[caret-users] Map2Surface

John Harwell john at pulvinar.wustl.edu
Wed Oct 1 09:04:17 CDT 2003


Hi Mark,

Map2Surface is an older program that has been replaced with  
map_fmri_to_surface which is included in the Caret distribution.   
map_fmri_to_surface has a graphical user interface but can also run in  
a command line mode.  Some documentation on map_fmri_to_surface is at  
"http://brainmap.wustl.edu/caret/html/map_fmri_to_surface/ 
map_fmri_to_surface_dialog.html" and some notes on mapping functional  
data to a surface are at  
"http://brainmap.wustl.edu/SureFit/mapper.html".

In map_fmri_to_surface set the volume type to AFNI, select the  
functional .HEAD file as the volume, set the Mapping Surface Type to  
"Map to Individual" (As for the parameters I believe you can disable  
cropping and padding and set the orientation to match your surface VTK  
file), and add the VTK file as the Surface.  The Average Voxel  
algorithm with zero neighbors is commonly used.  Pressing the Run  
Mapper button should then create a metric file containing the  
functional data mapped to the surface.

John Harwell

On Tuesday, September 30, 2003, at 11:09 PM, Mark A. Pinsk wrote:

>
> Hi, I'm attempting to use Map2Surface now.  It fails on me with a  
> dimension error, so i wanted to outline what I'm doing to see if i'm  
> missing something:
>
> 1. I get my experimental anatomical volume (expvol) to the same  
> dimensions and orientation as my surface anatomical volume (surfvol)  
> using the instructions on the AFNI FAQ site for Warp on Demand and  
> 3daxialize.
> 2. I register the expvol to the surfvol using 3dvolreg.
> 3. Now I take my functional BRIK containing my zscore subbriks and  
> also place it in the same dimensions and orientation as my surfvol  
> using same procedures as above.
> 4. And I register it to the surfvol using the 3drotate parameters  
> outputted to me by step 2 above.
> 5. If I now look at my new functional brik overlayed on my surfvol,  
> everything is nicely in register, except the clusters of activity look  
> "funny" (I imagine due to the resampling and interpolation it has gone  
> through, but maybe I should be doing something differently?)
>
> 6. Now I try Map2Surface:
> Map2Surface zmap_Algnd_to_surfvol+orig.BRIK  
> v.L.full.segment_corr10.fiducial.26032.vtk v.L.full.sMRI.params
>
> And I get the following message:
> No multi-bucket volumes or non-Minc with embedded header.
> Actual filesize = 587202560
> xdimydimzdim = 8388608
> xdimydimzdim2=16777216
> xdimydimzdim4=33554432
> Exiting--double check your dimensions.
>
> Where have I gone wrong? Thanks!!!! Mark
>
>
>
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