Sorry for asking same question here again. I asked Dung before holiday about the criteria of good registration of fMRI and thickness map. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08913.html
I paste my question again: what is the best registration of example_func and orig.mgz? In another word, what should I check besides things in the FS tutorial when I check/modify the registration in tkregister2? Is there golden reference points I can use?
 
I will appreciate if Dave could give more explanation or references of "beautiful match between functional and structural images".  

Thank you in advance.

Xin Wang    

From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu]
Sent: Mon 1/5/2009 2:03 PM
To: Dave Brohawn
Cc: jroffman@partners.org; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Problem with post-spm registered data

Hi Dave, I'm not sure where to begin with this. Can you give more info?
In particular, you might look at
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for ways to report issues
efficiently.

doug

Dave Brohawn wrote:

>Hello,
>
>Josh Roffman and I recently ran an fMRI scan. Our subject's data viewed in
>tkmedit seemed to be shifted inferiorly in the coronal view by a wide
>margin (an inch or so), leaving no functional activation in the top of the
>cortex, even when set at an extremely low threshold.
>
>When running the fMRI scan, we checked our slice prescription and ensured
>the area of view covered the entire cortex. We also checked the raw data
>output during the scan in the viewing window, and functional activity was
>present.
>
>After running the unpacking and recon-all processes, I ran the pre-proc
>command and spm-register, and viewed the output using tkregister2. The
>registered functional data matched up beautifully with the underlying
>anatomy, and went right to the top of the cortex in the coronal view.
>
>We ran our analysis using the appropriate paradigm files (has worked
>without fail for our previous subjects) and there is no functional
>activity in the top inch or so of the cortex whatsoever.
>
>Please let me know if you have an answer to how this could have happened.
>
>Dave Brohawn
>_______________________________________________
>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

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting