Debugging the last connectome steps

[sebastientourbier]

1. To convert tck tractogram to trk fromat, CMP3 uses the Tck2Trk interface:

connectomemapper3/cmtklib/diffusion.py

Lines 376 to 387 in 249e4e5

	class Tck2Trk(BaseInterface):
	"""Convert a tractogram in `mrtrix` TCK format to `trackvis` TRK format.
	Examples
	--------
	>>> from cmtklib.diffusion import Tck2Trk
	>>> tck_to_trk = Tck2Trk()
	>>> tck_to_trk.inputs.in_tracks = 'sub-01_tractogram.tck'
	>>> tck_to_trk.inputs.in_image = 'sub-01_desc-preproc_dwi.nii.gz'
	>>> tck_to_trk.inputs.out_tracks = 'sub-01_tractogram.trk'
	>>> tck_to_trk.run() # doctest: +SKIP
	"""

2. To map the structural connectome, CMP3 uses the cmat() function:

connectomemapper3/cmtklib/connectome.py

Lines 156 to 184 in 249e4e5

	def cmat(intrk, roi_volumes, roi_graphmls, parcellation_scheme, compute_curvature=True, additional_maps={},
	output_types=['gPickle'], atlas_info={}):
	"""Create the connection matrix for each resolution using fibers and ROIs.
	Parameters
	----------
	intrk : TRK file
	Reconstructed tractogram
	roi_volumes : list
	List of parcellation files for a given parcellation scheme
	roi_graphmls : list
	List of graphmls files that describes parcellation nodes
	parcellation_scheme : ['NativeFreesurfer','Lausanne2008','Lausanne2018']
	compute_curvature : Boolean
	additional_maps : dict
	A dictionary of key/value for each additional map where the value
	is the path to the map
	output_types : ['gPickle','mat','graphml']
	atlas_info : dict
	Dictionary storing information such as path to files related to a
	parcellation atlas / scheme.
	"""