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

[Alessandro Calamuneri]

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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