The Schaefer-Yeo atlases exist in volumetric form here:
Note that they are in MNI-2009c space. If you followed Example 11b, were you using TT_N27 as the alignment template, instead? If that is the case... I am not sure if we have a version of these in the TT_N27. Would have to ask @dglen . (Also, might have to ask him where the 1000-parcellation is, since I don't see it in that download directory?) Also, note that the 1000-parcellation is quite fine, and so you might want to see how typically large those regions are compared to your voxels---if they are similar, I am not sure it would make much sense to use those.
Note also that Example 11b is for a voxelwise analysis, and therefore includes blurring. You probably would not want to include blurring if you are running and ROI-based analysis, because you will artificially spread information across ROI boundaries before estimating time series. Example 11b uses FS information not for ROI-based analysis, but for ventricle and WM maps for ANATICOR regressor estimation.
But to the functionality you had asked about, for when those initial issues/questions are resolved:
You will want to resample the atlas to match your final EPI data resolution. If you are doing a resting state analysis (which is what Example 11b does), then this would be your
errts* file in the afni_proc.py results directory. To resample that Schaefer_7N_400.nii.gz atlas to the DSET_ERRTS file, as well as retain the label information that AFNI includes in atlases you can run:
# resample the SY-400 to the errts data, with nearest-neighbor interp
# NB: 'NN' is actually an all-caps keyword to keep in the cmd
-input Schaefer_7N_400.nii.gz \
-master DSET_ERRTS \
-prefix sy7n400_in_errts.nii.gz \
# reattach labels and other header niceties for the atlas
# NB: 'INT_CMAP' is actually an all-caps keyword to keep in the cmd
3drefit -copytables Schaefer_7N_400.nii.gz sy7n400_in_errts.nii.gz
3drefit -cmap INT_CMAP sy7n400_in_errts.nii.gz
You can verify that the DSET_ERRTS and new atlas are on the same grid by running:
3dinfo -same_all_grid DSET_ERRTS sy7n400_in_errts.nii.gz
... which should produce five 1s if the five examined properties all match (woe betides if that is not the case---please ping back if so).
Finally, the way I would get the time courses would be to do so as an output of 3dNetCorr, which will also calculate a correlation matrix (command below has been amended from the original post, as @pmetzak correctly noted in the reply to this message: the option I should have put here originally was
-ts_out, which is now included, as that dumps out the set of average ROI time series to a text file):
-inset DSET_ERRTS \
-in_rois sy7n400_in_errts.nii.gz \