Problems with fMRIPrep Outputs

Software Support
1

Summary of what happened:

I’m new to fMRIPrep and have a question. I ran it on a 30-min resting-state session, and it seems to have finished successfully. But the inflated surface (like inflated.surf.gii) is missing, and I can’t find the functional data projected onto the surface (e.g., func.gii or .dtseries.nii). Any idea what might be wrong?

Command used (and if a helper script was used, a link to the helper script or the command generated):

fmriprep dataset dataset/derivatives participant \
         --fs-license-file license.txt \
         --omp-nthreads 8 \
         --nthreads 32 \
         --stop-on-first-crash \
         --mem_mb 30000 \
         --output-space MNI152NLin2009cAsym T1w \
         --random-seed 34 \
         -w work

Version:

fMRIPrep 24.1.1.

Environment (Docker, Singularity / Apptainer, custom installation):

PUT ENVIRONMENT HERE

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

PASTE LOG OUTPUT HERE

Screenshots / relevant information:

2

Hi @Ibai_Azpeitia_Loiti1,

In the future please fill out the entire software support template. You can see I edited in for you this time, you can edit your post to add the missing information.

You did not specify any CIFTI (e.g., —cifti-output)or GIFTI (e.g.,—output-spaces fsnative) output.

Best,
Steven

3

Hi Steven, thanks a lot for the response, I will try with those flags!

4

Just a note on the inflated surfaces. I believe that running smriprep will still output them, but they are not produced by fMRIPrep because they are not necessary for fMRI preprocessing.

They are mainly useful for visualization. If you can load a GIFTI inflated surface, you can probably load a FreeSurfer [lr]h.inflated surface, and if not, you can just run mris_convert.

For an inflated fsLR mesh in subject space, that’s a different matter, and needs implementation. feat: Output fsLR meshes on subject surfaces by effigies · Pull Request #460 · nipreps/smriprep · GitHub I think it would probably be best as a standalone tool after the fact.