Hi Philipp,

ROI (average or multiple PC) regression can be done via -regress_ROI or -regress_ROI_PC, where masks are passed via either -anat_follower_ROI or -mask_import (or via the internal 3dSeg generation).

Example 11 shows use of -anat_follower_ROI (with FreeSurfer ROIs), which can then be applied with either -regress_ROI or -regress_ROI_PC. In this case, the ROIs start of in "original anat" space, and are warped to the final space on the EPI grid.

Example 11b shows use of -mask_import, which can be similarly applied. This ROI must already be in the final space on the EPI grid. It will not be warped at all. A "brain" mask could even start as a standard space mask this way.

You can even give multiple ROIs to apply this way, and even mixing -regress_ROI and -regress_ROI_PC across them. Note that the default use of "brain" means the EPI brain mask, not the anatomical one, if that matters.


Getting to your case, assuming the cortex sheet is like a FreeSurfer mask, pass it with -anat_follower_ROI and apply it with -regress_ROI, e.g.

-anat_follower_ROI   cortex  epi  FS_cortex.nii.gz \
-regress_ROI            cortex

Does that seem reasonable?

- rick