added missing doc file

Author: chrisgorgo

doc/users/nipypecmd.rst

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+.. _nipypecmd:
+
+============================================================
+Running Nipype Interfaces from the command line (nipype_cmd)
+============================================================
+
+The primary use of Nipype_ is to build automated non-interactive pipelines.
+However, sometimes there is a need to run some interfaces quickly from the command line.
+This is especially useful when running Interfaces wrapping code that does not have 
+command line equivalents (nipy or SPM). Being able to run Nipype interfaces opens new
+possibilities such as inclusion of SPM processing steps in bash scripts.
+
+To run Nipype Interafces you need to use the nipype_cmd tool that should already be installed.
+The tool allows you to list Interfaces available in a certain package:
+
+.. testcode::
+	
+	
+	$nipype_cmd nipype.interfaces.nipy
+
+	Available Interfaces:
+	    SpaceTimeRealigner
+	    Similarity
+	    ComputeMask
+	    FitGLM
+	    EstimateContrast
+	    FmriRealign4d
+		
+After selecting a particular Interface you can learn what inputs it requires:
+
+.. testcode::
+	
+	
+	$nipype_cmd nipype.interfaces.nipy ComputeMask --help
+	
+	usage:nipype_cmd nipype.interfaces.nipy ComputeMask [-h] [--M M] [--cc CC]
+	                                                     [--ignore_exception IGNORE_EXCEPTION]
+	                                                     [--m M]
+	                                                     [--reference_volume REFERENCE_VOLUME]
+	                                                     mean_volume
+
+	Run ComputeMask
+
+	positional arguments:
+	  mean_volume           mean EPI image, used to compute the threshold for the
+	                        mask
+
+	optional arguments:
+	  -h, --help            show this help message and exit
+	  --M M                 upper fraction of the histogram to be discarded
+	  --cc CC               Keep only the largest connected component
+	  --ignore_exception IGNORE_EXCEPTION
+	                        Print an error message instead of throwing an
+	                        exception in case the interface fails to run
+	  --m M                 lower fraction of the histogram to be discarded
+	  --reference_volume REFERENCE_VOLUME
+	                        reference volume used to compute the mask. If none is
+	                        give, the mean volume is used.
+							
+Finally you can run run the Interface:
+
+.. testcode::
+	
+	$nipype_cmd nipype.interfaces.nipy ComputeMask mean.nii.gz
+
+All that from the command line without having to start python interpreter manually.
+
+.. include:: ../links_names.txt