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.

 

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. 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.

 

 

 

 

 

 

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://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac

https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux

 

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

 

 

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