Hi all:
We ran FreeSurfer's recon sequence of anatomy files that had already been aligned to the MNI template - so spatially normalized. We're doing all of our processing in AFNI and the resulting segmentation output files open in AFNI's orig space, not in tlrc space. So basically we can't overlay the segmentation files on our anat+tlrc files where they should already be aligned to each other. When we converted the file to a .tlrc file with the AFNI command 3dcopy we could then overlay the mask on the normalized anatomy but it was no longer aligned.
So I suppose my question is - is there any way to have the segmentation files maintain their positioning or output in .tlrc space so they are still aligned to our anatomy files?
Thanks for any insight.
Lauren