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


:class:`CreateMatrix`
---------------------


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

Example
~~~~~~~

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

Inputs:: 

	[Mandatory]
	dict_file : (an existing file name)
		Pickle file containing the label dictionary (see ROIGen)
	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]
	out_endpoint_array_name : (a file name)
		Name for the generated endpoint arrays
	out_matrix_file : (a file name)
		NetworkX graph describing the connectivity
	out_matrix_mat_file : (a file name)
		Matlab matrix describing the connectivity


Outputs:: 

	endpoint_file : (a file name)
		Saved Numpy array with the endpoints of each fiber
	endpoint_file_mm : (a file name)
		Saved Numpy array with the endpoints of each fiber (in millimeters)
	fiber_label_file : (a file name)
		Saved Numpy array with the labels for each fiber
	fiber_length_file : (a file name)
		Saved Numpy array with the lengths of each fiber
	matrix_file : (a file name)
		NetworkX graph describing the connectivity
	matrix_mat_file : (a file name)
		Matlab matrix describing the connectivity

:class:`ROIGen`
---------------


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

Example
~~~~~~~

>>> import nipype.interfaces.cmtk.cmtk as ck
>>> rg = ck.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)
		exclusive: use_freesurfer_LUT
	freesurfer_dir : (a directory name)
		Freesurfer main directory
		requires: use_freesurfer_LUT
	ignore_exception : (a boolean)
		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
		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
