[caret-users] Mapping Functional Volume to flattened partial hemisphere

Donna Dierker donna at brainvis.wustl.edu
Wed Jun 20 07:44:46 CDT 2007

Hi Jed,

I'm guessing this is the dataset we looked at a couple of weeks ago, 
when I was there for the fMRI course.  I vaguely recall translating the 
surface and saving the resulting coord file by a different name (e.g., 
fiducial_ACorigin or fiducial_orig).  Do "ls *coord |grep -i fiducial" 
in your directory to see all the fiducial coord files.  Make sure you're 
mapping the volume to that fiducial surface.  If you still are having 
trouble, then put all the relevant files in a zip archive and upload here:


It's amazing how quickly these details disappear from memory, but it 
seems like it was either a deal where you generated the surface using 
SureFit, which puts the origin at the cropped bounding box lower left 
corner, or the origin of the volume used to generate the surface (with 
which the functional now aligns) was translated off the AC.


On 06/19/2007 04:43 PM, John Harwell wrote:
> Jed,
> First, make sure you are mapping the functional volume to the 3D 
> fiducial surface.
> Second, both the anatomical and functional volumes must be in the same 
> stereotaxic space.  Load the anatomical and functional volumes into 
> Caret and verify that the functional data properly overlays the 
> anatomical data.  In addition, if you load your 3D surface into Caret, 
> there is an option on the Overlay/Underlay-Volume Settings page that 
> allows the display of the 3D surface where it intersects the displayed 
> volume slice.
> ----------------------------------------------------------
> John Harwell
> john at brainvis.wustl.edu
> 314-362-3467
> Department of Anatomy and Neurobiology
> Washington University School of Medicine
> 660 S. Euclid Ave.    Box 8108
> St. Louis, MO 63110   USA
> On Jun 19, 2007, at 4:31 PM, Jed Mathis wrote:
>> We have a flat map of an occipital lobe and are trying to map a 
>> functional
>> dataset onto it. I've tried using the Map Volume to Surface command 
>> and it
>> does map the data set on but it appears to be off in the Anterior to
>> Posterior Direction.
>> The spgr used for the flatmap is from the same exam used to collect the
>> functional dataset. Anything in particular I need to do to the 
>> functional
>> dataset before trying to align to the flat map?
>> Thanks
>> Jed

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