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

.. _example_smoothing_comparison:


===========================
Paper: Smoothing comparison
===========================

::
  
  
  import nipype.interfaces.io as nio           # Data i/o
  import nipype.interfaces.spm as spm          # spm
  import nipype.interfaces.freesurfer as fs    # freesurfer
  import nipype.interfaces.nipy as nipy
  import nipype.interfaces.utility as util
  import nipype.pipeline.engine as pe          # pypeline engine
  import nipype.algorithms.modelgen as model   # model specification
  import nipype.workflows.fmri.fsl as fsl_wf
  from nipype.interfaces.base import Bunch
  import os                                    # system functions
  
  preprocessing = pe.Workflow(name="preprocessing")
  
  iter_fwhm = pe.Node(interface=util.IdentityInterface(fields=["fwhm"]),
                      name="iter_fwhm")
  iter_fwhm.iterables = [('fwhm', [4, 8])]
  
  iter_smoothing_method = pe.Node(interface=util.IdentityInterface(fields=["smoothing_method"]),
                      name="iter_smoothing_method")
  iter_smoothing_method.iterables = [('smoothing_method',['isotropic_voxel',
                                             'anisotropic_voxel',
                                             'isotropic_surface'])]
  
  realign = pe.Node(interface=spm.Realign(), name="realign")
  realign.inputs.register_to_mean = True
  
  isotropic_voxel_smooth = pe.Node(interface=spm.Smooth(),
                                   name="isotropic_voxel_smooth")
  preprocessing.connect(realign, "realigned_files", isotropic_voxel_smooth,
                        "in_files")
  preprocessing.connect(iter_fwhm, "fwhm", isotropic_voxel_smooth, "fwhm")
  
  compute_mask = pe.Node(interface=nipy.ComputeMask(), name="compute_mask")
  preprocessing.connect(realign, "mean_image", compute_mask, "mean_volume")
  
  anisotropic_voxel_smooth = fsl_wf.create_susan_smooth(name="anisotropic_voxel_smooth",
                                                        separate_masks=False)
  anisotropic_voxel_smooth.inputs.smooth.output_type = 'NIFTI'
  preprocessing.connect(realign, "realigned_files", anisotropic_voxel_smooth,
                        "inputnode.in_files")
  preprocessing.connect(iter_fwhm, "fwhm", anisotropic_voxel_smooth,
                        "inputnode.fwhm")
  preprocessing.connect(compute_mask, "brain_mask", anisotropic_voxel_smooth,
                        'inputnode.mask_file')
  
  
  
  recon_all = pe.Node(interface=fs.ReconAll(), name = "recon_all")
  
  surfregister = pe.Node(interface=fs.BBRegister(),name='surfregister')
  surfregister.inputs.init = 'fsl'
  surfregister.inputs.contrast_type = 't2'
  preprocessing.connect(realign, 'mean_image', surfregister, 'source_file')
  preprocessing.connect(recon_all, 'subject_id', surfregister, 'subject_id')
  preprocessing.connect(recon_all, 'subjects_dir', surfregister, 'subjects_dir')
  
  isotropic_surface_smooth = pe.MapNode(interface=fs.Smooth(proj_frac_avg=(0,1,0.1)),
                                        iterfield=['in_file'],
                                        name="isotropic_surface_smooth")
  preprocessing.connect(surfregister, 'out_reg_file', isotropic_surface_smooth,
                        'reg_file')
  preprocessing.connect(realign, "realigned_files", isotropic_surface_smooth,
                        "in_file")
  preprocessing.connect(iter_fwhm, "fwhm", isotropic_surface_smooth,
                        "surface_fwhm")
  preprocessing.connect(iter_fwhm, "fwhm", isotropic_surface_smooth, "vol_fwhm")
  preprocessing.connect(recon_all, 'subjects_dir', isotropic_surface_smooth,
                        'subjects_dir')
  
  merge_smoothed_files = pe.Node(interface=util.Merge(3),
                                 name='merge_smoothed_files')
  preprocessing.connect(isotropic_voxel_smooth, 'smoothed_files',
                        merge_smoothed_files, 'in1')
  preprocessing.connect(anisotropic_voxel_smooth, 'outputnode.smoothed_files',
                        merge_smoothed_files, 'in2')
  preprocessing.connect(isotropic_surface_smooth, 'smoothed_file',
                        merge_smoothed_files, 'in3')
  
  select_smoothed_files = pe.Node(interface=util.Select(),
                                  name="select_smoothed_files")
  preprocessing.connect(merge_smoothed_files, 'out', select_smoothed_files,
                        'inlist')
  
  def chooseindex(roi):
      return {'isotropic_voxel':range(0,4), 'anisotropic_voxel':range(4,8),
              'isotropic_surface':range(8,12)}[roi]
  
  preprocessing.connect(iter_smoothing_method, ("smoothing_method", chooseindex),
                        select_smoothed_files, 'index')
  
  rename = pe.MapNode(util.Rename(format_string="%(orig)s"), name="rename",
                      iterfield=['in_file'])
  rename.inputs.parse_string = "(?P<orig>.*)"
  
  preprocessing.connect(select_smoothed_files, 'out', rename, 'in_file')
  
  specify_model = pe.Node(interface=model.SpecifyModel(), name="specify_model")
  specify_model.inputs.input_units             = 'secs'
  specify_model.inputs.time_repetition         = 3.
  specify_model.inputs.high_pass_filter_cutoff = 120
  specify_model.inputs.subject_info = [Bunch(conditions=['Task-Odd','Task-Even'],
                                             onsets=[range(15,240,60),
                                                     range(45,240,60)],
                                             durations=[[15], [15]])]*4
  
  level1design = pe.Node(interface=spm.Level1Design(), name= "level1design")
  level1design.inputs.bases = {'hrf':{'derivs': [0,0]}}
  level1design.inputs.timing_units = 'secs'
  level1design.inputs.interscan_interval = specify_model.inputs.time_repetition
  
  level1estimate = pe.Node(interface=spm.EstimateModel(), name="level1estimate")
  level1estimate.inputs.estimation_method = {'Classical' : 1}
  
  contrastestimate = pe.Node(interface = spm.EstimateContrast(),
                             name="contrastestimate")
  contrastestimate.inputs.contrasts = [('Task>Baseline','T',
                                        ['Task-Odd','Task-Even'],[0.5,0.5])]
  
  modelling = pe.Workflow(name="modelling")
  modelling.connect(specify_model, 'session_info', level1design, 'session_info')
  modelling.connect(level1design, 'spm_mat_file', level1estimate, 'spm_mat_file')
  modelling.connect(level1estimate,'spm_mat_file', contrastestimate,
                    'spm_mat_file')
  modelling.connect(level1estimate,'beta_images', contrastestimate,'beta_images')
  modelling.connect(level1estimate,'residual_image', contrastestimate,
                    'residual_image')
  
  main_workflow = pe.Workflow(name="main_workflow")
  main_workflow.base_dir = "smoothing_comparison_workflow"
  main_workflow.connect(preprocessing, "realign.realignment_parameters",
                        modelling, "specify_model.realignment_parameters")
  main_workflow.connect(preprocessing, "select_smoothed_files.out",
                        modelling, "specify_model.functional_runs")
  main_workflow.connect(preprocessing, "compute_mask.brain_mask",
                        modelling, "level1design.mask_image")
  
  datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'],
                                                 outfields=['func', 'struct']),
                       name = 'datasource')
  datasource.inputs.base_directory = os.path.abspath('data')
  datasource.inputs.template = '%s/%s.nii'
  datasource.inputs.template_args = info = dict(func=[['subject_id',
                                                       ['f3','f5','f7','f10']]],
                                                struct=[['subject_id','struct']])
  datasource.inputs.subject_id = 's1'
  datasource.inputs.sort_filelist = True
  
  main_workflow.connect(datasource, 'func', preprocessing, 'realign.in_files')
  main_workflow.connect(datasource, 'struct', preprocessing,
                        'recon_all.T1_files')
  
  datasink = pe.Node(interface=nio.DataSink(), name="datasink")
  datasink.inputs.base_directory = os.path.abspath('smoothing_comparison_workflow/output')
  datasink.inputs.regexp_substitutions = [("_rename[0-9]", "")]
  
  main_workflow.connect(modelling, 'contrastestimate.spmT_images', datasink,
                        'contrasts')
  main_workflow.connect(preprocessing, 'rename.out_file', datasink,
                        'smoothed_epi')
  
  main_workflow.run()
  main_workflow.write_graph()


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


        
.. admonition:: Example source code

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

