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Dear Yujing,

Thank you for your response and help. I’m replying to your two points below.

1. make sure ‘tcsh’ is in her PATH I can confirm that I’ve loaded tcsh via the module system and it’s correctly in my PATH. Running which tcsh returns: /apps/fsv2/software/2024a/tcsh/6.24.10-GCCcore-12.3.0/bin/tcsh.

Initially, as the system doesn’t have tcsh at /bin/tcsh, this caused errors (e.g., even recon-all --version would fail), but Roberto kindly provided a workaround. Since then, I’ve been able to run recon-all --help and recon-all --version without issues. However, when I try to run the full recon-all command on a subject, it exits within a few seconds due to UpdateNeeded being looked for in an inaccessible location. I’ve included the full console output below for context. This happens regardless of whether I run it from a bash or tcsh shell.

1. It looks like she has ‘/opt/cycle/jetpack/bin/’ in her PATH. Is ‘/campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup’ her Freesurfer install directory? I’m assuming she sourced Freesurfer environment correctly. After sourcing Freesurfer environment correctly, ‘echo $PATH’ should show $FREESURFER_HOME/bin in the very beginning. Also, check if executables in $FREESURFER_HOME/bin have executable permissions.

* Yes, /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup is my FreeSurfer installation directory. * I believe I’ve sourced the FreeSurfer environment correctly — I’ve successfully tried sourcing from both bash and tcsh and did not previously have these issues on a local Linux machine. * Running echo $PATH confirms that $FREESURFER_HOME/bin appears at the beginning: /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup/bin:… opt/cycle/jetpack/bin/ is also in my Path but at the very end.

Regarding the UpdateNeeded error — when I run which UpdateNeeded, it correctly returns: /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup/bin/UpdateNeeded. So I’m unsure why, at runtime, it's still attempting to use /opt/cycle/jetpack/bin/UpdateNeeded, which leads to the following error:

/opt/cycle/jetpack/bin/UpdateNeeded: Permission denied. if: Expression Syntax.

Please let me know if there is anything else I can check of provide to help resolves this – and thank you again for your support.

Best wishes, Marlene

$ recon-all -s sub-315A_T1w -i /campaign/VB-FM5HPC-001/Marlene/Data_tmp/input/sub-315A_T1w.nii -sd $SUBJECTS_DIR -all fs-check-version --s sub-315A_T1w --o /tmp/tmp.eCskko Tue Jun 17 17:43:12 BST 2025

setenv SUBJECTS_DIR /campaign/VB-FM5HPC-001/Marlene/Data_tmp/output cd /campaign/VB-FM5HPC-001/Marlene/Data_tmp/output /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup/bin/fs-check-version --s sub-315A_T1w --o /tmp/tmp.eCskko -rwxr-xr-x 1 ms2290 rce_VB-FM5HPC-001 18565 Jun 17 09:40 /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup/bin/fs-check-version

freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 $Id$ Linux nimbus-1-spot-fsv2-2-4 4.18.0-553.50.1.el8_10.x86_64 #1 SMP Tue Apr 15 08:09:22 EDT 2025 x86_64 x86_64 x86_64 GNU/Linux pid 15581 Current FS Version freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 Subject does not have a bstampfile, copying /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup/build-stamp.txt Subject FS Version: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /campaign/VB-FM5HPC-001/Marlene/Data_tmp/output Actual FREESURFER_HOME /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup Linux nimbus-1-spot-fsv2-2-4 4.18.0-553.50.1.el8_10.x86_64 #1 SMP Tue Apr 15 08:09:22 EDT 2025 x86_64 x86_64 x86_64 GNU/Linux /campaign/VB-FM5HPC-001/Marlene/Data_tmp/output/sub-315A_T1w

mri_convert /campaign/VB-FM5HPC-001/Marlene/Data_tmp/input/sub-315A_T1w.nii /campaign/VB-FM5HPC-001/Marlene/Data_tmp/output/sub-315A_T1w/mri/orig/001.mgz

mri_convert /campaign/VB-FM5HPC-001/Marlene/Data_tmp/input/sub-315A_T1w.nii /campaign/VB-FM5HPC-001/Marlene/Data_tmp/output/sub-315A_T1w/mri/orig/001.mgz reading from /campaign/VB-FM5HPC-001/Marlene/Data_tmp/input/sub-315A_T1w.nii... TR=7.80, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 0.999974, 0.00720242) k_ras = (0, -0.00720242, 0.999974) writing to /campaign/VB-FM5HPC-001/Marlene/Data_tmp/output/sub-315A_T1w/mri/orig/001.mgz... @#@FSTIME 2025:06:17:17:43:13 mri_convert N 2 e 5.88 S 0.03 U 5.81 P 99% M 54872 F 0 R 1094 W 0 c 20 w 109 I 0 O 30376 L 0.07 0.10 0.14 @#@FSLOADPOST 2025:06:17:17:43:19 mri_convert N 2 0.15 0.12 0.14 #-------------------------------------------- #@# MotionCor Tue Jun 17 17:43:20 BST 2025 Found 1 runs /campaign/VB-FM5HPC-001/Marlene/Data_tmp/output/sub-315A_T1w/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... /opt/cycle/jetpack/bin/UpdateNeeded: Permission denied. if: Expression Syntax.

From: Huang, Yujing YHUANG43@mgh.harvard.edu Sent: 17 June 2025 15:50 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: Running Freesurfer on HPC (Almalinux OS, CycleCloud Compute nodes)

1. make sure ‘tcsh’ is in her PATH 2. It looks like she has ‘/opt/cycle/jetpack/bin/’ in her PATH. Is ‘/campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup’ her Freesurfer install directory? I’m assuming she sourced Freesurfer environment correctly.

https://secure-web.cisco.com/1OPa-utClpZzYVZAm7UT1FwJaDX8H6HzbnM9eZHYpViNrGZ... https://secure-web.cisco.com/1C3fygtctOGKgwcSFtU7swK_Up5CoYO6M1TZ7S739PLgjU8...

After sourcing Freesurfer environment correctly, ‘echo $PATH’ should show $FREESURFER_HOME/bin in the very beginning. Also, check if executables in $FREESURFER_HOME/bin have executable permissions.

Yujing

From: Roberto Scipioni <roberto.scipioni@redoakconsulting.co.ukmailto:roberto.scipioni@redoakconsulting.co.uk> Sent: Tuesday, June 17, 2025 10:34 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Running Freesurfer on HPC (Almalinux OS, CycleCloud Compute nodes)

External Email - Use Caution Dear Sir or Madam,

I am an HPC admin who has been contacted by a user who has installed the Freesurfer in his local directory. However, she keeps getting errors in using the software., for instance:

1. tcsh ONLY works if it is actually present in /bin . This defeats the purpose of using the HPC and its module environment especially using the Cloud as compute nodes are ephemeral.

1. Update needed is searched in /opt/cycle/jetpack/bin/UpdateNeeded rather than in the Software folder /campaign/VB-FM5HPC-001/Marlene/software/freesurfer/freesurfer_backup/bin where it is.

Is there any obvious reason why this may happen. The user is knowledgeable and she has already trying different environment options like those suggested in: https://secure-web.cisco.com/1CCwHd0B7yIez3RoL6XJ5pWTdKUBQ8lUK_gtbn0lLhpB5CQ...https://secure-web.cisco.com/1MlpAewP0l0b-LfNakbZ011g7UhgKbNFb1Xo5kZEtuRQnXEAECu9FmWBZm65-GZQWdvjcO5hkdZoZkHg0wxkpxalrCyIv-Hz2MjKulkVmPp4Jgceh-yH1R8Su4ULTsjJWVmROXuxOFVdbKcfgN_ob42Yz6zYYYxTKSq1HEYGlHhnEHTACMaUXyZ8Tn-MlMhG91GrhSAZS5qi_ecW_7aMnqkB0VWXDgx0xkX3zEno1zcTX1HPWteHEPhzZ512aSjt6ZbiPBerZServOdUOh2ZTab8hINMTmeZn7G40uMxocANYL1X81bZ9lxS15OL_9VzsO723Ea2vQwI8OzZ7kOyfDQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel6downloads

Your help with this would be greatly appreciated. Kind regards

Dr Roberto Scipioni Senior HPC specialist, Red Oak Consulting, UK