Hi Steve,
I think the builtin routine we have expects the coordinate center for each
image to be the point in all three images that has the value 0mm (e.g. the
AC if the image has been talirach transformed). We have already tried just
applying the transform as is and it didn't align things properly with our
surfaces. This is why I was thinking we needed to do something with the
sforms, but perhaps it is a combination of the sforms and the image
dimensions to convert the coordinate center from the corner to mm origin
that is needed?
The diffusion image dimensions are:
dim1 128
dim2 128
dim3 68
The structural image dimensions are:
dim1 176
dim2 208
dim3 176
Where the first image is 2mm isotropic and the second is 1mm isotropic.
We just need to figure out how to convert the affine matrix so that it is
relative to the image origins, rather than the first corner voxels.
Thanks,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Steve Smith
Sent: Friday, July 24, 2009 12:52 AM
To: [log in to unmask]
Subject: Re: [FSL] FLIRT Affine Matricies Applied to mm Coordinates
Hi Matt - I would think that to transform the vectors from diffusion
into structural space you only need the diff2str.mat transform, and
can ignore the sform settings.
The values in the affine transform are all wrt mm in both images, with
the coordinate centre for each imaging being in the centre of the
first (corner) voxel so you should be able to use that pretty easily.
Cheers.
On 24 Jul 2009, at 05:26, Matt Glasser wrote:
> My group is having difficulty implementing the application of a
> FLIRT affine transform outside of FLIRT on mm coordinates.
> Basically, we have vectors in diffusion space that need to be moved
> into structural space without resampling (or we would just use
> vecreg). To avoid resampling, we are converting the vectors to a
> format that stores the mm coordinates of their origin (the center of
> the voxel in diffusion space) and x y and z components of the unit
> vector. Thus, we need to apply a diff2str.mat FLIRT transform to
> each set of mm coordinates to find out where they will be in
> structural space (where we have cortical surfaces). This is proving
> less than straightforward for our programmer to implement in Caret,
> potentially because of differences in how the origin of the volumes
> are defined. We have the following example situation (which works
> in flirt or vecreg, but, we need to do it on mm coordinates):
>
> A diffusion volume with the vectors has the following sform:
>
> sto_xyz:1 -2.000000 0.000000 0.000000 121.510132
> sto_xyz:2 0.000000 2.000000 0.000000 -101.654175
> sto_xyz:3 0.000000 0.000000 2.000000 -36.245544
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Right-to-Left
> sform_yorient Posterior-to-Anterior
> sform_zorient Inferior-to-Superior
>
> An affine matrix diff2str.mat:
>
> 0.954197 0.0818732 -0.00957881 -45.0519
> -0.0968743 1.04984 0.0603049 -21.6026
> 0.0306892 -0.0608188 1.09415 25.3402
> 0 0 0 1
>
> And a structural volume with the following sform:
>
> sto_xyz:1 1.000000 0.000000 0.000000 -88.500000
> sto_xyz:2 0.000000 1.000000 0.000000 -123.500000
> sto_xyz:3 0.000000 0.000000 1.000000 -74.500000
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Left-to-Right
> sform_yorient Posterior-to-Anterior
> sform_zorient Inferior-to-Superior
>
> My intuition tells me that some appropriate combination of these
> matrices will lead to a mm to mm affine transform that we can apply
> to the vectors. The separate issue of rotating the vectors to
> account for the affine transform, once we have the correct mm 2 mm
> one, has been addressed elsewhere.
>
> Thanks,
>
> Matt.
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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