DWI models: Define "bvec" orientation reference#98
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- FSL bedpostx command fibre orientations stored as spherical coordinates are confirmed to use the "bvec" reference frame. - Enforcing azimuth angle to obey the right hand rule about the zenith axis would necessitate direct modification of image intensities from bedpostx outputs to store. Therefore it would be preferable to instead define the sign of the azimuth angle based on the direction of the second reference axis. Closes #95. Closes #94.
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I think this is ready to go, right? Could you take a look/resolve the conflicts? I just updated the bep-16 branch with a merge from bids-standard/bids-specification:master |
Conflicts: src/derivatives/05-diffusion-derivatives.md
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I'm not 100% happy with the description of the azimuth angle. I wonder if it needs to be explicit about the trigonometric relationships involved in either direction. Another prospect to consider would be tailored figures showing the interpretations of coefficients relative to any arbitrary reference frame. But it's good enough, so I'll merge and if a better idea comes across anyone we can revisit. |
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Addresses part of #94.
While I have not yet completed all of the relevant work, I have at least convinced myself of the fact that the eigenvector images produced by FSL's
dtifitare not defined with respect to the image axes; rather, they use the same convention as thebvecsformat. Therefore, to be able to write such data to a BIDS-compliant dataset without image intensity modification, that coordinate system needs to be included in the specification.While I suspect the
bedpostxoutputs use the same convention, I've not yet confirmed that for #94, so I'm deferring that for now.