[caret-users] SPM users: Set your AC to SPM originator voxel minus one

Donna Hanlon donna at brainvis.wustl.edu
Thu Jul 29 13:35:25 CDT 2004


SPM users,

I agree with John that using the caret built-in mapper is often quicker 
and easier than using the map_fmri_to_surface program.  But I'd like to 
qualify this statement in John's reply below:

> * Your fiducial surface should have its origin at the anterior 
> commissure.

This is true if:

* Your SPM volume's originator voxel minus one is set to the anterior 
commissure.  (For example, with volumes that have not been spatially 
normalized, it might be the magnet center, which could be anywhere -- 
brainstem or elsewhere.) -- AND
* The voxel you selected during SureFit volume preparation matched the 
SPM volume's originator voxel minus one.

If your SPM originator voxel is the AC, then I recommend you use this 
voxel (minus one, because SPM calls 1,1,1 what we Caret/SureFit/AFNI 
calls 0,0,0).  Then, you can use the Transforms: Subtract params file AC 
to translate your surface to AC origin.

Otherwise, you need to first translate your surface like so:

+Xmin,+Ymin,+Zmin (to align it with the uncropped volume)
-SPMOx-1,-SPMOy-1,-SPMOz-1

You can do it in a single translation step like this:

Xmin-SPMOx-1,Ymin-SPMOy-1,Zmin-SPMOz-1

If the SPM originator voxel isn't the AC, then you can save the 
resulting fiducial coord file by an appropriate alternate name (e.g., 
*fiducial-magctr*coord rather than *fiducial-ACorigin*coord).

Donna

On 07/29/2004 12:08 PM, John Harwell wrote:

> 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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>
>
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