I would like to use the cifti output in fsaverage5 space from fmriprep. The output has 9402 (L) & 9422 ® vertices out of 10242. I would like to know which vertices from fsaverage5 are excluded.
I am trying to use the aparc and aparc.a2009s parcellations. I assume the medial wall was excluded. Is there a file that defines these vertices?

Thank you for your question. What version of fmriprep are you running? It appears there may be a solution to this cifti vertex mismatch in the new fmriprep version (1.3.0)

Looking deeper - you are correct that the medial wall is being removed. Current cifti outputs are not HCP-compatible. We are planning to add HCP-ciftis compatibility soon.

I am using fmriprep-1.3.0.post1 (with the tf patch).

In my output, the *bold.dtseries.nii has 49112 vertices with 9402 and 9422 vertices in the left and right hemispheres respectively. The fsaverage5 space has 10242 vertices in each hemisphere and the label files of the medial wall in freesurfer have 888 and 881 vertices. Therefore I expected the cifti file to show 9354 (10242-888) and 9361 (10242-881) vertices in the left and right hemispheres. So, I was wondering if another labeling of the medial wall was used and where to find this information.

Also, could you please confirm whether the *bold.dtseries.nii and hemi-L.func.gii do not have any of the confound variables regressed out? Thanks!

We are actively working on the HCP-compatibility with the ciftis. Regarding the labeling - it uses the [lr]h.aparc.annot files and it excludes “unknown” vertices

fMRIPrep does not run confounds regressions or any other filtering. We provide the confound.tsv file to regress confounds out with your preferred tool.

Did you solve the cifti vertex mismatch problem between CIFTI dense time series and fsaverage5?
I’m trying to find the index of excluded vertices of CIFTI output (9402(L) & 9422® vertices out of 10242).