My problem is the following: I have some CIFTI data obtained by using fMRIprep. The data is in fsaverage5 space and I would like to adapt a cortical/subcortical version of the Glasser atlas (dlabel file) that I have been using for HCP style data to parcellate this data.
I was able to successfully resample the atlas to the fsaverage5 space by using connectome workbench. However, when I try to extract the timeseries of the parcels from the fMRIprep preprocessed data, 2 parcels of the Glasser atlas only return nan: “R_H_ROI” and “L_H_ROI” . These are cortical regions that seem to be very close to the hippocampus.
On the HCP mailing list, I have been told that the reason could be a different type of masking in fMRIprep, which “cuts off” these two regions so that they are completely missing from the resulting CIFTI file. In this case, they argue that “This would mean that fmriprep-processed results, with their current settings/templates, would never contain data inside those parcels.”
Would you have any insights on where this might be happening along the pipeline and/or any suggestions to recover the missing regions?
Thank you very much.
This could be case. When forming the CIFTI file, we first load up FreeSurfer’s aparc annotation for the specific surface (in this case, fsaverage5's ?h.aparc.annot) and remove all the unknown parcellations. The purpose of this was to remove vertices within the medial wall (to be more in-line with HCP), but may remove more than intended. However, fmriprep outputs the BOLD data resampled to each fsaverage5 hemisphere, and these GIFTI files include the unknown parcellations… though you would have to generate a new CIFTI file from these surfaces yourself.
At present, fmriprep-generated CIFTI files consist of two different spaces:
fsaverage5 or fsaverage6 cortex
MNI152NLin2009cAsym subcortex
but will shortly allow users to output their data to HCP grayordinates.
It helped a lot and solved the problem! Here is the solution in case it is useful to anyone.
First, I got the subcortical labels from the original CIFTI: