protected]
https://mail.nmr.mgh.harvard.edu/mailman3/lists/[email protected]/
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
