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!
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Attached both bbregister.log and reg_feat2anat.log.
Thanks for help! Xi-Nian
On Mon, Dec 14, 2009 at 9:44 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Xinian Zuo