Hi Sophie,
Okay, then let's stick with the separate map_fmri_to_surface program then.
If you realigned your EPIs with the cubic 1mm anatomical, then I think
you should be able to follow the steps shown here:
http://brainmap.wustl.edu/help/map_individual.html
Loading the cropped params file *should* load the appropriate parameters
(Xmin,Ymin,Zmin and any padding) for you.
Don't translate your surface in caret; just use the SureFit-generated
"native" vtk file.
If this fails, then upload the following files:
1. sample epi hdr/img
2. cropped params file
3. vtk file
It wouldn't hurt to include the anatomical to which the EPIs were aligned.
Donna
On 07/30/2004 11:01 AM, Sophie Riches wrote:
Sorry I being really thick, but I need more help!
I cannot use the in-built mapper becasue it seems to crash whenever I
try and load any file not in a spec file ( the same problem I had last
week!)
My SPM volume has the origin aligned with the AC at 31.8, 35.1, 8.92,
after it has been aligned with the structural data.
My surface was reconstructed in SUREfit aligned on the AC.
So when I run the map_fmri_to_surface program, should I enter:
-30.8, -34.1, -7.92 in the maptoindividual parameters cropping box to
align them together?
Sophie
*/Donna Hanlon <[EMAIL PROTECTED]>/* wrote:
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
> [EMAIL PROTECTED]
> 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
>>
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>
>
>
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