[caret-users] misaligned metric and structural file

John Harwell john at brainvis.wustl.edu
Thu Jul 29 12:08:13 CDT 2004


Sophie,

Probably the easiest way to map functional data is to map the data in 
Caret5 using Attributes:Metric:Map Functional Volume to Metric.

Steps:

* Load your fiducial surface, functional volume, and anatomical volume 
into Caret5.
* Your fiducial surface should have its origin at the anterior 
commissure.
* Switch to a volume display and verify that the functional volume 
properly overlays the anatomical volume.
* On the Display Control's Overlay/Underlay - Volume panel, check the 
"Show Surface Outline" check box in the Miscellaneous section.  This 
should show a green outline of the fiducial surface on the volume.  If 
it does not or the green outline does not overlay the cortex in the 
anatomical volume, either your surface is not AC centered or the 
volumes stereotaxic coordinates are incorrect.
* Select Attributes:Metric:Map Functional Volume to Metric.
* In the Map Functional Volume To Surface Dialog make sure your 
fiducial surface is selected.  Use the dialogs controls to select your 
functional volume.
* Press the Apply button.
* Use the Display Control Dialog Overlay/Underlay Surface panel to set 
the primary overlay to Metric and make sure the newest metric column is 
selected.  You should now see your functional data on the surface.

There is also a short section on mapping functional data in the Caret 
5.1 User's Manual and Tutorial.

----------------------------------------------------------
John Harwell
john at pulvinar.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 Jul 29, 2004, at 11:30 AM, Sophie Riches wrote:

>  
> Hello again! Sorry to keep bothering you but i keep getting foiled!
> I have aligned a set of EPI fMRI scans to a structural T1 scan in SPM 
> 99 before processing the fMRI data.
>  
> The output from SPM looks okay - the activation is where I expected so 
> I think the orientation is ok and in normal SPM orientation. When 
> overlaid on slices it appears to be nicely aligned.
>  
> However when I map the fMRI to the reconsrtucted surface (from 
> SureFit) it is quite clearly not aligned at all. I am using the 
> map_frmi program on windows and have put in the fidiucial file as the 
> mapping surface,
>   
> Have I missed out a step? I have used the parameter file for the 
> surface and it has set the origin automatically .(although I thought 
> the origin of a surface made in SureFit would be 0,0,0 so I tried that 
> and still get it misaligned.) It certainly looks as though it is in 
> the right orientation but is not centred on the same origin.
>  
> Any ideas?
>  
> Sophei
>
> ALL-NEW Yahoo! Messenger - all new features - even more fun! 
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