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 unicode string)
        Creator
data_files: (a list of items which are an existing file name)
        list of external data files (i.e. Numpy, HD5, XML)
description: (a unicode string, nipype default value: Created with
         the Nipype CFF converter)
        Description
email: (a unicode string)
        Email address
gifti_labels: (a list of items which are an existing file name)
        list of GIFTI labels
gifti_surfaces: (a list of items which are an existing file name)
        list of GIFTI surfaces
gpickled_networks: (a list of items which are an existing file name)
        list of gpickled Networkx graphs
graphml_networks: (a list of items which are 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 unicode string)
        License
nifti_volumes: (a list of items which are an existing file name)
        list of NIFTI volumes
out_file: (a file name, nipype default value: connectome.cff)
        Output connectome file
publisher: (a unicode string)
        Publisher
references: (a unicode string)
        References
relation: (a unicode string)
        Relation
rights: (a unicode string)
        Rights
script_files: (a list of items which are an existing file name)
        list of script files to include
species: (a unicode string, nipype default value: Homo sapiens)
        Species
timeseries_files: (a list of items which are an existing file name)
        list of HDF5 timeseries files
title: (a unicode string)
        Connectome Title
tract_files: (a list of items which are 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 list of items which are an existing 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