Print

---

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
>         -------------------------------------------------
>         This mail sent through IMP: http://horde.org/imp/
>
>
>
>          
>
>
>
>
> -- 
> Best Regards, Donald McLaren
> =====================
> D.G. McLaren
> University of Wisconsin - Madison
> Neuroscience Training Program
> Tel: (773) 406 2464
> =====================
> This e-mail contains CONFIDENTIAL INFORMATION which may contain 
> PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED 
> and which is intended only for the use of the individual or entity 
> named above. If the reader of the e-mail is not the intended recipient 
> or the employee or agent responsible for delivering it to the intended 
> recipient, you are hereby notified that you are in possession of 
> confidential and privileged information. Any unauthorized use, 
> disclosure, copying or the taking of any action in reliance on the 
> contents of this information is strictly prohibited and may be 
> unlawful. If you have received this e-mail unintentionally, please 
> immediately notify the sender via telephone at (773) 406 2464 or email.