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
On Wed, Mar 25, 2009 at 7:39 AM, John Ashburner <[log in to unmask]> wrote:
> 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,
> 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