Hi Guys:

So we're in the process of making some anatomy-based ROIs from FreeSurfer segmentation files. We've run our EPI and anatomy data through most of a uber_subject preprocessing pipeline and will ultimately be wanting to do all of our analyses in a standardized space. I had figured that we could just take the aparc_aseg.mgz file that comes out of FreeSurfer and use the cat_matvec transformation matrix on this file to get it to be aligned with the subject anatomy in MNI space.
So we did this and the segmentation file is aligned fine to the anatomy, EPI, and MNI template (which are all aligned with each other well enough). The problem is, we used the following command: 3dallineate -base anat.al_strip+tlrc -input aparcaseg_shft+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -prefix FS-SEG
The anat.al_strip+tlrc file has a grid space of 1x.97x.97 and the aparcaseg_shft+orig file has a grid space of 1x1x1.

So we didn't use the -master or -mast_dxyz flags. The segmentation file should default to the grid space of the anat.al_strip file, is my understanding but instead the normalized segmentation file turns into a 2x2x2 file so it looks really blocky and bad. Is this because we're using the 1Dmatrix we are? I'm not sure how it's transforming into that voxel size.
Would it be kosher to just try align_epi_anat.py on the segmentation file to try to just the segmentation file into MNI space as an alternative? Ultimately we just want a high res segmentation file aligned with the EPI so that we can extract more precise ROI timecourses but as it stands these normalized segmentation files look too coarse to do that.

Thanks for your help.