Hi Doug,<div><br></div><div>Thank you, I think that will work. Right now my anatomical ROIs are in subject native space and I would like to register the third-level group (across subject) fmri activation map to subject native space as well before crossing the two. Is that possible? I have the anat2exf.register.dat files for each subjects&#39;s group feat (across runs) but I don&#39;t know how to do it for the third level?</div>
<div><br></div><div>Thanks so much,</div><div>Huiting</div><div><br></div><div><br><div class="gmail_quote">On Mon, Jul 16, 2012 at 2:03 PM, Douglas N Greve <span dir="ltr">&lt;<a href="mailto:greve@nmr.mgh.harvard.edu" target="_blank">greve@nmr.mgh.harvard.edu</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">You can create a binary mask of the ROI, then use mri_mask to mask out<br>
the non-ROI part from the fMRI. does that work?<br>
doug<br>
<div><div class="h5"><br>
On 07/11/2012 11:25 AM, Huiting Liu wrote:<br>
&gt;<br>
&gt; Hello,<br>
&gt;<br>
&gt;<br>
&gt; I&#39;m trying to do an ROI analysis that crosses the group-level<br>
&gt; functional activation with specific anatomical structures. Currently<br>
&gt; the clusters found for our group-level functional activation are too<br>
&gt; large and need to be separated into many structures. Is there a<br>
&gt; command I could use that would cross the group level map with each<br>
&gt; cortical structure generated by freesurfer&#39;s recon-all?<br>
&gt;<br>
&gt;<br>
&gt; Thanks.<br>
&gt;<br>
&gt;<br>
&gt;<br>
</div></div>&gt; _______________________________________________<br>
&gt; Freesurfer mailing list<br>
&gt; <a href="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer@nmr.mgh.harvard.edu</a><br>
&gt; <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a><br>
<br>
--<br>
Douglas N. Greve, Ph.D.<br>
MGH-NMR Center<br>
<a href="mailto:greve@nmr.mgh.harvard.edu">greve@nmr.mgh.harvard.edu</a><br>
Phone Number: <a href="tel:617-724-2358" value="+16177242358">617-724-2358</a><br>
Fax: <a href="tel:617-726-7422" value="+16177267422">617-726-7422</a><br>
<br>
Bugs: <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting" target="_blank">surfer.nmr.mgh.harvard.edu/fswiki/BugReporting</a><br>
FileDrop: <a href="http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html" target="_blank">www.nmr.mgh.harvard.edu/facility/filedrop/index.html</a><br>
<br>
_______________________________________________<br>
Freesurfer mailing list<br>
<a href="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer@nmr.mgh.harvard.edu</a><br>
<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a><br>
<br>
<br>
The information in this e-mail is intended only for the person to whom it is<br>
addressed. If you believe this e-mail was sent to you in error and the e-mail<br>
contains patient information, please contact the Partners Compliance HelpLine at<br>
<a href="http://www.partners.org/complianceline" target="_blank">http://www.partners.org/complianceline</a> . If the e-mail was sent to you in error<br>
but does not contain patient information, please contact the sender and properly<br>
dispose of the e-mail.<br>
<br>
</blockquote></div><br></div>