Thanks for reporting the bug. We have fixed it in our dev version.
To locate and fix surfreg in your Freesurfer 7.4.1 environment:
1. which surfreg
2. open the surfreg reported from step #1 in a text editor, fix the bug in line 107 - change “freesurfer/subjets” should be “freesurfer/subjects”
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Suzanne Witt
Sent: Tuesday, December 3, 2024 12:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] surfreg error: typo in mris_convert command
External Email - Use Caution
Hello,
I recently updated to Freesurfer 7.4.1 (previously running 7.2.0) and am trying to get my full workflow to run. I am getting the following error when I try to run “surfreg –s test –t fsaverage_sym –lh –xhemi –no-annot”:
#CMD# mris_convert --center --vol-geom /usr/local/freesurfer/subjets/fsaverage/mri/orig.mgz /usr/local/freesurfer/subjects/test/xhemi/surf/lh.fsaverage_sym.sphere.reg /usr/local/freesurfer/subjects/test/xhemi/surf/lh.fsaverage_sym.sphere.reg
centering surface
error: mghRead(/usr/local/freesurfer/subjets/fsaverage/mri/orig.mgz, -1): could not open file
It looks as if there is a typo in the path to “orig.mgz”, where “freesurfer/subjets” should be “freesurfer/subjects”.
I’ve not found anything searching for “surfreg” in the message board that points to a corrected surfreg binary.
- Freesurfer version: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460
- Platform: python:3.9-debian Docker image
- uname -a: Linux 828abe00572a 6.5.0-1024-gcp #26~22.04.1-Ubuntu SMP Fri Jun 14 18:48:45 UTC 2024 x86_64 GNU/Linux
- Full terminal dump attached
Thanks and cheers.
Suzanne T. Witt, PhD
Scientific Solutions Engineer
she/her
