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# interfaces.cmtk.convert

## CFFConverter

Link to code

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()

Inputs:

    [Mandatory]

    [Optional]
    creator: (a string)
            Creator
    data_files: (an existing file name)
            list of external data files (i.e. Numpy, HD5, XML)
    description: (a string, nipype default value: Created with the Nipype CFF converter)
            Description
    email: (a string)
            Email address
    gifti_labels: (an existing file name)
            list of GIFTI labels
    gifti_surfaces: (an existing file name)
            list of GIFTI surfaces
    gpickled_networks: (an existing file name)
            list of gpickled Networkx graphs
    graphml_networks: (an existing file name)
            list of graphML networks
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the interface fails to
            run
    license: (a string)
            License
    nifti_volumes: (an existing file name)
            list of NIFTI volumes
    out_file: (a file name, nipype default value: connectome.cff)
            Output connectome file
    publisher: (a string)
            Publisher
    references: (a string)
            References
    relation: (a string)
            Relation
    rights: (a string)
            Rights
    script_files: (an existing file name)
            list of script files to include
    species: (a string, nipype default value: Homo sapiens)
            Species
    timeseries_files: (an existing file name)
            list of HDF5 timeseries files
    title: (a string)
            Connectome Title
    tract_files: (an existing file name)
            list of Trackvis fiber files

Outputs:

    connectome_file: (an existing file name)
            Output connectome file

## MergeCNetworks

Link to code

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()

Inputs:

    [Mandatory]
    in_files: (a file name)
            List of CFF files to extract networks from

    [Optional]
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the interface fails to
            run
    out_file: (a file name, nipype default value: merged_network_connectome.cff)
            Output CFF file with all the networks added

Outputs:

    connectome_file: (an existing file name)
            Output CFF file with all the networks added