MULTI_SHELL_Estimate
====================

MULTI\_SHELL Estimate

:Command: ``dmriprep``
:Module version: 0.1
:Module type: ``prep``
:Attributes: ``utility``, ``identity``
:Notes: `MULTI_SHELL_Estimate README <https://github.com/NIRALUser/DTIPlayground/blob/master/dtiplayground/dmri/preprocessing/modules/MULTI_SHELL_Estimate/README.md>`_
:Source: `dtiplayground/dmri/preprocessing/modules/MULTI_SHELL_Estimate <https://github.com/NIRALUser/DTIPlayground/blob/master/dtiplayground/dmri/preprocessing/modules/MULTI_SHELL_Estimate>`_

Global variables
----------------

Values this module shares with the other modules of the pipeline (``dmriprep run -g <name>=<value>`` sets one).

- ``dti_path``

Protocol options
----------------

``tool``
    Tools to estimate multi-shell models (dipy / AMICO NODDI / mrtrix3)

    :Type: ``list``
    :Default: ``dipy``
    :Choices:
        - ``dipy`` -- Use DIPY library
        - ``amico`` -- NODDI model of AMICO (NDI, ODI, FWF)
        - ``mrtrix3`` -- mrtrix3 dwi2adc (S0, ADC)


``model``
    Model

    :Type: ``list``
    :Default: ``dti``
    :Used when: ``tool`` is ``dipy``
    :Choices:
        - ``dti`` -- Diffusion Tensor
        - ``dki`` -- Diffusion Kurtosis (tensor, FA/MD/AD/RD, MK/AK/RK/MKT/KFA, kurtosis tensor)
        - ``msdki`` -- Mean Signal Diffusion Kurtosis (MSD, MSK)
        - ``fwdti`` -- Free Water Elimination Diffusion
        - ``ivim`` -- Intravoxel Incoherent Motion


``optimizationMethod_dti``
    Optimizaition Method

    :Type: ``list``
    :Default: ``wls``
    :Used when: ``model`` is ``dti``, ``tool`` is ``dipy,amico``
    :Choices:
        - ``wls`` -- Weighted Least Squares
        - ``lls`` -- Linear Least Squares
        - ``nls`` -- Non-Linear Least Squares
        - ``ols`` -- Ordinary Least Squares
        - ``restore`` -- RESTORE


``optimizationMethod_fwdti``
    Optimization Method

    :Type: ``list``
    :Default: ``nls``
    :Used when: ``model`` is ``fwdti``, ``tool`` is ``dipy``
    :Choices:
        - ``wls`` -- Weighted Least Squares
        - ``nls`` -- Non-linear Least Square


``optimizationMethod_dki``
    Optimization Method

    :Type: ``list``
    :Default: ``wls``
    :Used when: ``model`` is ``dki,msdki``, ``tool`` is ``dipy``
    :Choices:
        - ``wls`` -- Weighted Least Squares
        - ``ols`` -- Ordinary Least Squares
        - ``nls`` -- Non-linear Least Square


``split_b_D``
    The b-value to split the data on for two-stage fit. This will be used while estimating the value of D

    :Type: ``float``
    :Default: ``400``
    :Used when: ``model`` is ``ivim``, ``tool`` is ``dipy``


``split_b_S0``
    The b-value to split the data on for two-stage fit. This will be used while estimating the value of S0

    :Type: ``float``
    :Default: ``200``
    :Used when: ``model`` is ``ivim``, ``tool`` is ``dipy``


``maskPath``
    Brain mask (NRRD or NIfTI); if empty, the mask of BRAIN\_Mask is used, else the whole image

    :Type: ``filepath-remote``
    :Default: not set
    :Used when: ``tool`` is ``dipy,amico``