On Mon, Dec 14, 2009 at 9:44 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Can you send the reg-feat2anat log file?

doug

Xinian Zuo wrote:

Hi FSers,

I am new to freesurfer. now start to use it for looking at struc-func relationship. Normally, in fsl, I employ bet for both example_func and highresh anat. it means that the func_brain and anat_brain are fed into flirt to estimate the co-registration.
here, i try to use reg_feat2anat to do this. but in this new version (4.5), it told me the betfunc command can not be found. thus I just used the version without --bet. the results in tksurfer looked not good. I am guessing it was caused by the highres with large neck areas. MY QUESTION is
how can I trigger reg_feat2anat (or whatever other commands) to take skull-stripped highres for the co-registration (in fact, the brainmask.mgz already there)? Or I was wrong, reg_feat2anat did this consideration?
Any suggestions would be appreciated!
--
Xinian Zuo, Ph.D
Associate Research Scientist
Institute for Pediatric Neuroscience
NYU Child Study Center
215 Lexington Ave., 14th Floor
New York, NY 10016
Phone: 212-263-4735
Public: www.AboutOurKids.org <http://www.AboutOurKids.org>

Academic: http://publicationslist.org/xinian.zuo
Personal: zuoxinian.googlepages.com <http://zuoxinian.googlepages.com>

Blog: http://restbrain.blogspot.com
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422

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