Dear Sir or Madam,

Indeed we run into the same issues again:

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 2025:06:19:12:23:46 mri_convert N 2 e 5.96 S 0.03 U 5.86 P 98% M 54352 F 0 R 1082 W 0 c 22 w 164 I 0 O 30376 L 32.16 32.15 32.10

@#@FSLOADPOST 2025:06:19:12:23:52 mri_convert N 2 32.22 32.16 32.10

#--------------------------------------------

#@# MotionCor Thu Jun 19 12:23:52 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...

UpdateNeeded: Command not found.

if: Expression Syntax.

It looks like the code may use bash,csh and tcsh at different stages and therefore the scripts get confused and do not run properly.

Also, the UpdateNeeded is NOT found in the FreeSurfer/bin directory although it IS there!

Why does the code not find it?

Any suggestion?

Kind regards


	Dr Roberto Scipioni Senior HPC Specialist, Red Oak Managed Services
	T: +44 (0) 1242 806188 M: +44 (0) 7821 656925 E: roberto.scipioni@redoakconsulting.co.uk W: https://www.redoakconsulting.co.uk

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From: fsbuild <fsbuild@contbay.com>
Sent: 17 June 2025 23:40
To: freesurfer@nmr.mgh.harvard.edu
Cc: Roberto Scipioni <roberto.scipioni@redoakconsulting.co.uk>
Subject: Re: [Freesurfer] Running Freesurfer on HPC (Almalinux OS, CycleCloud Compute nodes)

Currently the tcsh scripts assume a normal Linux .rpm or .deb package installation with a dependency on csh/tcsh being installed under /bin. We do not assume spack, modules, etc. as may be used on clusters is going to configure software images such that it will conflict with that setup. So the tcsh scripts will not run unless /bin/tcsh exists or maybe an alias would work.

If it’s not possible to do a normal install of the .deb or .rpm package to directly install all the system command and library dependencies, then I recommend analyzing the package files to check all the dependencies are otherwise installed.

"If: expression syntax errors" can be from executing the wrong shell. In the case of trying to execute bash scripts, that error might be from running something like “dash” on an Ubuntu flavor of Linux instead of the full-blown “bash" shell.

- R