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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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 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 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