fMRI Prep v1.3.0_ Command error

fmriprep
multiecho

#1

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


#2

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.


#3

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


#4

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


#5

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:


#6

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


#7

Awesome! Thanks @trungn :slight_smile: