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# nipype.interfaces.cmtk.cmtk module

## CreateMatrix

Link to code

> Bases: BaseInterface

> 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()

> resolution_network_filea pathlike object or string representing an existing file

>   Parcellation files from Connectome Mapping Toolkit.

> roi_filea pathlike object or string representing an existing file

>   Freesurfer aparc+aseg file.

> tract_filea pathlike object or string representing an existing file

>   Trackvis tract file.

> count_region_intersectionsa boolean

>   Counts all of the fiber-region traversals in the connectivity matrix (requires significantly more computational time). (Nipype default value: `False`)

> out_endpoint_array_namea pathlike object or string representing a file

>   Name for the generated endpoint arrays.

> out_fiber_length_std_matrix_mat_filea pathlike object or string representing a file

>   Matlab matrix describing the deviation in fiber lengths connecting each node.

> out_intersection_matrix_mat_filea pathlike object or string representing a file

>   Matlab connectivity matrix if all region/fiber intersections are counted.

> out_matrix_filea pathlike object or string representing a file

>   NetworkX graph describing the connectivity.

> out_matrix_mat_filea pathlike object or string representing a file

>   Matlab matrix describing the connectivity. (Nipype default value: `cmatrix.mat`)

> out_mean_fiber_length_matrix_mat_filea pathlike object or string representing a file

>   Matlab matrix describing the mean fiber lengths between each node.

> out_median_fiber_length_matrix_mat_filea pathlike object or string representing a file

>   Matlab matrix describing the mean fiber lengths between each node.

> endpoint_filea pathlike object or string representing an existing file

>   Saved Numpy array with the endpoints of each fiber.

> endpoint_file_mma pathlike object or string representing an existing file

>   Saved Numpy array with the endpoints of each fiber (in millimeters).

> fiber_label_filea pathlike object or string representing an existing file

>   Saved Numpy array with the labels for each fiber.

> fiber_labels_noorphansa pathlike object or string representing an existing file

>   Saved Numpy array with the labels for each non-orphan fiber.

> fiber_length_filea pathlike object or string representing an existing file

>   Saved Numpy array with the lengths of each fiber.

> fiber_length_std_matrix_mat_filea pathlike object or string representing an existing file

>   Matlab matrix describing the deviation in fiber lengths connecting each node.

> filtered_tractographies : a list of items which are a pathlike object or string representing an existing file filtered_tractography : a pathlike object or string representing an existing file

> > TrackVis file containing only those fibers originate in one and terminate in another region.

> filtered_tractography_by_intersectionsa pathlike object or string representing an existing file

>   TrackVis file containing all fibers which connect two regions.

> intersection_matrix_filea pathlike object or string representing an existing file

>   NetworkX graph describing the connectivity.

> intersection_matrix_mat_filea pathlike object or string representing an existing file

>   Matlab matrix describing the mean fiber lengths between each node.

> matlab_matrix_files : a list of items which are a pathlike object or string representing an existing file matrix_file : a pathlike object or string representing an existing file

> > NetworkX graph describing the connectivity.

> matrix_files : a list of items which are a pathlike object or string representing an existing file matrix_mat_file : a pathlike object or string representing an existing file

> > Matlab matrix describing the connectivity.

> mean_fiber_length_matrix_mat_filea pathlike object or string representing an existing file

>   Matlab matrix describing the mean fiber lengths between each node.

> median_fiber_length_matrix_mat_filea pathlike object or string representing an existing file

>   Matlab matrix describing the median fiber lengths between each node.

> stats_filea pathlike object or string representing an existing file

>   Saved Matlab .mat file with the number of fibers saved at each stage.

## CreateNodes

Link to code

> Bases: BaseInterface

> 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()

> resolution_network_filea pathlike object or string representing an existing file

>   Parcellation file from Connectome Mapping Toolkit.

> roi_filea pathlike object or string representing an existing file

>   Region of interest file.

> out_filenamea pathlike object or string representing a file

>   Output gpickled network with the nodes defined. (Nipype default value: `nodenetwork.pck`)

> node_networka pathlike object or string representing a file

>   Output gpickled network with the nodes defined.

## ROIGen

Link to code

> Bases: BaseInterface

> 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()

> 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)
>     >>> labelDict

> aparc_aseg_filea pathlike object or string representing an existing file

>   Freesurfer aparc+aseg file.

> LUT_filea pathlike object or string representing an existing file

>   Custom lookup table (cf. FreeSurferColorLUT.txt). Mutually exclusive with inputs: `use_freesurfer_LUT`.

> freesurfer_dira pathlike object or string representing a directory

>   Freesurfer main directory. Requires inputs: `use_freesurfer_LUT`.

> out_dict_filea pathlike object or string representing a file

>   Label dictionary saved in Pickle format.

> out_roi_filea pathlike object or string representing a file

>   Region of Interest file for connectivity mapping.

> use_freesurfer_LUTa boolean

>   Boolean value; Set to True to use default Freesurfer LUT, False for custom LUT. Mutually exclusive with inputs: `LUT_file`.

> dict_filea pathlike object or string representing a file

>   Label dictionary saved in Pickle format.

> roi_filea pathlike object or string representing a file

>   Region of Interest file for connectivity mapping.

nipype.interfaces.cmtk.cmtk.cmat(track_file, roi_file, resolution_network_file, matrix_name, matrix_mat_name, endpoint_name, intersections=False)

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

nipype.interfaces.cmtk.cmtk.create_allpoints_cmat(streamlines, roiData, voxelSize, n_rois)

  Create the intersection arrays for each fiber

nipype.interfaces.cmtk.cmtk.create_endpoints_array(fib, voxelSize)

  Create the endpoints arrays for each fiber.

  Parameters:

    - fib (array-like) – the fibers data

    - voxelSize (tuple) – 3-tuple containing the voxel size of the ROI image

  Returns:

    - endpoints (ndarray of size [#fibers, 2, 3]) – containing for each fiber the index of its first and last point in the voxelSize volume

    - endpointsmm (ndarray of size [#fibers, 2, 3]) – endpoints in millimeter coordinates

nipype.interfaces.cmtk.cmtk.create_nodes(roi_file, resolution_network_file, out_filename)

nipype.interfaces.cmtk.cmtk.get_connectivity_matrix(n_rois, list_of_roi_crossed_lists)

nipype.interfaces.cmtk.cmtk.get_rois_crossed(pointsmm, roiData, voxelSize)

nipype.interfaces.cmtk.cmtk.length(xyz, along=False)

  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 in case of along == False, giving total length, array if along == True, giving cumulative lengths.

  Return type:

    scalar or array shape (N-1,)

  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([])
      0
      >>> length([[1, 2, 3]])
      0
      >>> length([], along=True)
      array([0])

nipype.interfaces.cmtk.cmtk.save_fibers(oldhdr, oldfib, fname, indices)

  Stores a new trackvis file fname using only given indices