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MRtrix3 / mrtrix3

MRtrix3 provides a set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and apparent fibre density
http://www.mrtrix.org
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dwipreproc: LR/AP/IS behaviour for non-axial axquisitions #847

Open Lestropie opened 7 years ago

Lestropie commented 7 years ago

Just thinking about this while I read this post.

The axis indices (0, -0, 1, -1, 2, -2) and NIfTI axis codes (i, -i, j, -j, k, -k) should be fine.

However currently the 'lr' / 'rl' / 'ap' / 'pa' / 'is' / 'si' flags are just used to select an axis index. For non-axial acquisitions, these won't map directly, the image transform needs to be read.

jdtournier commented 7 years ago

Not sure I follow this. What's the problem exactly? One of the first things to happen in dwipreproc is the mrconvert -stride -1,2,3,4 call - wouldn't that avoid any issues with this?