[Mrtrix-discussion] DISCREPANCY in voxel2world matrices between mrtrix and spm

[romain valabregue]

Hello,

from what I understand this is 2 view of the same transformation matrix
mrtrix give the transformation matrix relative to a fix given order of 
the voxel
so the Data layout says [-0 1 2]
this is why the first number 1 is then -1.75 (-1*voxelsize) in spm

This flip will then change also the corresponding translation
the discrepencie in y and z translation are due to the fact that matlab 
indices start at 1

Anyway you should use the transformation given by spm

Romain

Le 21/05/2014 16:01, Alessandro Calamuneri a écrit :
> Hi there,
> I am triyng to get some paremeters sampling at coordinates of tracks 
> got after a probabilistic tractography. When I look at an image, e.g., 
> FA.nii, I get, among others, the following info using mrview
>
> Dimensions: 128x128x4
> voxel size: 1.75x1.75x2
> Data layout: [-0 1 2]
> data scaling: offset=0 multiplier=1
> Transform 1    0    0    -109.8
>                0    1    0    -100.2
>                0    0    1    -44.73
>                0    0    0         1
>
> Now, when I look at the same transformation matrix by using SPM on 
> matlab, I get the following transformation matrix
>
> V.mat=
>
> -1.75         0             0          114.7
>    0          1.75          0         -101.95
>    0           0             2           -46.729
>    0           0             0              1
>
> In the translation column, there is a consistent offset according, for 
> two out of three of those parameters, to voxel dimension, as dTz=2 
> dTy=1.75, whereas there seems not to be a reletionship between 114.7 
> and -109.8. I assume this is due to the way in which data are stored 
> and read within mrtrix, as a flip should have been occured. By 
> flipping coordinates I get 128*-1.75+114.7=109.3., which turns out to 
> show an offset of a few millimiters.
> As I want to sample MRI data along the tracts using an own matlab 
> implementation, I need to go to volume voxel space by multiplying 
> tracts coordinates (that are in mm) by the inverse transformation 
> matrix. But given this discrepancy, which transformation matrix should 
> I use? I have also tried to overlap tracts to, e.g, the same FA map, 
> on matlab, and this displacement seems to occur indeed.
> How can I be sure to get the correct intensities at proper voxel 
> coordinates?
>
> Thanks,
> Alessandro
>
>
>
>
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