Hi Shahin, One way I normally use create a paint file by freesurfer by using vol2surf command and create w file. You can create a caret paint file from that and apply the deformation from fsaverage to Pals or FS_LR to that paint file. Then you can see the surface based based on Freesurfer data. The atlases are available in following link
http://sumsdb.wustl.edu/sums/directory.do?id=679528&dir_name=HUMAN Best Rouhi On Fri, Nov 8, 2013 at 8:11 AM, SHAHIN NASR <[email protected]>wrote: > Thanks. Would you tell me where I can get these deformation maps (what's > their exact name)? > On Nov 7, 2013 10:24 PM, "Matt Glasser" <[email protected]> wrote: > >> You need to save the file as a GIFTI .func.gii file. Then you can use >> the fsaverage to FS_LR and FS_LR to PALS deformation maps to resample the >> data onto the PALS mesh. >> >> Peace, >> >> Matt. >> >> From: SHAHIN NASR <[email protected]> >> Reply-To: "Caret, SureFit, and SuMS software users" < >> [email protected]> >> Date: Thursday, November 7, 2013 7:42 PM >> To: <[email protected]> >> Subject: [caret-users] mapping fMRI maps generated in freesurfer on >> >> Hi, >> I have generated a group-averaged fmri activity map in freesurfer to >> be overlaid on fsaverage (freesurfer brain template). Analysis was in the >> surface space (rather than MNI305 space) and output is a sig.nii file. >> Now I want to overlay it on the PALS brain template using caret. As >> far as I see, this is not supported. When I try to use Attribute>Map >> Volumes to surfaces I can load my sig.nii file but when I use "Map to Spec >> File with Atlas", there is no fsaverage space and also when I use SPM5 >> space instead, registration is off. >> Is there any solution? Should I reanalyze my data in MNI305 space? >> Or is there anyway to correct the registration? >> >> -- >> Shahin Nasr >> >> PhD in Cognitive Neuroscience >> Martinos Imaging Center, MGH >> Harvard Medical School >> >> _______________________________________________ caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > -- Best Regards Rouhollah Abdollahi
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