.. AUTO-GENERATED FILE -- DO NOT EDIT!

interfaces.cmtk.cmtk
====================


.. _nipype.interfaces.cmtk.cmtk.CreateMatrix:


.. index:: CreateMatrix

CreateMatrix
------------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/interfaces/cmtk/cmtk.py#L430>`__

Performs connectivity mapping and outputs the result as a NetworkX graph and a Matlab matrix

Example
~~~~~~~

>>> import nipype.interfaces.cmtk as cmtk
>>> conmap = cmtk.CreateMatrix()
>>> conmap.roi_file = 'fsLUT_aparc+aseg.nii'
>>> conmap.tract_file = 'fibers.trk'
>>> conmap.run()                 # doctest: +SKIP

Inputs::

        [Mandatory]
        resolution_network_file: (an existing file name)
                Parcellation files from Connectome Mapping Toolkit
        roi_file: (an existing file name)
                Freesurfer aparc+aseg file
        tract_file: (an existing file name)
                Trackvis tract file

        [Optional]
        count_region_intersections: (a boolean, nipype default value: False)
                Counts all of the fiber-region traversals in the connectivity matrix
                (requires significantly more computational time)
        out_endpoint_array_name: (a file name)
                Name for the generated endpoint arrays
        out_fiber_length_std_matrix_mat_file: (a file name)
                Matlab matrix describing the deviation in fiber lengths connecting
                each node.
        out_intersection_matrix_mat_file: (a file name)
                Matlab connectivity matrix if all region/fiber intersections are
                counted.
        out_matrix_file: (a file name)
                NetworkX graph describing the connectivity
        out_matrix_mat_file: (a file name, nipype default value: cmatrix.mat)
                Matlab matrix describing the connectivity
        out_mean_fiber_length_matrix_mat_file: (a file name)
                Matlab matrix describing the mean fiber lengths between each node.
        out_median_fiber_length_matrix_mat_file: (a file name)
                Matlab matrix describing the mean fiber lengths between each node.
        resolution_network_file: (an existing file name)
                Parcellation files from Connectome Mapping Toolkit
        roi_file: (an existing file name)
                Freesurfer aparc+aseg file
        tract_file: (an existing file name)
                Trackvis tract file

Outputs::

        endpoint_file: (an existing file name)
                Saved Numpy array with the endpoints of each fiber
        endpoint_file_mm: (an existing file name)
                Saved Numpy array with the endpoints of each fiber (in millimeters)
        fiber_label_file: (an existing file name)
                Saved Numpy array with the labels for each fiber
        fiber_labels_noorphans: (an existing file name)
                Saved Numpy array with the labels for each non-orphan fiber
        fiber_length_file: (an existing file name)
                Saved Numpy array with the lengths of each fiber
        fiber_length_std_matrix_mat_file: (an existing file name)
                Matlab matrix describing the deviation in fiber lengths connecting
                each node.
        filtered_tractographies: (an existing file name)
        filtered_tractography: (an existing file name)
                TrackVis file containing only those fibers originate in one and
                terminate in another region
        filtered_tractography_by_intersections: (an existing file name)
                TrackVis file containing all fibers which connect two regions
        intersection_matrix_file: (an existing file name)
                NetworkX graph describing the connectivity
        intersection_matrix_mat_file: (an existing file name)
                Matlab matrix describing the mean fiber lengths between each node.
        matlab_matrix_files: (an existing file name)
        matrix_file: (an existing file name)
                NetworkX graph describing the connectivity
        matrix_files: (an existing file name)
        matrix_mat_file: (an existing file name)
                Matlab matrix describing the connectivity
        mean_fiber_length_matrix_mat_file: (an existing file name)
                Matlab matrix describing the mean fiber lengths between each node.
        median_fiber_length_matrix_mat_file: (an existing file name)
                Matlab matrix describing the median fiber lengths between each node.
        stats_file: (an existing file name)
                Saved Matlab .mat file with the number of fibers saved at each stage

.. _nipype.interfaces.cmtk.cmtk.CreateNodes:


.. index:: CreateNodes

CreateNodes
-----------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/interfaces/cmtk/cmtk.py#L747>`__

Generates a NetworkX graph containing nodes at the centroid of each region in the input ROI file.
Node data is added from the resolution network file.

Example
~~~~~~~

>>> import nipype.interfaces.cmtk as cmtk
>>> mknode = cmtk.CreateNodes()
>>> mknode.inputs.roi_file = 'ROI_scale500.nii.gz'
>>> mknode.run() # doctest: +SKIP

Inputs::

        [Mandatory]
        resolution_network_file: (an existing file name)
                Parcellation file from Connectome Mapping Toolkit
        roi_file: (an existing file name)
                Region of interest file

        [Optional]
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the
                interface fails to run
        out_filename: (a file name, nipype default value: nodenetwork.pck)
                Output gpickled network with the nodes defined.
        resolution_network_file: (an existing file name)
                Parcellation file from Connectome Mapping Toolkit
        roi_file: (an existing file name)
                Region of interest file

Outputs::

        node_network: (a file name)
                Output gpickled network with the nodes defined.

.. _nipype.interfaces.cmtk.cmtk.ROIGen:


.. index:: ROIGen

ROIGen
------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/interfaces/cmtk/cmtk.py#L578>`__

Generates a ROI file for connectivity mapping and a dictionary file containing relevant node information

Example
~~~~~~~

>>> import nipype.interfaces.cmtk as cmtk
>>> rg = cmtk.ROIGen()
>>> rg.inputs.aparc_aseg_file = 'aparc+aseg.nii'
>>> rg.inputs.use_freesurfer_LUT = True
>>> rg.inputs.freesurfer_dir = '/usr/local/freesurfer'
>>> rg.run() # doctest: +SKIP

The label dictionary is written to disk using Pickle. Resulting data can be loaded using:

>>> file = open("FreeSurferColorLUT_adapted_aparc+aseg_out.pck", "r")
>>> file = open("fsLUT_aparc+aseg.pck", "r")
>>> labelDict = pickle.load(file) # doctest: +SKIP
>>> print labelDict                     # doctest: +SKIP

Inputs::

        [Mandatory]
        aparc_aseg_file: (an existing file name)
                Freesurfer aparc+aseg file

        [Optional]
        LUT_file: (an existing file name)
                Custom lookup table (cf. FreeSurferColorLUT.txt)
                mutually_exclusive: use_freesurfer_LUT
        aparc_aseg_file: (an existing file name)
                Freesurfer aparc+aseg file
        freesurfer_dir: (a directory name)
                Freesurfer main directory
                requires: use_freesurfer_LUT
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the
                interface fails to run
        out_dict_file: (a file name)
                Label dictionary saved in Pickle format
        out_roi_file: (a file name)
                Region of Interest file for connectivity mapping
        use_freesurfer_LUT: (a boolean)
                Boolean value; Set to True to use default Freesurfer LUT, False for
                custom LUT
                mutually_exclusive: LUT_file

Outputs::

        dict_file: (a file name)
                Label dictionary saved in Pickle format
        roi_file: (a file name)
                Region of Interest file for connectivity mapping

.. module:: nipype.interfaces.cmtk.cmtk


.. _nipype.interfaces.cmtk.cmtk.cmat:

:func:`cmat`
------------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/interfaces/cmtk/cmtk.py#L165>`__



Create the connection matrix for each resolution using fibers and ROIs.


.. _nipype.interfaces.cmtk.cmtk.create_allpoints_cmat:

:func:`create_allpoints_cmat`
-----------------------------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/interfaces/cmtk/cmtk.py#L95>`__



Create the intersection arrays for each fiber


.. _nipype.interfaces.cmtk.cmtk.create_endpoints_array:

:func:`create_endpoints_array`
------------------------------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/interfaces/cmtk/cmtk.py#L120>`__



Create the endpoints arrays for each fiber
Parameters
~~~~~~~~~~
fib: the fibers data
voxelSize: 3-tuple containing the voxel size of the ROI image
Returns
~~~~~~~
(endpoints: matrix of size [#fibers, 2, 3] containing for each fiber the
index of its first and last point in the voxelSize volume
endpointsmm) : endpoints in milimeter coordinates


.. _nipype.interfaces.cmtk.cmtk.create_nodes:

:func:`create_nodes`
--------------------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/interfaces/cmtk/cmtk.py#L726>`__






.. _nipype.interfaces.cmtk.cmtk.get_connectivity_matrix:

:func:`get_connectivity_matrix`
-------------------------------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/interfaces/cmtk/cmtk.py#L84>`__






.. _nipype.interfaces.cmtk.cmtk.get_rois_crossed:

:func:`get_rois_crossed`
------------------------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/interfaces/cmtk/cmtk.py#L71>`__






.. _nipype.interfaces.cmtk.cmtk.length:

:func:`length`
--------------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/interfaces/cmtk/cmtk.py#L27>`__



Euclidean length of track line

Parameters
~~~~~~~~~~
xyz : array-like shape (N,3)
   array representing x,y,z of N points in a track
along : bool, optional
   If True, return array giving cumulative length along track,
   otherwise (default) return scalar giving total length.

Returns
~~~~~~~
L : scalar or array shape (N-1,)
   scalar in case of `along` == False, giving total length, array if
   `along` == True, giving cumulative lengths.

Examples
~~~~~~~~
>>> xyz = np.array([[1,1,1],[2,3,4],[0,0,0]])
>>> expected_lens = np.sqrt([1+2**2+3**2, 2**2+3**2+4**2])
>>> length(xyz) == expected_lens.sum()
True
>>> len_along = length(xyz, along=True)
>>> np.allclose(len_along, expected_lens.cumsum())
True
>>> length([])
~
>>> length([[1, 2, 3]])
~
>>> length([], along=True)
array([0])


.. _nipype.interfaces.cmtk.cmtk.save_fibers:

:func:`save_fibers`
-------------------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/interfaces/cmtk/cmtk.py#L385>`__



Stores a new trackvis file fname using only given indices

