Fmriprep not outputting gifti's with freesurfer enabled

I’m looking to generate a functional connectivity matrix from some fmri volumes (ideally mapped to vertex-corresponded freesurfer surfaces in fsnative). I have been run the raw data through fmriprep with freesurfer enabled.

According to the fmriprep documentation Outputs of fMRIPrep — fmriprep version documentation, I should expect to see a GIFTI in the func/ directory of the output of fmriprep that I’m not finding:

sub-<subject_label>/
func/
sub-<subject_label>_[specifiers]space-T1w_desc-aparcaseg_dseg.nii.gz
sub-<subject_label>
[specifiers]space-T1w_desc-aseg_dseg.nii.gz
**sub-<subject_label>
[specifiers]_space-<space_label>_hemi-[LR]_bold.func.gii**

Whereas my output is (for each run):
func/
sub-22_ses-2_task-rest_run-1_space-MNI152NLin2009cAsym_boldref.nii.gz
sub-22_ses-2_task-rest_run-1_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
sub-22_ses-2_task-rest_run-1_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz

Any ideas what’s going on?

Can you share your full fmriprep command?

Sure, it’s:

sudo docker run -ti --rm -v /home/quintin_frerichs/data/mdma-fmri-imperial-copy:/data:ro -v /home/quintin_frerichs/data/fmriprep-output/mdma-fmri-imperial-output:/out -v /home/quintin_frerichs/license.txt:/opt/freesurfer/license.txt nipreps/fmriprep:latest /data /out participant --participant_label sub-22

Thanks. It looks like you’re just taking the default output space, which is --output-spaces MNI152NLin2009cAsym, and are not specifying a surface space. If you want fsnative in addition to MNI, use --output-spaces MNI152NLin2009cAsym fsnative.

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