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
