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.
1. Freesurfer version: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 2. Platform: python:3.9-debian Docker image 3. 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 4. Full terminal dump attached
Thanks and cheers.
Suzanne T. Witt, PhD Scientific Solutions Engineer suzannewitt@flywheel.iomailto:suzannewitt@flywheel.io she/her flywheel.iohttps://secure-web.cisco.com/1EXwUbHzeZQUocP35tQvPjHOZdzbGXFKv82eXyK4my6MCW-5rZ9eaLh7zmJ0LXjh2XTegk-0GKWUiZT90E-lzfCghn2Ja6IIe5Kb1elllft6YbCzjeyLYThDyZnEjVRIBuA2uHGwzwQcxJAEyPaXouW8qq7a8PGnYvmoS7YeWypr_UZZo-QVWcxjmXEkJ9JpsmjeK5R9VDUF1h9ZZyQdGu46hyfRRWHBmDtypUjCHX9znPb5RNS-LDXcz58lFiDy1D8Vy1KK7goCjzLfVCnOD7BsSvpfmhuR6jEEsL9R5PgK7RnCCBP15iNJAOZaJbbMf/https%3A%2F%2Fflywheel.io%2F%3Futm_source%3Demail%26utm_medium%3Dsignature%26utm_campaign%3Demployeesignature [A close-up of a logo Description automatically generated] Sign up to receive our monthly updateshttps://secure-web.cisco.com/1EcNbd--t7q66h14Fxl_ENEIp5a1umwwa3y9OXMrD5_xUeVkMKa5oa2C2-MMgKv2tDeyjeueUhcM3cMOLKPv_QF_upOw3BZ97rc8370-RAKiDki6eu38J1ab_Rne_qbsN9rn40aKh4zgwCHfe_9VXdtKkZ2WtHx6brHduZw6mLBAtljbsTQqhkaT-Mbpam_060PNxRrC_RK5pez25vKaUGgb2uQ6Ri-J3Mh4uhTRPwin5aDUYym15p7FEvFv4JGOAA49DeYW7Bnh9xfl9-8wYAn1m_CrkDP5Vik8c1Ne1PFvGLAd36Y9f_66ii86PfJVf/https%3A%2F%2Fflywheel.io%2Fsubscribe-to-newsletter%2F%3Futm_source%3Demail%26utm_medium%3Dsignature%26utm_campaign%3Demployeesignature
