If you import a Freesurfer surface into Caret, it won't align with the volume in mri/orig.mgz until you apply an offset transformation defined by something like mri_info -cras (I forget the exact command). Depending on which surface you apply that transformation -- before or after cras offset -- you could get the behavior you describe.
On Dec 24, 2012, at 7:51 PM, Colin Reveley wrote: > Hey, merry christmas. > > I have a surface. and a volume. they are in register in caret. the volume has > an origin reported in the nifti header. > > If I apply a rigid body transform to both, they are both rotated the way I > want (the way I want is so that the surface, and MR data in the slice plane > as some microscope slides of the sample) but the surface is no longer in > register with the volume. > > the rotations are right. but the translations aren't (there aren't any > translations intended actually) > > I can > > a) manually translate the surface around in caret till it roughly fits (which > I did, it's fine for now) > b) adjust the origin of the nifti (the origin isn't changed by applying the > transform with flirt) > > or I guess c) adjust something in the surface header. couldn't see what. > > It occurred to me to treat the original volume origin as a vector and apply > the transform to it, then set the origin of the rotated volume to those > values. > > Probably that would work. But it's a bit too much linear algebra for me. > > Moving on from the obvious fact that I'm not that bright, surely doing > exactly this kind of thing ought to be pretty easy? > > > _______________________________________________ > 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
