DTI_Estimate
============

Estimate DTI

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

``method``
    Method to estimate DTI (dipy/dtiestim)

    :Type: ``list``
    :Default: ``dipy``
    :Choices:
        - ``dipy`` -- Use DIPY library
        - ``dtiestim`` -- Use NIRAL dtiestim software


``optimizationMethod``
    Optimizaition Method

    :Type: ``list``
    :Default: ``wls``
    :Choices:
        - ``wls`` -- Weighted Least Squares
        - ``lls`` -- Linear Least Squares
        - ``nls`` -- Non-Linear Least Squares
        - ``ml`` -- Maximum Likelihood (dtiestim Only)
        - ``restore`` -- RESTORE (DIPY Only)


``correctionMethod``
    Tensor correction method when a computed tensor is not positive semi-definite (dtiestim only)

    :Type: ``list``
    :Default: ``zero``
    :Choices:
        - ``zero`` -- Substitute to zero value
        - ``nearest`` -- Nearest (dtiestim only)
        - ``abs`` -- Absolute (dtiestim only)
        - ``none`` -- None (dtiestim only)