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?