Parcellating hcp cifti data

Hi All,

Hope someone might be able to shed some light!

I have processed some HCP data using the HCP pipelines. I have my fix cleaned data in cifti format:


I wish to get to use the desikan-killiany parcellation and get mean time series for each of the rois:

wb_command -cifti-parcellate concat_Atlas_hp2000_clean.dtseries.nii $subject_id.aparc.32k_fs_LR.dlabel.nii
COLUMN dk.ptseries.nii

This seems to work and gives me a 70*num_timepoints matrix

The issue I have is that a few of the ROIS have a value of 0 for all time points. For two this corresponds to the corpus callosum which makes sense, but also the right lateral occipital.

When I look at the data in there is no signal drop out that might explain this

Does anyone have any ideas as to what might be going on?