Whole-Brain-Tractography-Wizard

The Idea of a Wizard

Make a simple set of steps that will guide the user through a complex process. An example of this is the simple wizard that takes the user from a DICOM or NRRD Diffusion Weighted Image to a Full brain tractography. There are 4 steps to this process:

• 

  [DICOM to DWI]

• 

  [DWI to DTI]

• 

  [DTI to Fibers]

• 

  [Fibers]

In order to generate this wizard, we will use the For each step, we must:

• Obtain the input from the interface
• Validate the input
• Set up the parameters for the next step

Obtaining the input from the Interface

You can find the example at

 Modules/Scripted/Scripts/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/full_tractography_workflow.py

Declaring the Modules

   step_widget_files = [
       'dicom2nrrd',
       'dwi2dti',
       'dti2fibers',
       'done',
   ]

Declaring Each Module's Fields

   step_widget_fields = {
       'dicom2nrrd':[
           ('DICOMRadioButton', 'checked'),
           ('NRRDDWIRadioButton', 'checked'),
           ('inputDicomDirectory', 'directory'),
           ('outputVolume', 'currentPath'),
           ('useBMatrixGradientDirections','checked'),
           ('inputNRRDVolume','currentPath'),
       ],
       'dwi2dti':[
           ('leastSquaresEstimation', 'checked'),
           ('weightedLeastSquaresEstimation', 'checked'),
           ('thresholdParameter', 'value'),
           ('removeIslands', 'checked'),
           ('applyMask', 'checked'),
       ],
       'dti2fibers':[
           ('seedSpacing','value'),
           ('stoppingFAValue','value'),
           ('minimumFAValueSeed','value'),
           ('stoppingTrackCurvature','value'),
       ],
       'done':[],
   }

Validating Data for a Field

 def validate_dicom2nrrd(self, step_object, data):
       if data[step_object.id()]['DICOMRadioButton']:

Running a CLI module from a python script

           self.dicomtonrrdconverter_parameter_node = slicer.cli.run(
               slicer.modules.dicomtonrrdconverter, self.dicomtonrrdconverter_parameter_node,
               data[step_object.id()],
               wait_for_completion = True)

Validating the result of a CLI module

          if self.dicomtonrrdconverter_parameter_node.GetStatusString() == 'Completed':
               file_path = data[step_object.id()]['outputVolume']
               result_status, node = slicer.util.loadVolume(
                   file_path,
                   True
               )
           else:
               result_status = False

Setting data for the next module

           if result_status:
               self.dwi_node = node
               self.dwi_node_name = node.GetID()

Output errors if needed

       if not result_status:
           display_error("Error in DICOM to NRRD conversion, please see log")
       return result_status