Hi Daniel,

Thank you for your input. I have a follow up question. I also watched your video online as a reference (https://cbmm.mit.edu/video/09-alignment-and-atlases-part-1-2).

Questions pertaining my use: I want to register the EPI data set to say it's 5th brik. I wasn't originally trying to register it to an anatomical set. Would the following code be appropriate?

align_epi_anat.py \
-anat $AnimalID/$FolderID/${AnimalID}_${FolderID}+orig  \
-epi $AnimalID/$FolderID/${AnimalID}_${FolderID}+orig \
-rigid_equiv \
-anat_has_skull no \
-epi_strip None \
-epi_base 5

My first attempt with this code produced a registered set ($AnimalID/$FolderID/${AnimalID}_${FolderID}_al+orig) that was completely off. Any feedback or clarity to the source code to use would be greatly appreciated. Thank you.

Edwin