fMRI Prep v1.3.0_ Command error

Hi NeuroStars,

I’m trying to run fMRI Prep v1.3.0 on ME-data. However, when I run fMRI Prep v1.3.0, I seem to run into the error shown below. This is observed even when I run it with Python 3.7 set in the environment.

Here are the flags used:

module load fmriprep/1.3.0
unset PYTHONPATH

Run fmriprep

fmriprep
–participant-label ${subject}
–output-space {T1w,template}
–t2s-coreg
–fs-no-reconall
–use-syn-sdc
–mem_mb 80000
-n-cpus 8
–fs-license-file ${fslicense}
-w ${workdir}
${bidsdir}
${derivsdir}
participant

Any idea why this could be happening?

Cheers,
Thapa

It seems like you are using containers here, Singularity in particular. Can you give more details about your settings? More specifically, what is that module fmriprep/1.3.0 exactly loading?

Most likely, you’ll need to apply this workaround FMRIPREP from Singularity: UnboundLocalError, if fmriprep 1.3.0-post1 does not fix this particular problem for you.

Finally, there is an error on your command line: --output-space {T1w,template} should be --output-space T1w template instead.

Hi @oesteban

Thank you for your reply.

I’ve followed the link, really helpful :slight_smile:

Also, I’ve managed to run fMRI Prep v1.3.0 by having a temp-templateflow folder saved to the environment where I want to run it (see image for details on templates within the temp-templateflow folder).

I am currently working to set this in the fMRI Prep container so that I don’t run into this error when looping fMRI prep over multiple subjects.

Here’s my workaround with this issue: @effigies

@TribikramT, could you clarify the workaround that helped you?

Hi @oesteban

Here are the details:

  1. Re-created the singularity image to make it writable

  2. Inside the container, renamed the /opt/templateflow to /opt/templateflow.bkup. Then created a new, empty directory /opt/templateflow

  3. Created a read-only singularity image

  4. Using SINGULARITY_BIND to bind the /opt/templateflow directory inside the container with a writable directory on M3 filesystem

Hope this helps :slight_smile:

Hi @TribikramT, feel free to tag me if there is any question re the fix. Trung.

1 Like

Awesome! Thanks @trungn :slight_smile:

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