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NA-MIC Project Weeks

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Key Investigators

Project Description

A new extension, SlicerPipelines, is currently being developed and allows for GUI create-able modules (pipelines) in 3DSlicer. The term “pipeline” in this context is a module whose logic has a specific interface (or is wrapped to meet the interface), which allows for one MRML node input to one MRML node output algorithms.

In general, the SlicerPipelines extension is meant to help improve efficiency when dealing with simple workflows. Two main modules currently exist, a PipelineCreator module that allows for the creation of pipelines, and a PipelineCaseIterator module that allows for automated running of a pipeline over all files in a directory.

Pipeline Creator

Pipeline Creator Select Module

Pipeline Case Iterator


  1. Increase usefulness and useability of the extension
  2. Allow easier creation of new pipelines from existing modules

Approach and Plan

  1. Wrap more existing modules as pipelines to increase usefulness of the extension
    • Pipelines to convert between MRML types (segmentation to model, scalar volume to label map volume, etc). Some of these already exist, but finish them out for the core MRML types.
  2. Update existing wrapper generator for CLI modules to be able to be used for more CLIs. Currently implementation is limited in types it supports.
  3. Add ability to load newly created pipeline module when it is created, and add it to the additional module paths


  1. Added new pipelines
    1. Export Segmentation to Model
    2. Export LabelMap to Scalar Volume
    3. Export Scalar Volume to LabelMap
    4. Export LabelMap to Segmentation
  2. Added ability to load new created pipeline module on creation and add it to the additional module paths (similar to ExtensionWizard)
  3. Update select module pop up to default the next input type to the last output type

Next Steps

  1. Pipeline for Surface Wrap Solidify segment editor effect
  2. Add to extension manager

Background and References