I think what Nate was asking about was coregistering EPI data to the structural scans. The AFNI program 3dAnatNudge can help with this to some extent. It uses simple iterative translational movements to find the best fit between a "skull-stripped" anatomy volume and an EPI volume. No rotation or resizing is done.
To use this program you remove the skull and other non-brain voxels from the anatomy volume. The AFNI programs 3dIntracranial and a newer program called 3dSkullStrip both do this.
Jeff
From: Graham Wideman <[EMAIL PROTECTED]>
Date: Wed, 12 Oct 2005 11:57:15 -0700
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Coregistration?
Nate Parks wrote:
> Does AFNI have an automated coregistration tool?
> I thought you could only do manual coreg in AFNI.
AFNI coregistration program is 3dvolreg.
See docs:
http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dvolreg.html
And if you are having trouble finding which AFNI program does what, you might like my "all afni helps on one page":
http://www.grahamwideman.com/gw/brain/afni/alldocs_afni.htm
Graham
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