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<div class="moz-cite-prefix">Hello,<br>
<br>
from what I understand this is 2 view of the same transformation
matrix<br>
mrtrix give the transformation matrix relative to a fix given
order of the voxel<br>
so the Data layout says [-0 1 2]<br>
this is why the first number 1 is then -1.75 (-1*voxelsize) in spm<br>
<br>
This flip will then change also the corresponding translation<br>
the discrepencie in y and z translation are due to the fact that
matlab indices start at 1<br>
<br>
Anyway you should use the transformation given by spm<br>
<br>
Romain<br>
<br>
Le 21/05/2014 16:01, Alessandro Calamuneri a écrit :<br>
</div>
<blockquote
cite="mid:CAOw1OkpYLMzmQyovjw5cV9xu1L=m7pf_zckN4+502v6J0LXyog@mail.gmail.com"
type="cite">
<div dir="ltr">Hi there,
<div>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 </div>
<div><br>
</div>
<div>Dimensions: 128x128x4</div>
<div>voxel size: 1.75x1.75x2</div>
<div>Data layout: [-0 1 2]<br>
</div>
<div>data scaling: offset=0 multiplier=1</div>
<div>Transform 1 0 0 -109.8</div>
<div> 0 1 0 -100.2</div>
<div> 0 0 1 -44.73</div>
<div> 0 0 0 1</div>
<div><br>
</div>
<div>Now, when I look at the same transformation matrix by using
SPM on matlab, I get the following transformation matrix</div>
<div><br>
</div>
<div>V.mat=</div>
<div><br>
</div>
<div>-1.75 0 0 114.7</div>
<div> 0 1.75 0 -101.95</div>
<div> 0 0 2 -46.729</div>
<div>
0 0 0 1</div>
<div><br>
</div>
<div>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.</div>
<div>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.</div>
<div>How can I be sure to get the correct intensities at proper
voxel coordinates?</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Alessandro</div>
<div><br>
</div>
<div>
<div dir="ltr">
<div><br>
</div>
</div>
</div>
</div>
<br>
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</blockquote>
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