Hi Rick,

Based on your message, I've tried several things (including the -mast_dxyz option in some cases), but nothing worked.

First thing, trying to answer your question: The ROI is in the correct spatial location when overlayed on the anatomical T1 original dataset from freesurfer. Although I'm not sure if that's the anatomical I should be using in -source as you mentioned. I tried that as well, just in case, and it didn't work either.

Also, you mentioned that resampling shouldn't be necessary because the matrix applied is a xyz-to-xyz matrix. I wanted to ask you, just to make sure that's the case. I run 3dinfo to compare the freesurfer mask/ROI in the orig space that I'm trying to transform to tlrc, and the anat_w_skull_warped+tlrc. that I'm using as the master. Here are the results:
-freesurfer ROI in orig space:
Geometry String: "MATRIX(1,0,0,-136.7615,0,-1.49012e-08,-1.,133.7361,1.862645e-09,-1.,0,132.4308):256,256,256"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Superior-to-Inferior
third (z) = Posterior-to-Anterior [-orient RSP]
R-to-L extent: -136.761 [R] -to- 118.239 [L] -step- 1.000 mm [256 voxels]
A-to-P extent: -121.264 [A] -to- 133.736 [P] -step- 1.000 mm [256 voxels]
I-to-S extent: -122.569 -to- 132.431 [S] -step- 1.000 mm [256 voxels]


-master anat_w_skull_warped+tlrc (generated when I run uber_subject.py for resting state data):
Geometry String: "MATRIX(1,0,0,-80,0,1,0,-80,0,0,1,-65):161,191,151"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -80.000 [R] -to- 80.000 [L] -step- 1.000 mm [161 voxels]
A-to-P extent: -80.000 [A] -to- 110.000 [P] -step- 1.000 mm [191 voxels]
I-to-S extent: -65.000 -to- 85.000 [S] -step- 1.000 mm [151 voxels]

I still think that resampling may be necessary and that could be the problem, but please let me know what your thoughts are. I don't know what else to try. Thanks!
Ana