Shahin et al., In the SumsDB database you can go to http://sumsdb.wustl.edu/sums/directory.do?id=8291757&dir_name=Inter-atlas_deformation_maps
and download http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8293223&archive_name=inter-atlas_deformation_maps.zip The README.inter-atlas-registration_March2012.txt document (copied below) provides instructions on how to carry out the inter-atlas deformations using the accompanying dataset. If this doesn't work for you, please send another post detailing the problem. David README.inter-atlas-registration_March2012.txt How to convert (register) data between 164k_fs_LR and 74k_pals meshes 21 March 2012 * Download and unzip inter-atlas_deformation_maps.zip archive: http://sumsdb.wustl.edu/sums/directory.do?id=8291757&dir_name=Inter-atlas_deformation_maps * In a terminal window, change (cd) to whichever target directory (fs_L, fs_LR, fs_R, pals_L, pals_R) represents the mesh you desire for the output files. * Enter “caret_command –deformation-map-apply”, then follow the displayed command-line instructions (see below) in order to register the files of interest. caret_command -deformation-map-apply DEFORMATION MAP APPLY caret_command -deformation-map-apply <deformation-map-file-name> <data-file-type> <input-data-file-name> <output-data-file-name> [source-topology-file-name source-deformed-topology-file-name target-topology-file-name] Deform a data file. Note: "source-topology-file-name", "source-deformed-topology-file-name", and "target-topology-file-name" are only required when deforming coordinate FLAT files. "data-file-type" is one of: AREAL_ESTIMATION BORDER_FLAT BORDER_PROJECTION BORDER_SPHERICAL CELL CELL_PROJECTION COORDINATE COORDINATE_FLAT FOCI FOCI_PROJECTION LAT_LON METRIC_AVERAGE_TILE METRIC_NEAREST_NODE PAINT PROB_ATLAS RGB_PAINT SURFACE_SHAPE TOPOGRAPHY NOTE: METRIC_AVERAGE_TILE assigns target surface node average of nodes from the nearest tile in source surface. METRIC_NEAREST_NODE assigns target surface node metric value from nearest source node. Use this mode when it is important that the metric values are NOT modified. Run "caret_command -help-global-options" for parameters available to all commands. On Nov 8, 2013, at 1:11 AM, SHAHIN NASR <sha...@nmr.mgh.harvard.edu> 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" <m...@ma-tea.com> 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 <sha...@nmr.mgh.harvard.edu> > Reply-To: "Caret, SureFit, and SuMS software users" > <caret-users@brainvis.wustl.edu> > Date: Thursday, November 7, 2013 7:42 PM > To: <caret-users@brainvis.wustl.edu> > 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 > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users
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