Hi Rick,
It is possible that this was the one patient the tech pulled out to put the physio on so there was a shift in location. Unfortunately I was not there that day for the scan. I checked 3 files with 3dCM:
1) Resting state :
++ Oblique dataset:./EP_001.RS+orig.BRIK is 12.110529 degrees from plumb.
-1.69794 -24.4452 4.27884

2) T1 (raw):
++ Oblique dataset:EP_001.T1.nii is 10.193717 degrees from plumb.
-0.617424 9.77996 29.0229

3) T1 (Freesurfer skullstripped processed and converted back to rawavg coordinates which overlays with original T1)
++ Oblique dataset:brain.native.nii is 10.193736 degrees from plumb.
0.148247 12.7344 41.6709


I am not sure if using dcm2niigui to convert the Siemens Trio dicoms could have anything to do with the locations (reading wrong or converting improperly but not likely I would assume). Also these scans were several scans apart unfortunataely for this trial data so it could be that the patient did move. However it seems that the Resting state scan is just within the bottom of the grid of the freesurfer processed file. Would a possible fix be to crop the brain.nii file and aseg file so that the window is smaller and force extra zpadding to recenter it during alignment? I know the temporary steps _tt during alignment recenters the T1, however the final output goes back to the original grid.