BRAIN_Tractography
==================

Brain tractography (whole/single region) using DIPY library

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

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

``whiteMatterMaskThreshold``
    Manual or Otsu threshold on FA to get a white matter mask of the brain

    :Type: ``list``
    :Default: ``manual``
    :Choices:
        - ``manual`` -- Use manual threshold on FA to create a white matter mask


``thresholdLow``
    Lower value of threshold to apply on FA

    :Type: ``number``
    :Default: ``0.4``


``thresholdUp``
    Upper value of threshold to apply on FA

    :Type: ``number``
    :Default: ``0.98``


``method``
    Method used to generate the peaks used to generate the streamlines

    :Type: ``list``
    :Default: ``tensor``
    :Choices:
        - ``csa`` -- Constant Solid Angle method
        - ``opdt`` -- Orientation Probability Density Transform method
        - ``tensor`` -- DTI tensor method


``shOrder``
    sh order used for peak generation model

    :Type: ``number``
    :Default: ``2``


``relativePeakThreshold``
    Only keeps peaks greater than relativePeakThreshold \* m where m is the largest peak

    :Type: ``number``
    :Default: ``0.9``


``minPeakSeparationAngle``
    The minimum distance between directions. If two peaks are too close only the larger of the two is returned. Number between 0 and 90.

    :Type: ``number``
    :Default: ``25``


``stoppingCriterionThreshold``
    Threshold on FA to stop tracts

    :Type: ``number``
    :Default: ``0.3``


``vtk42``
    Save output tractogram in VTK format 4.2 (instead of 5.0)

    :Type: ``boolean``
    :Default: ``false``
    :Note: not shown in the user interface
    :Note: disabled


``removeShortTracts``
    Remove short tracts from tractogram

    :Type: ``boolean``
    :Default: ``false``


``shortTractsThreshold``
    Minimal length for tracts to be conserved.

    :Type: ``number``
    :Default: ``100``


``removeLongTracts``
    Remove long tracts from tractogram

    :Type: ``boolean``
    :Default: ``false``


``longTractsThreshold``
    Maximal length for tracts to be conserved.

    :Type: ``number``
    :Default: ``100``


``singleTract``
    If checked, the module performs single region tractography instead of whole brain

    :Type: ``boolean``
    :Default: ``false``


``referenceTractFile``
    Path of the reference tract file (.vtk)

    :Type: ``filepath-remote``
    :Default: not set
    :Used when: ``singleTract`` is ``True``


``displacementFieldFile``
    Path of the displacement file for transform

    :Type: ``filepath-remote``
    :Default: not set
    :Used when: ``singleTract`` is ``True``


``dilationRadius``
    Dilation radius

    :Type: ``number``
    :Default: ``2``
    :Used when: ``singleTract`` is ``True``