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()                 # doctest: +SKIP

creator : a unicode 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 unicode string

Description. (Nipype default value: Created with the Nipype CFF converter)

email : a unicode 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 unicode 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 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 a pathlike object or string representing an existing file

List of script files to include.

species : a unicode 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 unicode 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.

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()                  # doctest: +SKIP

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.

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)

connectome_file : a pathlike object or string representing an existing file

Output CFF file with all the networks added.