nipype.interfaces.cmtk.convert module¶
CFFConverter¶
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¶
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.