<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>
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