nipype.interfaces.cmtk.convert module

CFFConverter

Link to code

Bases: CFFBaseInterface

Creates a Connectome File Format (CFF) file from input networks, surfaces, volumes, tracts, etcetera….

Example

>>> import nipype.interfaces.cmtk as cmtk
>>> cvt = cmtk.CFFConverter()
>>> cvt.inputs.title = 'subject 1'
>>> cvt.inputs.gifti_surfaces = ['lh.pial_converted.gii', 'rh.pial_converted.gii']
>>> cvt.inputs.tract_files = ['streamlines.trk']
>>> cvt.inputs.gpickled_networks = ['network0.gpickle']
>>> cvt.run()
Optional Inputs:

  • creator (a string) – Creator.

  • data_files (a list of items which are a pathlike object or string representing an existing file) – List of external data files (i.e. Numpy, HD5, XML) .

  • description (a string) – Description. (Nipype default value: Created with the Nipype CFF converter)

  • email (a string) – Email address.

  • gifti_labels (a list of items which are a pathlike object or string representing an existing file) – List of GIFTI labels.

  • gifti_surfaces (a list of items which are a pathlike object or string representing an existing file) – List of GIFTI surfaces.

  • gpickled_networks (a list of items which are a pathlike object or string representing an existing file) – List of gpickled Networkx graphs.

  • graphml_networks (a list of items which are a pathlike object or string representing an existing file) – List of graphML networks.

  • license (a string) – License.

  • nifti_volumes (a list of items which are a pathlike object or string representing an existing file) – List of NIFTI volumes.

  • out_file (a pathlike object or string representing a file) – Output connectome file. (Nipype default value: connectome.cff)

  • publisher (a string) – Publisher.

  • references (a string) – References.

  • relation (a string) – Relation.

  • rights (a string) – Rights.

  • script_files (a list of items which are a pathlike object or string representing an existing file) – List of script files to include.

  • species (a string) – Species. (Nipype default value: Homo sapiens)

  • timeseries_files (a list of items which are a pathlike object or string representing an existing file) – List of HDF5 timeseries files.

  • title (a string) – Connectome Title.

  • tract_files (a list of items which are a pathlike object or string representing an existing file) – List of Trackvis fiber files.

Outputs:

connectome_file (a pathlike object or string representing an existing file) – Output connectome file.

MergeCNetworks

Link to code

Bases: CFFBaseInterface

Merges networks from multiple CFF files into one new CFF file.

Example

>>> import nipype.interfaces.cmtk as cmtk
>>> mrg = cmtk.MergeCNetworks()
>>> mrg.inputs.in_files = ['subj1.cff','subj2.cff']
>>> mrg.run()
Mandatory Inputs:

in_files (a list of items which are a pathlike object or string representing an existing file) – List of CFF files to extract networks from.

Optional Inputs:

out_file (a pathlike object or string representing a file) – Output CFF file with all the networks added. (Nipype default value: merged_network_connectome.cff)

Outputs:

connectome_file (a pathlike object or string representing an existing file) – Output CFF file with all the networks added.