nipype.interfaces.cmtk.nbs module¶
NetworkBasedStatistic¶
Bases: LibraryBaseInterface
Calculates and outputs the average network given a set of input NetworkX gpickle files
See also
For
https
//github.com/LTS5/connectomeviewer/blob/master/cviewer/libs/pyconto/groupstatistics/nbs/_nbs.py
Example
>>> import nipype.interfaces.cmtk as cmtk >>> nbs = cmtk.NetworkBasedStatistic() >>> nbs.inputs.in_group1 = ['subj1.pck', 'subj2.pck'] >>> nbs.inputs.in_group2 = ['pat1.pck', 'pat2.pck'] >>> nbs.run()
- Mandatory Inputs:
in_group1 (a list of items which are a pathlike object or string representing an existing file) – Networks for the first group of subjects.
in_group2 (a list of items which are a pathlike object or string representing an existing file) – Networks for the second group of subjects.
- Optional Inputs:
edge_key (a string) – Usually “number_of_fibers, “fiber_length_mean”, “fiber_length_std” for matrices made with CMTKSometimes “weight” or “value” for functional networks. (Nipype default value:
number_of_fibers
)node_position_network (a pathlike object or string representing a file) – An optional network used to position the nodes for the output networks.
number_of_permutations (an integer) – Number of permutations to perform. (Nipype default value:
1000
)out_nbs_network (a pathlike object or string representing a file) – Output network with edges identified by the NBS.
out_nbs_pval_network (a pathlike object or string representing a file) – Output network with p-values to weight the edges identified by the NBS.
t_tail (‘left’ or ‘right’ or ‘both’) – Can be one of “left”, “right”, or “both”. (Nipype default value:
left
)threshold (a float) – T-statistic threshold. (Nipype default value:
3
)- Outputs:
nbs_network (a pathlike object or string representing an existing file) – Output network with edges identified by the NBS.
nbs_pval_network (a pathlike object or string representing an existing file) – Output network with p-values to weight the edges identified by the NBS.
network_files (a list of items which are a pathlike object or string representing an existing file) – Output network with edges identified by the NBS.
- nipype.interfaces.cmtk.nbs.ntwks_to_matrices(in_files, edge_key)¶