Hi Rouhi, Thanks for the answer. The main problem is, data has been analyzed in surface space from the beginning so I assume that mri_vol2surf won't work here. As far as I see, I either have to follow what you said by re-analyzing data in volume or have to convert file to gifti format as Matt suggested yesterday.
Thanks for your suggestion Shahin > 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 > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
