Hi Simone,Actually, when I look at it in Caret, the functional and anatomical appear aligned, so that's good.
When I use AFNI's to3d to create an AFNI .HEAD and .BRIK of rHerkules_1_18.hdr that specifies the orientation as ARI (anterior-to-posterior, right-to-left, inferior-to-superior), Caret flips it appropriately when opening. The attached capture before_translation.jpg shows that the orientation is good at least in the y and z planes, although I'm not sure about the x-flipping. (It might be left-to-right rather than right-to-left, as I asserted when using to3d.) But the origin is off, no doubt because you set the AC in Caret. The trick is finding the translation offset between the AC-centered and original volume.
Using my own guess at the AC (-53,-65,-85) in Caret, I can get the volume and surface closer, but I suspect the x-flipping may still be wrong and the AC is probably still not set identically to your actual setting.
I'm hoping you can take these clues and run with them on your own for a bit.Eventually, you'll need to either translate and flip your surface coordinate file (using AFNI's Vecwarp or Caret's Window: Transformation matrix editor) to match your volume file, or write your volume out with an orientation and origin that matches your surface. But first you need to get the magic numbers that specify the affine transform from your surface to your volume.
On 11/07/2006 10:27 AM, Simone Kamphuis wrote:
Donna Dierker schrieb:Hi Simone,In your case, your anatomical volume, functional volume, and surface are not aligned to one another.The anatomical is in a different orientation (and probably different origin) than the surface (which is LPI - http://brainmap.wustl.edu/SureFit/orient.html, as Caret expects it to be). The functional is in yet a different orientation.Step one is to get the anatomical and surface aligned, and then find some way to align the functional with the anatomical. This may require using some other software such as AFNI or SPM. If your anatomical and functional volume are in some different orientation, but there is an AFNI or NIfTI header that tells Caret what the orientation actually is, then Caret can flip it accordingly. But even if it gets the orientation right, there's still no guarantee the origins will align.Unfortunately, I'm real busy for the next three weeks, so I can't play around with them to figure it out on my own. See how far you can get on your end, and let me know tomorrow if you make no progress.On 11/07/2006 05:46 AM, Simone Kamphuis wrote:Dear Donna Dierker, I have read your answer to John Arsenault's e-mail.I also have problems to map functional data onto my monkey caret fiducial surface.I was wondering if you could have a look at the files that I used. (I will upload them to http://pulvinar.wustl.edu/cgi-bin/upload.cgi) I used CARET v5.3 (Jun 20 2005). Thank you in advance. Simone Materna _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-usersDear Donna,I guess I should have send you my '......AC_left+orig.HEAD' file as well (I uploaded this file now). This file is in the same orientation as the surface. I used SPM to get the functional volume (T-map) in the same orientation as the anatomy (this might not seem to be the case at first sight, because the quality of the functional volume is not very good).I don't know how to get the anatomy (and functional volume) in the same orientation as the surface, since I can't open the '......AC_left+orig.HEAD' file in SPM.Thanks again, Simone _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
-- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.)
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