Update build.sh

[lucsanara]

Hi!

Could you please update aslprep version?

Thanks in advance

[lucsanara]

Hi!

I think there has been a bug with this. Could you please keep us updated in case the update successes?

[stebo85]

dear @lucsanara - yes, there was a problem, which is fixed now. So the updated version should be live in a couple of hours.

[lucsanara]

Dear @stebo85, We are struggling when aslprep through Neurodesk. It is arising the following error: traits.trait_errors.TraitError: The 'subjects_dir' trait of a RobustTemplateInputSpec instance must be a pathlike object or string representing an existing directory, but a value of '/home/jovyan/freesurfer-subjects-dir' <class 'str'> was specified. Even when we are not providing --fs-subjects-dir. We have already contacted aslprep developers, though we wanted to ask you it case it could be because of using a singularity container. Thank you in advance!

[stebo85]

1. Can you try to create this directory and then run again?

2. Can you try to run this before you start aslprep:

export SINGULARITYENV_SUBJECTS_DIR=~/freesurfer-output export APPTAINERENV_SUBJECTS_DIR=~/freesurfer-output

Thank you

Steffen

--

W: https://mri.sbollmann.nethttps://mri.sbollmann.net/ | W: https://www.neurodesk.orghttps://www.neurodesk.org/ | T: https://twitter.com/sbollmann_MRI | G: https://github.com/stebo85

Book meeting: https://calendly.com/s-bollmann/meeting

---

From: lucsanara @.> Sent: Tuesday, September 24, 2024 7:31:31 PM To: NeuroDesk/neurocontainers @.> Cc: Steffen Bollmann @.>; Mention @.> Subject: Re: [NeuroDesk/neurocontainers] Update build.sh (PR #807)

Dear @stebo85https://github.com/stebo85, We are struggling when aslprep through Neurodesk. It is arising the following error: traits.trait_errors.TraitError: The 'subjects_dir' trait of a RobustTemplateInputSpec instance must be a pathlike object or string representing an existing directory, but a value of '/home/jovyan/freesurfer-subjects-dir' <class 'str'> was specified. Even when we are not providing --fs-subjects-dir. We have already contacted aslprep developers, though we wanted to ask you it case it could be because of using a singularity container. Thank you in advance!

— Reply to this email directly, view it on GitHubhttps://github.com/NeuroDesk/neurocontainers/pull/807#issuecomment-2370762309, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AA6V2W7U25MLYUN33AIBIX3ZYEWPHAVCNFSM6AAAAABOKZUPACVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZQG43DEMZQHE. You are receiving this because you were mentioned.Message ID: @.***>

[stebo85]

@lucsanara - did any of my suggestions work? If yes, then I can document it.

[lucsanara]

@stebo85 sorry for the late reply. At first it seemed to work, but it then raised a new error:

Not sure which is the problem as outside neurodesk it works.

[stebo85]

@lucsanara - that's great to know!

What command line options are you running ASLprep with?

What do you mean with "outside neurodesk it works"? Does it mean the singularity/apptainer container works and this error only comes up when running it through the neurodesktop interface?

[lucsanara]

Hi! thanks for your answer @stebo85 Here I show you the command: aslprep neurodesktop-storage/Agueda/BIDS neurodesktop-storage/Agueda/BIDS/derivatives/aslprep participant --participant-label sub-388 --force-bbr --basil --ignore t2w --fs-subjects-dir /Users/agueda/neurodesktop-storage/Agueda/BIDS/derivatives/freesurfer/sourcedat/freesurfer_pre/sourcedata --bids-filter-file neurodesktop-storage/Agueda/BIDS/BIDS_filter_file.json --fs-license-file neurodesktop-storage/Agueda/BIDS/license.txt --skip_bids_validation -vv -w neurodesktop-storage/Agueda/BIDS By outside neurodesktop I mean when running aslprep in the computer terminal.

[stebo85]

Ok, is this on apple silicon or on an x86 processor?

If on apple silicon: is it running through podman or docker?

[stebo85]

@lucsanara - can you also share the crash file or anything that contains more information about the error? I can currently not reproduce the problem.