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