Dwigradcheck

Hi @rsmith or @jdtournier

Simple question: How do I read the dwigradcheck table? Is this suggesting a x-axis flip?

Mean length     Axis flipped    Axis permutations    Axis basis
60.26            0                (0, 1, 2)           image
59.74            0                (0, 1, 2)           scanner
37.79            2                (0, 1, 2)           image
37.24         none                (0, 2, 1)           scanner
37.21            0                (0, 2, 1)           image
37.07            2                (0, 1, 2)           scanner
36.54         none                (0, 2, 1)           image
36.39            0                (0, 2, 1)           scanner
35.52            2                (2, 1, 0)           scanner
35.38            1                (1, 0, 2)           scanner
34.92            0                (2, 1, 0)           image
34.91            2                (2, 1, 0)           image
34.89            0                (2, 1, 0)           scanner
34.88            1                (0, 1, 2)           image
34.83         none                (0, 1, 2)           image
34.79         none                (0, 1, 2)           scanner
34.75            0                (1, 0, 2)           image
34.54            1                (0, 1, 2)           scanner
34.51            1                (1, 0, 2)           image
34.36            0                (1, 0, 2)           scanner
29.04            2                (0, 2, 1)           scanner
29.02            1                (0, 2, 1)           image
28.18            2                (2, 0, 1)           scanner
27.78         none                (2, 0, 1)           image
27.53            1                (1, 2, 0)           scanner
27.36            1                (2, 0, 1)           image
27.27            1                (0, 2, 1)           scanner
27.16         none                (1, 0, 2)           image
27.14            2                (1, 0, 2)           scanner
27.11            0                (2, 0, 1)           scanner
27.10            2                (1, 2, 0)           image
27.03         none                (1, 2, 0)           image
27.00            2                (0, 2, 1)           image
26.80            0                (1, 2, 0)           scanner
26.80            2                (1, 2, 0)           scanner
26.39            0                (1, 2, 0)           image
26.39         none                (1, 0, 2)           scanner
26.36            1                (2, 0, 1)           scanner
26.34         none                (2, 0, 1)           scanner
26.28         none                (2, 1, 0)           scanner
26.25         none                (1, 2, 0)           scanner
26.25            1                (1, 2, 0)           image
26.22            2                (2, 0, 1)           image
26.18            0                (2, 0, 1)           image
25.99         none                (2, 1, 0)           image
25.99            2                (1, 0, 2)           image
25.79            1                (2, 1, 0)           image
25.60            1                (2, 1, 0)           scanner

Hey Adam,

Yep: if you flip the x-axis, the mean streamline length is almost double that compared to if you perform no such flip, and it’s a pretty clear standout winner.

The ambiguity is whether this flip should be applied in image space (equivalent to negating values in the first row of the bvec file) or scanner space (equivalent to negating values in the first column of the gradient table in MRtrix format). If your image axes are very close to the scanner principal axes, then it’s just about impossible to figure out which of the two should be applied based on this heuristic. But your prior processing might provide a clue. E.g. If you’ve just imported DICOM data, and the nature of the data coming from your scanner vendor means that the gradient orientations are stored within the DICOM headers in scanner space, then you probably want to do the flip in scanner space. If your data have been somehow processed by some other software package, which has involved conversion to/from NIfTI / bvecs at some point, and especially if that software isn’t guaranteed to deal with the bvecs coordinate system handedness issue, more likely the error has been applied in image space and so should be corrected there. But the closer your images axes are to the scanner axes, the less important the distinction becomes.

Cheers
Rob

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