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()                 # doctest: +SKIP

resolution_network_file : a pathlike object or string representing an existing file

Parcellation files from Connectome Mapping Toolkit.

roi_file : a pathlike object or string representing an existing file

Freesurfer aparc+aseg file.

tract_file : a pathlike object or string representing an existing file

Trackvis tract file.

count_region_intersections : a boolean

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

out_endpoint_array_name : a pathlike object or string representing a file

Name for the generated endpoint arrays.

out_fiber_length_std_matrix_mat_file : a pathlike object or string representing a file

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

out_intersection_matrix_mat_file : a pathlike object or string representing a file

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

out_matrix_file : a pathlike object or string representing a file

NetworkX graph describing the connectivity.

out_matrix_mat_file : a pathlike object or string representing a file

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

out_mean_fiber_length_matrix_mat_file : a pathlike object or string representing a file

Matlab matrix describing the mean fiber lengths between each node.

out_median_fiber_length_matrix_mat_file : a pathlike object or string representing a file

Matlab matrix describing the mean fiber lengths between each node.

endpoint_file : a pathlike object or string representing an existing file

Saved Numpy array with the endpoints of each fiber.

endpoint_file_mm : a pathlike object or string representing an existing file

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

fiber_label_file : a pathlike object or string representing an existing file

Saved Numpy array with the labels for each fiber.

fiber_labels_noorphans : a pathlike object or string representing an existing file

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

fiber_length_file : a pathlike object or string representing an existing file

Saved Numpy array with the lengths of each fiber.

fiber_length_std_matrix_mat_file : a 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_intersections : a pathlike object or string representing an existing file

TrackVis file containing all fibers which connect two regions.

intersection_matrix_file : a pathlike object or string representing an existing file

NetworkX graph describing the connectivity.

intersection_matrix_mat_file : a 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_file : a pathlike object or string representing an existing file

Matlab matrix describing the mean fiber lengths between each node.

median_fiber_length_matrix_mat_file : a pathlike object or string representing an existing file

Matlab matrix describing the median fiber lengths between each node.

stats_file : a 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() # doctest: +SKIP

resolution_network_file : a pathlike object or string representing an existing file

Parcellation file from Connectome Mapping Toolkit.

roi_file : a pathlike object or string representing an existing file

Region of interest file.

out_filename : a pathlike object or string representing a file

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

node_network : a 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() # 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
>>> labelDict                     # doctest: +SKIP

aparc_aseg_file : a pathlike object or string representing an existing file

Freesurfer aparc+aseg file.

LUT_file : a pathlike object or string representing an existing file

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

freesurfer_dir : a pathlike object or string representing a directory

Freesurfer main directory. Requires inputs: use_freesurfer_LUT.

out_dict_file : a pathlike object or string representing a file

Label dictionary saved in Pickle format.

out_roi_file : a pathlike object or string representing a file

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 with inputs: LUT_file.

dict_file : a pathlike object or string representing a file

Label dictionary saved in Pickle format.

roi_file : a 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