.. AUTO-GENERATED FILE -- DO NOT EDIT!

.. _example_dmri_group_connectivity_mrtrix:


==================================================
dMRI: Group connectivity - MRtrix, FSL, FreeSurfer
==================================================

Introduction
============

This script, dmri_group_connectivity_mrtrix.py, runs group-based connectivity analysis using
the dmri.mrtrix.connectivity_mapping Nipype workflow. Further detail on the processing can be
found in :ref:`dmri_connectivity_advanced. This tutorial can be run using:

    python dmri_group_connectivity_mrtrix.py

We perform this analysis using one healthy subject and two subjects who suffer from Parkinson's disease.

The whole package (960 mb as .tar.gz / 1.3 gb uncompressed) including the Freesurfer directories for these subjects, can be acquired from here:

    * http://db.tt/b6F1t0QV

A data package containing the outputs of this pipeline can be obtained from here:

    * http://db.tt/elmMnIt1

Along with MRtrix, FSL, and Freesurfer, you must also have the Connectome File Format
library installed as well as the Connectome Mapper (cmp).

    * MRtrix: http://www.brain.org.au/software/mrtrix/
    * FSL: http://www.fmrib.ox.ac.uk/fsl/
    * Freesurfer: http://surfer.nmr.mgh.harvard.edu/
    * CTMK: http://www.cmtk.org/
    * CFF: sudo apt-get install python-cfflib

Or on github at:

    * CFFlib: https://github.com/LTS5/cfflib
    * CMP: https://github.com/LTS5/cmp

Output data can be visualized in ConnectomeViewer, TrackVis, Gephi,
the MRtrix Viewer (mrview), and anything that can view Nifti files.

    * ConnectomeViewer: https://github.com/LTS5/connectomeviewer
    * TrackVis: http://trackvis.org/
    * Gephi: http://gephi.org/

The fiber data is available in Numpy arrays, and the connectivity matrix
is also produced as a MATLAB matrix.



Import the workflows
--------------------
First, we import the necessary modules from nipype.

::
  
  import nipype.interfaces.fsl as fsl
  import nipype.interfaces.freesurfer as fs    # freesurfer
  import  os.path as op                     # system functions
  import cmp
  from nipype.workflows.dmri.mrtrix.group_connectivity import create_group_connectivity_pipeline
  from nipype.workflows.dmri.connectivity.group_connectivity import (create_merge_network_results_by_group_workflow, create_merge_group_network_results_workflow, create_average_networks_by_group_workflow)
  

Set the proper directories
--------------------------
First, we import the necessary modules from nipype.

::
  
  subjects_dir = op.abspath('groupcondatapackage/subjects/')
  data_dir = op.abspath('groupcondatapackage/data/')
  fs.FSCommand.set_default_subjects_dir(subjects_dir)
  fsl.FSLCommand.set_default_output_type('NIFTI')
  

Define the groups
-----------------
Here we define the groups for this study. We would like to search for differences between the healthy subject and the two
vegetative patients. The group list is defined as a Python dictionary (see http://docs.python.org/tutorial/datastructures.html),
with group IDs ('controls', 'parkinsons') as keys, and subject/patient names as values. We set the main output directory as 'groupcon'.

::
  
  group_list = {}
  group_list['controls'] = ['cont17']
  group_list['parkinsons'] = ['pat10', 'pat20']
  

The output directory must be named as well.

::
  
  global output_dir
  output_dir = op.abspath('dmri_group_connectivity_mrtrix')
  

Main processing loop
====================
The title for the final grouped-network connectome file is dependent on the group names. The resulting file for this example
is 'parkinsons-controls.cff'. The following code implements the format a-b-c-...x.cff for an arbitary number of groups.

.. warning::

    The 'info' dictionary below is used to define the input files. In this case, the diffusion weighted image contains the string 'dti'.
    The same applies to the b-values and b-vector files, and this must be changed to fit your naming scheme.

The workflow is created given the information input about the groups and subjects.

.. seealso::

    * nipype/workflows/dmri/mrtrix/group_connectivity.py
    * nipype/workflows/dmri/mrtrix/connectivity_mapping.py
    * :ref:`dmri_connectivity_advanced`

We set values for absolute threshold used on the fractional anisotropy map. This is done
in order to identify single-fiber voxels. In brains with more damage, however, it may be necessary
to reduce the threshold, since their brains are have lower average fractional anisotropy values.

We invert the b-vectors in the encoding file, and set the maximum harmonic order
of the pre-tractography spherical deconvolution step. This is done to show
how to set inputs that will affect both groups.

Next we create and run the second-level pipeline. The purpose of this workflow is simple:
It is used to merge each subject's CFF file into one, so that there is a single file containing
all of the networks for each group. This can be useful for performing Network Brain Statistics
using the NBS plugin in ConnectomeViewer.

.. seealso::

    http://www.connectomeviewer.org/documentation/users/tutorials/tut_nbs.html


::
  
  title = ''
  for idx, group_id in enumerate(group_list.keys()):
      title += group_id
      if not idx == len(group_list.keys()) - 1:
          title += '-'
  
      info = dict(dwi=[['subject_id', 'dti']],
                  bvecs=[['subject_id', 'bvecs']],
                  bvals=[['subject_id', 'bvals']])
  
      l1pipeline = create_group_connectivity_pipeline(group_list, group_id, data_dir, subjects_dir, output_dir, info)
  
      # This is used to demonstrate the ease through which different parameters can be set for each group.
      if group_id == 'parkinsons':
          l1pipeline.inputs.connectivity.mapping.threshold_FA.absolute_threshold_value = 0.5
      else:
          l1pipeline.inputs.connectivity.mapping.threshold_FA.absolute_threshold_value = 0.7
  
      # Here with invert the b-vectors in the Y direction and set the maximum harmonic order of the
      # spherical deconvolution step
      l1pipeline.inputs.connectivity.mapping.fsl2mrtrix.invert_y = True
      l1pipeline.inputs.connectivity.mapping.csdeconv.maximum_harmonic_order = 6
  
      # Here we define the parcellation scheme and the number of tracks to produce
      parcellation_name = 'scale500'
      l1pipeline.inputs.connectivity.mapping.Parcellate.parcellation_name = parcellation_name
      cmp_config = cmp.configuration.PipelineConfiguration()
      cmp_config.parcellation_scheme = "Lausanne2008"
      l1pipeline.inputs.connectivity.mapping.inputnode_within.resolution_network_file = cmp_config._get_lausanne_parcellation('Lausanne2008')[parcellation_name]['node_information_graphml']
      l1pipeline.inputs.connectivity.mapping.probCSDstreamtrack.desired_number_of_tracks = 100000
  
      l1pipeline.run()
      l1pipeline.write_graph(format='eps', graph2use='flat')
  
      # The second-level pipeline is created here
      l2pipeline = create_merge_network_results_by_group_workflow(group_list, group_id, data_dir, subjects_dir, output_dir)
      l2pipeline.inputs.l2inputnode.network_file = cmp_config._get_lausanne_parcellation('Lausanne2008')[parcellation_name]['node_information_graphml']
      l2pipeline.run()
      l2pipeline.write_graph(format='eps', graph2use='flat')
  

Now that the for loop is complete there are two grouped CFF files each containing the appropriate subjects.
It is also convenient to have every subject in a single CFF file, so that is what the third-level pipeline does.

::
  
  l3pipeline = create_merge_group_network_results_workflow(group_list, data_dir, subjects_dir, output_dir, title)
  l3pipeline.run()
  l3pipeline.write_graph(format='eps', graph2use='flat')
  

The fourth and final workflow averages the networks and saves them in another CFF file

::
  
  l4pipeline = create_average_networks_by_group_workflow(group_list, data_dir, subjects_dir, output_dir, title)
  l4pipeline.run()
  l4pipeline.write_graph(format='eps', graph2use='flat')


.. include:: ../../links_names.txt


        
.. admonition:: Example source code

   You can download :download:`the full source code of this example <../../../examples/dmri_group_connectivity_mrtrix.py>`.
   This same script is also included in the Nipype source distribution under the
   :file:`examples` directory.

