dmipy
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AthenaEPI
The open source toolbox for reproducible diffusion MRI-based microstructure estimation
MT-CSD doens't necessarily enforce unity on the volume fractions when fitting the signal. Since no penalty on non-unity fractions is imposed, this is the same as fitting the normalized signal...
To allow fitting of data without b0-measurements it should be possible to add S0 as an optimized parameter.
Alternative FOD optimizer taking into account non-Gaussian noise and enabling total variation spatial regularization. - Should click into the MultiCompartmentSphericalHarmonics model, but would need to be adapted to allow for...
The current parameter linking system works but is difficult to interact with and add custom functions into. - Parameter and optimization link descriptions should be passed as dictionaries. - each...
fvtk visualization in dipy has been deprecated. - create function in utils for specifically vizualizing the examples that uses the new visualization tools. - takes the fod field and the...
Current implementation in dmipy/dmipy/utils/spherical_mean.py is very slow and ugly with shell-wise for-loops. In spherical mean model fitting it is often half the estimation time. - precalculate and pre-invert multishell spherical...
Sphere implementation for Callaghan model does not pass tests yet. https://github.com/AthenaEPI/dmipy/blob/9ab40ee7e64b185a3deac990cba4191df36737db/dmipy/signal_models/sphere_models.py#L224
Astro-models are just spherical mean representations of cylinder models. This should be emphasized in the documentation.
Likely due to some kind of overflow error some cylinder models don't give meaninful signal attenuation values when giving huge diameters. There should be a catch for this.