T1 Volume Processing Nipype Error

[SHIYUN WA]

Hi Clinica Team,

There are some bugs when we run the command `clinica run t1-volume [OPTIONS] BIDS_DIRECTORY CAPS_DIRECTORY GROUP_LABEL` to process the MRI in the BIDS directory. I attached the complete error information and the sbatch script we used in a separate file.

Our clinica conda environment is built on a cluster server, and we have some built-in MATLAB modules in it:

`matlab/r2018a    matlab/r2021a    matlab/r2021b    matlab/r2023a    matlab/r2023b    matlab/r2024a    matlab/r2025a    matlab/r2025b`

We followed the SPM wiki instructions to install `spm_25.01.02.zip` and `spm12_updates_r7771.zip`. In the sbatch script file, we exported the path of spm and loaded the MATLAB module. I tried to explicitly add spm path to the loaded Matlab module, but the bug always exists no matter I include this or not.

So, based on some possible reasons about the bug, my question is:

1. When installing SPM, are we supposed to only use SPM12? If so, how can we find the old SPM12 zip file? Their Github release doesn’t provide it now, only the source code (https://github.com/spm/spm12) is available.
2. Regarding MATLAB, can we load the available modules in our cluster? Or do we still need to directly install a MATLAB runtime and then install SPM12 standalone accordingly?

Thank you for your time and help in advance!

Best,

Shiyun

[Alice Joubert]

Hello,

Sorry for the delayed response. 

- What version of clinica + SPM set-up (SPM standalone yes or no, version + MATLAB or MCR) did you use when you obtained that log file ? It looks like an error that was fixed in the previous months but I want to make sure.

- Yes we cannot find the old version of SPM12 either. We are currently working on a release to provide a solution for all clinica users to adapt for SPM25 standalone in T1-Volume and PET-Volume pipelines. It should be released next week if all goes well.

- With that solution you would need the MCR and SPM standalone versions and could not use your modules anymore. Would that be a problem for you ?

Best,

Alice

[Kai-Chun Yang]

Dear Alice,

Thank you for your great work on Clinica.

I am currently attempting to perform FDG PET quantification using clinica -v run t1-volume via WSL2 on Windows 11. However, I have encountered difficulties configuring MATLAB and SPM12. Specifically, Clinica/Nipype fails to launch MATLAB in batch mode, causing the pipeline to stall.

Given these issues, I suspect using the SPM Standalone version might be a more stable solution. However, I found the documentation regarding support for SPM Standalone in Clinica v0.10.1 to be slightly ambiguous:

One section states: "We are considering using only SPM25 standalone for next versions of clinica (v > 0.10.0)"  
(https://aramislab.paris.inria.fr/clinica/docs/public/dev/)

Another section suggests: "Clinica does not support this version [SPM25] yet... If you want to use pipelines relying on SPM please use SPM12." 
(https://aramislab.paris.inria.fr/clinica/docs/public/dev/Software/Third-party/#known-issue-with-matlab-and-spm12)

Could you clarify if SPM25 Standalone is currently supported in version 0.10.1, or if I should stick to configuring SPM12?

I appreciate your time and help.

Best regards,

Kai-Chun (David)

[Alice Joubert]

Hello,

Thanks for reaching out ! It is indeed a bit confusing. The support of spm25 is currently a work in progress. I have a PR that is supposed to be merged soon that will allow to use SPM25 standalone on the dev version. If you can wait a little (1 to 2 weeks maximum) I would drop SPM12 and configure spm25. I can update you when I have merged the PR into the dev version. The release containing that update could take some more time.

Hope that helps,

Alice

[David Yang]

Dear Alice,

Thanks for your kind reply and all your great support.

Best regards

Kai-Chun (David)

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Kai-Chun Yang MD, PhD

Department of Psychiatry
Taipei Veterans General Hospital, Taipei, Taiwan