I am trying to align the aparc+aseg file from freesurfer to my skull-stripped brain in AFNI (original space) by aligning the skull-stripped brain from freesurfer first, and applying that to aparc+aseg, as follows:


@Align_Centers -base mprage_ns+orig. -dset brain+orig -cm -child aparc+aseg+orig.


This creates a brain_shft+orig file that is perfectly aligned to the mprage_ns file, with the accompanying 1d transformation file. However, the aparc+aseg file is not shifted at all.

I have used this function before and it has worked (i.e. produced both brain_shft and aparc+aseg_shft files), so it seems like there may be an issue with the -child flag? Is this the case? If not, is there an equivalent workaround, perhaps using 3dAllineate?

I am using the current (2/13) version of AFNI.