Your recon-all command doesn't have the directive to tell it what to run - add option '-all' to your command.
See this wiki page for detail https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Weisholtz, Daniel S.,MD Sent: Thursday, January 25, 2024 12:51 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all ends prematurely without error Hello FreeSurfer team, I have been using FreeSurfer for some time without difficulty, but I recently encountered a problem that I cannot overcome. When I run recon-all using a command like this: recon-all -s b047test -i /Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz the process terminates in just a few seconds without error. The output reads as follows: fs-check-version --s b047test --o /var/folders/44/ndjzqbx515991v_9vt0j8spr0000gq/T//tmp.IMS2K1 Thu Jan 25 12:35:02 EST 2024 setenv SUBJECTS_DIR /Users/danielweisholtz/Coregistration/subjects cd /Users/danielweisholtz /Applications/freesurfer/7.4.1/bin/fs-check-version --s b047test --o /var/folders/44/ndjzqbx515991v_9vt0j8spr0000gq/T//tmp.IMS2K1 -rwxr-xr-x 1 root wheel 18565 Jun 14 2023 /Applications/freesurfer/7.4.1/bin/fs-check-version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 $Id$ Darwin i.partners.org<http://i.partners.org> 21.6.0 Darwin Kernel Version 21.6.0: Mon Aug 22 20:19:52 PDT 2022; root:xnu-8020.140.49~2/RELEASE_ARM64_T6000 arm64 pid 6977 Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying /Applications/freesurfer/7.4.1/build-stamp.txt Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /Users/danielweisholtz/Coregistration/subjects Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 Darwin i.partners.org<http://i.partners.org> 21.6.0 Darwin Kernel Version 21.6.0: Mon Aug 22 20:19:52 PDT 2022; root:xnu-8020.140.49~2/RELEASE_ARM64_T6000 arm64 /Users/danielweisholtz/Coregistration/subjects/b047test \n mri_convert /Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz /Users/danielweisholtz/Coregistration/subjects/b047test/mri/orig/001.mgz \n mri_convert /Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz /Users/danielweisholtz/Coregistration/subjects/b047test/mri/orig/001.mgz INFO: using NIfTI-1 qform reading from /Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz... INFO: This is an unsigined short. TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) writing to /Users/danielweisholtz/Coregistration/subjects/b047test/mri/orig/001.mgz... ~/Coregistration/subjects/b047test/mri/transforms ~/Coregistration/subjects/b047test ~/Coregistration/subjects/b047test Started at Thu Jan 25 12:35:02 EST 2024 Ended at Thu Jan 25 12:35:06 EST 2024 #@#%# recon-all-run-time-hours 0.001 recon-all -s b047test finished without error at Thu Jan 25 12:35:06 EST 2024 done The subject folder is created along with some of the files, but not much is actually there. I had been using FreeSurfer 7.2.0 but I upgraded to 7.4.1, and this did not resolve the problem. Initially, I thought the problem was with the source file I was using, but I tested it with an MRI that I had previously used successfully with recon-all, and I got the same error. So something seems to have changed with my system that is causing this problem. I am running FreeSurfer on a Mac using MacOS 12.6. Many thanks for any assistance you can provide. Sincerely, Dan Weisholtz
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