You missed the bit that writes the new orientation matrix to the header
of VF.
M = inv(spm_matrix(x));
MM = spm_get_space('moved.img');
spm_get_space('moved.img',M*MM);
Best regards,
-John
On Wed, 2010-03-17 at 12:50 +0100, Giorgio De Nunzio wrote:
> Hi all,
>
> this is my first post to the list, and I am an absolute beginner as far
> as SPM is concerned, so please excuse my trivial question.
> I have some brain MR images, and a template with which I wish to
> coregistrate the images.
> I am writing a matlab function: the input parameters are:
> - the template file name (it is a double-resolution, half voxel-size
> version of the SPM T1 template, nii format);
> - the moving-image file name
> The function should create a new nii file containing the coregistered
> image.
>
> Before trying to write this script, I already used SPM from its GUI, and
> I could with no problem insert the template and the input file name into
> the corresponding user fields of the SPM (fmri) form called "Coreg:
> Estimate and Reslice", obtaining the registered image as a file with the
> same name as my moving image, with a heading 'r' (something like
> 'rIm005.nii').
>
> This is now the code I am using (copied from somewhere, without fully
> understanding all the details):
>
> function coregister(filename)
> VG = spm_vol('T1_templateSPM2.nii');
> VF = spm_vol(filename);
> x = spm_coreg(VG,VF);
> spm_reslice([VG,VF],struct('which',1));
>
> I am somewhat confused: it looks like the part that is building the
> registered-image file is the second one (spm_reslice), because the
> spm_coreg does not create any file, and I see no communication between
> coreg and reslice.
> Moreover, this script also creates meanT1_templateSPM2.nii, which I did
> not see when using the GUI.
>
> Can someone please explain what is going up?
> Where can I find examples of SPM scripting, with some comments?
>
> When this peace of code works, and if nobody complains for the low level
> of this question, I'll be back with something about spm_segment syntax...
>
> Thanks
> Giorgio
>
--
John Ashburner <[log in to unmask]>
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