workflows.dmri.connectivity.nx

create_cmats_to_csv_pipeline()

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Creates a workflow to convert the outputs from CreateMatrix into a single comma-separated value text file. An extra column / field is also added to the text file. Typically, the user would connect the subject name to this field.

Example

>>> from nipype.workflows.dmri.connectivity.nx import create_cmats_to_csv_pipeline
>>> csv = create_cmats_to_csv_pipeline("cmats_to_csv", "subject_id")
>>> csv.inputs.inputnode.extra_field = 'subj1'
>>> csv.inputs.inputnode.matlab_matrix_files = ['subj1_cmatrix.mat', 'subj1_mean_fiber_length.mat', 'subj1_median_fiber_length.mat', 'subj1_fiber_length_std.mat']
>>> csv.run()

Inputs:

inputnode.extra_field
inputnode.matlab_matrix_files

Outputs:

outputnode.csv_file

Graph

digraph cmats_to_csv{ label="cmats_to_csv"; cmats_to_csv_inputnode[label="inputnode (utility)"]; cmats_to_csv_Matlab2CSV[label="Matlab2CSV (misc)"]; cmats_to_csv_MergeCSVFiles[label="MergeCSVFiles (misc)"]; cmats_to_csv_outputnode[label="outputnode (utility)"]; cmats_to_csv_inputnode -> cmats_to_csv_Matlab2CSV; cmats_to_csv_inputnode -> cmats_to_csv_MergeCSVFiles; cmats_to_csv_Matlab2CSV -> cmats_to_csv_MergeCSVFiles; cmats_to_csv_MergeCSVFiles -> cmats_to_csv_outputnode; }

create_networkx_pipeline()

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Creates a workflow to calculate various graph measures (via NetworkX) on an input network. The output measures are then converted to comma-separated value text files, and an extra column / field is also added. Typically, the user would connect the subject name to this field.

Example

>>> from nipype.workflows.dmri.connectivity.nx import create_networkx_pipeline
>>> nx = create_networkx_pipeline("networkx", "subject_id")
>>> nx.inputs.inputnode.extra_field = 'subj1'
>>> nx.inputs.inputnode.network_file = 'subj1.pck'
>>> nx.run()

Inputs:

inputnode.extra_field
inputnode.network_file

Outputs:

outputnode.network_files
outputnode.csv_files
outputnode.matlab_files

Graph

digraph networkx{ label="networkx"; networkx_inputnode[label="inputnode (utility)"]; networkx_NetworkXMetrics[label="NetworkXMetrics (cmtk)"]; networkx_mergeNetworks[label="mergeNetworks (utility)"]; networkx_Matlab2CSV_node[label="Matlab2CSV_node (misc)"]; networkx_Matlab2CSV_global[label="Matlab2CSV_global (misc)"]; networkx_MergeCSVFiles_global[label="MergeCSVFiles_global (misc)"]; networkx_MergeCSVFiles_node[label="MergeCSVFiles_node (misc)"]; networkx_mergeCSVs[label="mergeCSVs (utility)"]; networkx_outputnode[label="outputnode (utility)"]; networkx_inputnode -> networkx_mergeNetworks; networkx_inputnode -> networkx_MergeCSVFiles_global; networkx_inputnode -> networkx_MergeCSVFiles_global; networkx_inputnode -> networkx_NetworkXMetrics; networkx_inputnode -> networkx_MergeCSVFiles_node; networkx_inputnode -> networkx_MergeCSVFiles_node; networkx_inputnode -> networkx_MergeCSVFiles_node; networkx_NetworkXMetrics -> networkx_mergeNetworks; networkx_NetworkXMetrics -> networkx_Matlab2CSV_node; networkx_NetworkXMetrics -> networkx_outputnode; networkx_NetworkXMetrics -> networkx_Matlab2CSV_global; networkx_mergeNetworks -> networkx_outputnode; networkx_Matlab2CSV_node -> networkx_MergeCSVFiles_node; networkx_Matlab2CSV_global -> networkx_MergeCSVFiles_global; networkx_Matlab2CSV_global -> networkx_MergeCSVFiles_global; networkx_MergeCSVFiles_global -> networkx_outputnode; networkx_MergeCSVFiles_global -> networkx_mergeCSVs; networkx_MergeCSVFiles_node -> networkx_outputnode; networkx_MergeCSVFiles_node -> networkx_mergeCSVs; networkx_mergeCSVs -> networkx_outputnode; }

add_global_to_filename()

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add_nodal_to_filename()

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