MRIsSmooth is now SmoothTessellation. Tessellation example added

Author: Erik Ziegler

examples/tessellation_tutorial.py

@@ -0,0 +1,86 @@
+#!/usr/bin/env python
+"""
+=============================================
+sMRI: Regional Tessellation and Surface Smoothing
+=============================================
+
+Introduction
+============
+
+This script, tessellation_tutorial.py, demonstrates the use of create_tessellation_flow from nipype.workflows.smri.freesurfer, and it can be run with:
+
+ python tessellation_tutorial.py
+
+This example requires that the user has Freesurfer installed, and that the Freesurfer directory for 'fsaverage' is present.
+
+.. seealso::
+
+ConnectomeViewer
+The Connectome Viewer connects Multi-Modal Multi-Scale Neuroimaging and Network Datasets For Analysis and Visualization in Python.
+
+http://www.geuz.org/gmsh/
+Gmsh: a three-dimensional finite element mesh generator with built-in pre- and post-processing facilities
+
+http://www.blender.org/
+Blender is the free open source 3D content creation suite, available for all major operating systems under the GNU General Public License.
+
+.. warning::
+
+This workflow will take several hours to finish entirely, since smoothing
+ the larger cortical surfaces is very time consuming.
+
+Packages and Data Setup
+=======================
+
+Import the necessary modules and workflow from nipype.
+"""
+import nipype.pipeline.engine as pe # pypeline engine
+import nipype.interfaces.io as nio # Data i/o
+import os, os.path as op
+from nipype.workflows.smri.freesurfer import create_tessellation_flow
+
+"""
+Directories
+===========
+
+Set the default directory and lookup table (LUT) paths
+"""
+
+fs_dir = os.environ['FREESURFER_HOME']
+lookup_file = op.join(fs_dir,'FreeSurferColorLUT.txt')
+subjects_dir = op.join(fs_dir, 'subjects/')
+output_dir = './tessellate_tutorial'
+
+"""
+Inputs
+======
+
+Create the tessellation workflow and set inputs
+"""
+
+tessflow = create_tessellation_flow(name='tessflow')
+tessflow.inputs.inputspec.subject_id = 'fsaverage'
+tessflow.inputs.inputspec.subjects_dir = subjects_dir
+tessflow.inputs.inputspec.lookup_file = lookup_file
+
+"""
+Outputs
+=======
+
+Create a datasink to organize the smoothed meshes
+"""
+
+datasink = pe.Node(interface=nio.DataSink(), name="datasink")
+datasink.inputs.base_directory = 'meshes'
+
+"""
+Execution
+=========
+
+Finally, create and run another pipeline that connects the workflow and datasink
+"""
+
+tesspipe = pe.Workflow(name='tessellate_tutorial')
+tesspipe.base_dir = output_dir
+tesspipe.connect([(tessflow, datasink,[('outputspec.meshes', '@meshes.all')])])
+tesspipe.run()

nipype/interfaces/freesurfer/__init__.py

@@ -11,4 +11,4 @@
  SegStats, Label2Vol)
 from .utils import (SampleToSurface, SurfaceSmooth, SurfaceTransform,
  SurfaceSnapshots,ApplyMask, MRIsConvert, MRITessellate,
- MRIMarchingCubes, MRIsSmooth)
+ MRIMarchingCubes, SmoothTessellation)

nipype/interfaces/freesurfer/utils.py

@@ -894,7 +894,7 @@ def _gen_outfilename(self):
  _, name, ext = split_filename(self.inputs.in_file)
  return name + ext + '_' + str(self.inputs.label_value)
 
-class MRIsSmoothInputSpec(FSTraitedSpec):
+class SmoothTessellationInputSpec(FSTraitedSpec):
  """
  This program smooths the tessellation of a surface using 'mris_smooth'
  """
@@ -917,14 +917,14 @@ class MRIsSmoothInputSpec(FSTraitedSpec):
  out_curvature_file = File(argstr='-c ./%s', desc='Write curvature to ?h.curvname (default "curv")')
  out_area_file = File(argstr='-b ./%s', desc='Write area to ?h.areaname (default "area")')
 
-class MRIsSmoothOutputSpec(TraitedSpec):
+class SmoothTessellationOutputSpec(TraitedSpec):
  """
  This program smooths the tessellation of a surface using 'mris_smooth'
  """
  surface = File(exists=True, desc='Smoothed surface file ')
 
 
-class MRIsSmooth(FSCommand):
+class SmoothTessellation(FSCommand):
  """
  This program smooths the tessellation of a surface using 'mris_smooth'
 
@@ -936,13 +936,13 @@ class MRIsSmooth(FSCommand):
  Example:
 
  import nipype.interfaces.freesurfer as fs
- smooth = fs.MRIsSmooth()
+ smooth = fs.SmoothTessellation()
  smooth.inputs.in_file = 'lh.hippocampus.stl'
  smooth.run() # doctest: +SKIP
  """
  _cmd = 'mris_smooth'
- input_spec = MRIsSmoothInputSpec
- output_spec = MRIsSmoothOutputSpec
+ input_spec = SmoothTessellationInputSpec
+ output_spec = SmoothTessellationOutputSpec
 
  def _list_outputs(self):
  outputs = self.output_spec().get()

nipype/workflows/smri/freesurfer/utils.py

@@ -313,7 +313,7 @@ def create_tessellation_flow(name='tessellate', out_format='stl'):
  surfconvert = pe.MapNode(fs.MRIsConvert(out_datatype=out_format),
  iterfield=['in_file'],
  name='surfconvert')
- smoother = pe.MapNode(fs.MRIsSmooth(),
+ smoother = pe.MapNode(fs.SmoothTessellation(),
  iterfield=['in_file'],
  name='smoother')