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
ALL-NEW Yahoo! Messenger - all new features - even more fun!
_______________________________________________
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
_______________________________________________
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
