Modules:PolyDataToLabelmap-Documentation-3.6

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Module Name

PolyData to LabelMap

GUI panel

Surface model overlaid on ref image

Label map generated from surface

General Information

Module Type & Category

Type: CLI

Category: Surface Models

Authors, Collaborators & Contact

• Author: Xiaodong Tao and Nicole Aucoin
• Contact: taox at research.ge.com

Module Description

This module creates a label map of the interior of an input model within a reference volume. The module first label voxels that intersects the surface as foreground, then use a flood fill to label all interior.

Usage

Examples, Use Cases & Tutorials

• This module may be thought of as the inverse of Marching Cubes.

• A command line example:

./PolyDataToLabelmap --distance 1.0
    InputReferenceVolume.nrrd
    InputSurfaceModel.vtp
    OutputLabelMap.nrrd
 

Quick Tour of Features and Use

• Input/Output panels:

Input/Output panels

This module takes three input: Input Volume is the reference volume. Model is the surface model from whose interior is to be labeled as foreground, and Output Volume is the output label map. Output Volume has the same image parameters (size, resolution, orientation, etc) as Input Volume.

• Parameters panel:

Parameters Parameters

Since surface can be very sparsely triangulated, this module first resamples the input surface model in an appropriate resolution. The parameter Sample Distance controls how fine the surface is sampled. The ballpark value for this parameter is the smallest size of voxels (in mm) in Input Volume.

Development

Dependencies

This module depends only on the core "Volumes" module of slice for data IO.

Known bugs

None.

Usability issues

When the object has a geometry such that the centroid of all vertices lie outside of the object, the module will fail to generate the correct label for the object.

Source code & documentation

Source Code: PolyDataToLabelmap.cxx

XML Description: PolyDataToLabelmap.xml

Test: PolyDataToLabelmapTest.cxx

Usage:

./PolyDataToLabelmap --help

USAGE: 

   ./PolyDataToLabelmap  [--returnparameterfile <std::string>]
                         [--processinformationaddress <std::string>]
                         [--xml] [--echo] [--distance <float>] [--]
                         [--version] [-h] <std::string> <std::string>
                         <std::string>


Where: 

   --returnparameterfile <std::string>
     Filename in which to write simple return parameters (int, float,
     int-vector, etc.) as opposed to bulk return parameters (image,
     geometry, transform, measurement, table).

   --processinformationaddress <std::string>
     Address of a structure to store process information (progress, abort,
     etc.). (default: 0)

   --xml
     Produce xml description of command line arguments (default: 0)

   --echo
     Echo the command line arguments (default: 0)

   --distance <float>
     Sample distance (default: 1)

   --,  --ignore_rest
     Ignores the rest of the labeled arguments following this flag.

   --version
     Displays version information and exits.

   -h,  --help
     Displays usage information and exits.

   <std::string>
     (required)  Input volume

   <std::string>
     (required)  Model

   <std::string>
     (required)  The label volume


   Description: Intersects an input model with an reference volume and
   produces an output label map.

   Author(s): Nicole Aucoin BWH, Xiaodong Tao, GE

   Acknowledgements: This work is part of the National Alliance for Medical
   Image Computing (NAMIC), funded by the National Institutes of Health
   through the NIH Roadmap for Medical Research, Grant U54 EB005149.

More Information

Acknowledgment

This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from National Centers for Biomedical Computing.

OASIS datasets were used to generate images on this page.

References

Note: this CLI module requires .vtp format input (this is the "new" VTK data format that uses XML encoding).

If you need to do a batch conversion of .vtk to .vtp, you may want to use File:Vtk2xml.zip originally by Prabhu Ramachandran <prabhu@aero.iitm.ernet.in> and enhanced for this purpose by András Jakab MD <jakaba@med.unideb.hu>

Another option, from Thomas Ballinger <tomb@bwh.harvard.edu> is available here.