I'm not really sure what your aims are, so can't really comment much. I'm
guessing that you want to generate some form of average shaped image, in
which case you could try DARTEL in SPM5/8.
On Wednesday 25 March 2009 19:57, Anton Orlichenko wrote:
> Thanks John!
> I'm looking through the Woods paper right now.
> BTW to clarify I have been converting *_sn.mat to y_* files and
> working with those. Then you are saying I might try to factor out the
> affine transform from this y_* field, average the affine and local
> deformations separately, then apply these two average transforms to
> the image?
> On Wed, Mar 25, 2009 at 7:39 AM, John Ashburner <[log in to unmask]>
> > The sn.mat files combine an affine transform with a small deformation,
> > parameterised by a linear combination of a few 3D cosine transform basis
> > functions. You may find it easier to work with y_* files generated by
> > the deformations toolbox.
> > Creating an average will be a lot more difficult than you anticipate.
> > You probably need to combine the displacements with the affine
> > transforms. Averaging affine transforms can be achieved as described in
> > eg
> > Characterizing volume and surface deformations in an atlas framework:
> > theory, applications, and implementation
> > NeuroImage, Volume 18, Issue 3, March 2003, Pages 769-788
> > Roger P. Woods
> > You could probably also opt for a Procrustes method, which would involve
> > factoring out translations, rotations and possibly an isotropic zoom.
> > There is code for this in spm8/toolbox/Seg/spm_get_closest_affine.m or
> > spm8/spm_prep2sn.m . After factoring out the affine transforms, the
> > displacement fields could probably be dealt with is a relatively simple
> > way.
> > Shapes do not actually add and subtract in a nice linear way. However, if
> > displacements are small enough, then linear approximations are probably a
> > reasonably close Taylor series approximations. If you want the maths,
> > then there are a few textbooks by authors such as Ian Dryden. If you want
> > the full maths, then try books by Ron Kimmel or Ulf Grenander.
> > Best regards,
> > -John
> > On Wednesday 25 March 2009 02:58, Anton Orlichenko wrote:
> >> Dear SPM experts,
> >> This may sound like a dumb question, but how does spm5 warp images
> >> with displacement fields, such as those derived from an _sn.mat file?
> >> I have looked at the code but would be really grateful if someone
> >> could say a few words about the subject.
> >> The reason I ask is that I'm trying to get an average deformation from
> >> several different deformations. I read in displacement fields and take
> >> the average. This mostly works except but I apply the average
> >> deformation to an image I get a result that is to my eye the correct
> >> shape but shifted and rotated.
> >> Has anyone here tried doing something similar? If so how did you go
> >> about it.
> >> Best,
> >> Anton