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There's no actual code within SPM that allows you to transform the
Template_0-6.nii to MNI space.  If you really want to do this, then you can
do it with a little bit of MATLAB:

matfile = 'Template_6_2mni.mat';
imfile  = 'Template_6.nii';

t       = load(matfile);
Nii     = nifti(imfile);
mat     = t.mni.affine;
Nii.mat = t.mni.affine;
Nii.mat_intent = t.mni.code;
create(Nii)

Note that for Template_6_2mni.mat to exist, you have to have run a
Normalise to MNI space first.

Yes,  the rigid body transform is based on aligning with spm12\tpm\TPM.nii
, although it is actually extracted from the nonlinear deformation that is
estimated during segmentation.

The rigid bod transforms are encoded in the headers of the rc*.nii and
u_*.nii files.

Best regards,
-John


On 20 April 2017 at 11:53, FENG LIU <[log in to unmask]> wrote:

> Dear SPM experts,
>
>
>
> I performed the DARTEL analysis using SPM12. I have three questions in my
> experiment.
>
>
>
> First, I want to create a study specific template using DARTEL in MNI
> space. However, when I finish the steps “Run Dartel (create template)” and
> “Normalize to MNI space”, I found that the only the gray matter and white
> matter images normalized to the MNI space, the Template_0-6.nii are still
> in the dartel (group averaged) space. How could I transform these Templates
> to the MNI space?
>
>
>
> Second, in the step of “Run Dartel (create template)”, I inputted the
> rc1*.nii and rc2*.nii which generated by the previous “Segment” step. The
> rc1 and rc2 are the roughly aligned (via a rigid-body) gray matter and
> white matter images. Which image was used as the template for the
> rigid-body transformation? Is this image “spm12\tpm\TPM.nii”?
>
>
>
> Finally, after the “Run Dartel (create template)” step, a series of
> u_rc1*.nii were generated which parameterized the deformations. In the
> following step of “Normalize to MNI space”, I inputted the templated_6.nii,
> u_rc1*.nii and c1&2*.nii, and finally obtained a bunch of smwrc1&2*.nii
> files. Here, my question is that the u_rc1*.nii was obtained based on
> rc1&2, so the u_rc1*.nii I think is the deformation from the rigid-body
> images (rc1&2) to the dartel space. When I run “Normalize to MNI space”,
> why I need to input the c1&2 rather than rc1&2? Have the rigid body
> transformation parameters already imbedded into the u_rc1*.nii? When?
>
>
>
> Any help would be greatly appreciated!
>
>
>
> Best,
>
> Feng
>