Hi Donna, I tried converting to RAS (this converst the heder information, which apparently Caret does use) and the data matrix. The problem is the same: the axes are correct (i.e., R points to the right side, D is dorsal, etc). However, the surface and the volume still don't match in Caret just like before. The issue seems to be some sort of offset in the center of coordinates (when I click on the surface, the highlighted points seem to be on a sensible medio-lateral and dorso-ventral position. The problem is that the highlighted voxel is too posterior in the volume view). Does this make sense or hint to a possible solution to you perhaps? Worst case scenario, I could eyeball how big this translation offset is, open the volume in matlab and have it translate the data matrix. That way, it would roughly look okay, but perhaps there is a more graceful way of handling this. Thank you again, Pablo
On Fri, Jul 20, 2012 at 3:14 PM, Donna Dierker <[email protected]> wrote: > Be aware that what AFNI/Caret calls LPI, Freesurfer calls RAS. ;-) > > Can you try having mri_convert write the volume out as RAS, instead of > LPI? Freesurfer will read the header and do the right flipping/rotating > so that the surface aligns with it. Freesurfer did the right thing, as it > understands that label. But that understanding is not what other software > desires, in this case. (At least that's my read of your problem.) > > I think the axes don't need rotating anymore, but all three need flipping. > >> Dear List, >> >> I successfully completed the FS-to-F99 tutorial and now I am trying to >> reproduce the steps with my own FreeSurfer dataset. According to the >> FS-to-F99 tutorial, I need to have my mri volume "into LPI >> orientation" and "the surfaces and volume need to be in register". My >> original volume is in LIA orientation and is in register with my >> surface, in the sense that when I open both on FreeSurfer's tkmedit >> they are well-aligned to each other (I don't know how to check that >> they are in register otherwise). If I use this surface and volume on >> FS-to-F99's Stage-1 script and open the resulting spec file with >> Caret, the volume's axes are wrong and the points on the surface and >> in the volume don't match (I see this by clicking on the surface and >> looking what is then highlighted on the volume window). If I transform >> the volume into LPI orientation (using FreeSurfer's mri_convert >> command), the new volume has the desired orientation and, >> interestingly, it is still well-aligned to the surface in FreeSurfer's >> tkmedit. However, when I use this surface and volume on the FS-toF99's >> Stage-1 script, the volume and the surface are still not well-aligned, >> even though the axes labels are now correct. How could I fix things so >> that my volume and surface are in register when shown in Caret? >> >> Thank you very much, >> Pablo >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
