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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]> 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
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D.G. McLaren
University of Wisconsin - Madison
Neuroscience Training Program
Tel: (773) 406 2464
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