Actually that is better that you have done surface based and the final data are on surface! it will be more exact on the surface! then you just need to create the paint (w) files from your contrasts and import them to caret! use the deformation maps and it is done.
Best Rouhi On Fri, Nov 8, 2013 at 4:20 PM, <[email protected]> wrote: > 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 > -- Best Regards Rouhollah Abdollahi
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