Preprocessing for atlas based connectivity matrices

2

With regard to the FMRIPREP-related portions of this pipeline:

  1. ICA-AROMA is calculated in the MNI template space, which we do not calculate (to save time and disk space) if no MNI outputs are requested, so you’re going to need to use --output-space T1w template (output spaces are separated by a space, not a comma).

  2. That looks reasonable. I haven’t tried to denoise results in the subject native space, so I can’t attest that that works. Please let us know if you need to make any modifications, and we’ll updated the documentation.

  3. I don’t have experience here, so I’ll leave commentary to others.

  4. While we work to keep FreeSurfer and FMRIPREP outputs aligned, they aren’t always sampled exactly the same. For that you’re going to need to apply the FreeSurfer -> T1w transform. It’s not currently an output of fmriprep (though it probably ought to be), but you can create it with:

tkregister2 --noedit --mov /preproc/freesurfer/sub-<subject_label>/mri/T1.mgz \
    --targ /preproc/fmriprep/sub-<subject_label>/anat/sub-<subject_label>_T1w_preproc.nii.gz \
    --regheader --ltaout fs_to_t1w.lta

And then apply it:

mri_vol2vol --mov /preproc/freesurfer/sub-<subject_label>/mri/aparc+aseg.mgz \
    --targ /preproc/fmriprep/sub-<subject_label>/anat/sub-<subject_label>_T1w_preproc.nii.gz \
    --lta fs_to_t1w.lta --o aparc+aseg.nii.gz --nearest

Hopefully others can advise you more on the connectivity analysis-specific portions of your question.

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