Hi Matt - have you had a look at Mark's draft doc on these issues?
http://users.fmrib.ox.ac.uk/~mark/files/coordtransforms.pdf
Cheers.
On 24 Jul 2009, at 15:47, Matt Glasser wrote:
> 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.
>
>
> ---------------------------------------------------------------------------
> 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
> ---------------------------------------------------------------------------
>
---------------------------------------------------------------------------
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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