Hi Donald:
If you worry about the shear in affine. You can use spm_affreg, and set
the regtype to 'rigid' - almost rigid body.
That should have mainly translation+rotation.
Best,
Carlton
MCLAREN, Donald wrote:
> There is one issue with this approach. When you apply the Affine
> matrix to the mat filed of header, the resulting matrix has a shear
> component. This inhibits the use of ROI analyses with DARTEL data.
>
> Does anyone know how to eliminate the shear components when apply the
> Affine matrix to the mat field of the header? Can the mat fields be
> rounded to 3 decimal places????
>
> Any suggestions would be appreciated.
>
> On Wed, May 21, 2008 at 1:40 PM, Carlton Chu <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Hi Naroa:
>
> If you leave NaN in the bounding box option, you should have
> exactly the same dimensions as your native space.
> Initial import only roates and translates the image in the native
> space, I won't resize the brain. (ridge algnment)
>
> If you want to project your DARTEL warped brain into MNI space,
> you can affine reigster your DARTEL template to the MNI template
> (use normalization in SPM5, but set the iteration of non-linear
> warping to 0). Then you can apply the Affine matrix M in the
> parameter file generated to each of your dartel warped and
> modulated images before your statistical analysis. (multiply the
> transformation matrix to the .mat field in the header of each images).
>
> Then things will all work out. I believe John sent the script to
> apply the transformation in the email list a while ago...you can
> search for it
>
> Carlton
>
>
>
> NAROA IBARRETXE BILBAO wrote:
>
> Hi,
>
> I have a very basic question. I have just started to use
> Dartel tool.
>
> During "initial import" step I do define bounding box instead
> of using NaN. I
> put the following parameters: -90 -126 -72; 90 90 108 because
> leaving NaN by
> default the brain resulted smaller than normal.
>
> But now I don't know if it is the right decision. Should I
> conserve the original
> parameters?
>
> If I have changed the bounding box parameter, when I apply
> deformations to
> convert the average to MNI space should I put the same
> parameters used before?
>
> Thank you
> -------------------------------------------------
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>
>
>
>
>
>
>
>
> --
> Best Regards, Donald McLaren
> =====================
> D.G. McLaren
> University of Wisconsin - Madison
> Neuroscience Training Program
> Tel: (773) 406 2464
> =====================
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