dmipy
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AthenaEPI
The open source toolbox for reproducible diffusion MRI-based microstructure estimation
Following the recent publication of VERDICT-AMICO, It seems that AMICO can be implemented as a generalised optimizer instead of a model-wise one.
Implement equation (2) of [1] after IVIM parameter estimation. [1] Lemke, A., Laun, F. B., Simon, D., Stieltjes, B., & Schad, L. R. (2010). An in vivo verification of the...
- [x] includes function to remove specific isotropic signal contributions from fitted MT-CSD signal reconstruction - [x] test for the correct volume fraction removal. - [ ] Examples to apply...
slide 60 of : https://www.cs.jhu.edu/~misha/Spring15/17.pdf and explanation of anisotropic response function.
Extension of FittedMCSH model to fit the spherical FOD using one or more parametric distributions (watson/bingam), essentially making a bridge to standard MC models. This way you can get an...
Small extension to FittedMultiCompartmentSphericalHarmonicsModel to estimate the apparent fiber density. Raffelt, David, et al. "Apparent fibre density: a novel measure for the analysis of diffusion-weighted magnetic resonance images." Neuroimage 59.4...
Every framework should have a general catch for when the optimization errors-out for whatever reason, and then store that voxel in an "error map" or something. Much easier to inspect...
- Includes Anisotropic IVIM example. Slator, Paddy J., et al. "Quantifying placental microcirculation and microstructure with anisotropic IVIM models." Placenta 57 (2017): 290-291.
- Refactors parameter links as classes or dictionaries that can be easily adapted to apply any parameter relationship. - Is able to both link and remove a parameter (e.g. tortuosity),...
Right now a fractional parameter ranges between [0-1] * some_parameter, but that means that it can also take the value 0, which is typically not the case in some_parameter. fractional...