DOC/STY: Cleanups

Author: effigies

package/niflow/nipype1/examples/dmri_connectivity.py

@@ -26,9 +26,8 @@
 
     * http://db.tt/1vx4vLeP
 
-Along with `Camino <http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Main.HomePage>`_,
-`Camino-Trackvis <http://www.nitrc.org/projects/camino-trackvis/>`_, `FSL <http://www.fmrib.ox.ac.uk/fsl/>`_,
-and `Freesurfer <http://surfer.nmr.mgh.harvard.edu/>`_, you must also have the Connectome File Format
+Along with Camino_, Camino2Trackvis_, FSL_, and FreeSurfer_,
+you must also have the Connectome File Format
 library installed as well as the Connectome Mapper.
 
 These are written by Stephan Gerhard and can be obtained from:

package/niflow/nipype1/examples/dmri_preprocessing.py

@@ -130,6 +130,7 @@
 """
 
 bias = remove_bias()
+
 """
 Connect nodes in workflow
 =========================
@@ -148,10 +149,23 @@
             (prep, bias, [('outputnode.out_file', 'inputnode.in_file'),
                           ('outputnode.out_mask', 'inputnode.in_mask')]),
             (datasource, bias, [('bvals', 'inputnode.in_bval')])])
+
 """
 Run the workflow as command line executable
 """
 
 if __name__ == '__main__':
     wf.run()
     wf.write_graph()
+
+"""
+References
+----------
+
+.. [Jeurissen2014] Jeurissen et al., Multi-tissue constrained spherical deconvolution
+                   for improved analysis of multi-shell diffusion MRI data.
+                   NeuroImage 103:411--426. 2014.
+                   doi:`10.1016/j.neuroimage.2014.07.061
+                   <https://doi.org/10.1016/j.neuroimage.2014.07.061>`__.
+
+"""