I'm not sure that rotating the images would really help you so much.
If you have limited field of view in your original scans, and these
are tilted so that they miss some interesting part of the brain, then
you won't be able to recover this missing information by rotating the
images.

Best regards,
-John

On 10 May 2012 01:54, Zhijiang Wang <[log in to unmask]> wrote:
> Dear John,
>
> We have to rotate our brain template, because we found the posterior part
> was a litter higher while the anterior part was a litter lower, which caused
> the some lowest slices at Z-axis were not complete.
>
> So, we want rotate our image by some degree at the y-z space(but we don't
> know the degree value).
>
> If there is a function or tool in SPM, we can try and check.
>
> Many thanks again for your so valuable information.
>
>
>
> Best wishes,
>
> Ross Wang
>
> --------------------------------------------
>
> PhD Candidate
>
> Room 407, East Segment, Material Science Building,
>
> The International WIC Institute,
>
> Brain Informatics,
>
> College of Computer Science and Technology,
>
> Beijing University of Technology,
>
> Beijing, China.
>
>
> 于 2012-5-9 23:43, John Ashburner 写道:
>
> Make a copy of the old image.  Coregister the copy to whatever
> reference image you use.  Then use coreg->reslice only to reslice the
> old image to match the new one.  I don't really understand the
> motivation for doing this though.
>
> Just by having the updated matrix in the header, the image should be
> in alignment with the reference.  Maybe you just want to do a
> coreg->reslice only so that the image is resampled to the same
> orientation, voxel dimensions etc as the reference??
>
> Best regards,
> -John
>
>
> On 9 May 2012 16:34, Zhijiang Wang <[log in to unmask]> wrote:
>
> Dear John,
>
> Thanks for your answers！
>
> So if the aim is to rotate and translate the old img to a new one, is there
> a program in SPM?
>
> Thanks again！
>
>
> Best wishes,
>
> Ross Wang
>
> --------------------------------------------
>
> PhD Candidate
>
> Room 407, East Segment, Material Science Building,
>
> The International WIC Institute,
>
> Brain Informatics,
>
> College of Computer Science and Technology,
>
> Beijing University of Technology,
>
> Beijing, China.
>
>
> 于 2012-5-9 23:15, John Ashburner 写道:
>
> 1. You said "Personally, I would do it by relating together the old and new
> matrices in the header."
> How to relate?
> The transformation matrix is equal to new.head.mat / old.head.mat  ?
>
> You would divide one matrix by the other, either with a left division
> or a right division.  The exact way you do it would depend what you
> want to do with the resulting matrix.
>
> The old.head.mat is a mapping from voxel indices in the image to the
> old mm coordinate system.  The new.head.mat maps from the same voxel
> indices to the new mm coordinate system.  To map from the old mm
> coordinate system to the new one, you would do:
>
>     new.head.mat / old.head.mat
>
> This series of transforms begins by multiplying with the inverse of
> old.head.mat.  This inverse will map old mm coordinates to voxels.
> Because the operations are performed from right to left, the next
> operation is to multiply by new.head.mat.  This maps voxels to the new
> mm coordinates.  Combining the two will give a mapping from the old mm
> coordinate system to the new one.
>
> To map from new mm coords to old ones, you would use:
>
>     old.head.mat / new.head.mat
>
> 2. "The matrix shown in the graphics window relates the voxels in one image
> to those in the other".
>
> Could you please explain more details?
> I means is it relationship of pixel value or physical coordination or voxel
> indices?
>
> It provides a mapping from each voxel index in one image to its
> estimated corresponding location (in voxel indices) in the other
> image.
>
> Best regards,
> -John
>
> 于 2012-5-8 22:11, John Ashburner 写道:
>
> Personally, I would do it by relating together the old and new
> matrices in the header.  The matrix shown in the graphics window
> relates the voxels in one image to those in the other, which I don't
> think is what you want.
>
> Best regards,
> -John
>
>
> On 3 May 2012 09:51, Zhijiang Wang <[log in to unmask]> wrote:
>
> Hi, SPMers,
>
> After I do coregister/Estimate, there is a change in hdr.mat.
> But would anybody tell me how to get transformation matrix?
> I want to find the corresponding relationship of physical coordinates
> between two images peformed by coregister.
>
> In the results .ps file named by "spm_*.ps", there are 3 formulars about
> X1,Y1,Z1.
> Are they?
>
> Or through caculating the relationship between old.hdr.mat and new.hdr.mat?
>
> Great thanks!
>
>
> --
>
> Best wishes,
>
> Ross Wang
>
> --------------------------------------------
>
> PhD Candidate
>
> Room 407, East Segment, Material Science Building,
>
> The International WIC Institute,
>
> Brain Informatics,
>
> College of Computer Science and Technology,
>
> Beijing University of Technology,
>
> Beijing, China.