How to get specific outputs with fMRIPrep

Software Support
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1

Summary of what happened:

I am applying the fMRIPrep pipeline to data of a single subject to validate the command inputs I select so as to get the desired outputs and then apply the command to a whole dataset. In my case, I want to have at least the following outputs: The preprocessed structural T1w and T2w volumes in the MNI space, the preprocessed BOLD rs-fMRI volume in MNI space also, and when it comes to the surface space I need the inflated left and right hemisphere brain models, along with the volumetric BOLD rs-fMRI data projected on the surface (CIFTI format). Which are the command options I need to set?

I attach the command I used.

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

fmriprep \
  /home/jovyan/Desktop/dataset/raw \
  /home/jovyan/Desktop/dataset/derivatives \
  participant \
  --nprocs 120 \
  --omp-nthreads 4 \
  --mem 240000 \
  --skip_bids_validation \
  --output-spaces MNI152NLin2009cAsym:res-2 T1w T2w \
  --bold2anat-init t2w \
  --fs-license-file /home/jovyan/Desktop/freesurfer/license.txt

Version:

fmriprep 25.1.3

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

Neurodesktop

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

You need the —cifti-output flag.

Best,
Steven

3

Okay @Steven, thanks for the help. Do you know whether this command would output both the T1w and T2w structural volumes in MNI space?

Thank you!

4

If you specify an MNI output in your --output-spaces then yes.

5

In the outputs I do in fact get the T1w volume in the specified MNI space, but I do not seem to find the preprocessed T2w volume in MNI space.

6

For T2w in MNI, you might need to apply the T1w-to-MNI xfm to it after processing.