Difference between revisions of "Slicer3:Module:Fuzzy Surface Creation-Documentation"

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* '''Surface-, Middle-, Median value'''
+
* '''''Surface-, Middle-, Median value'''''
 
:These parameters are calculated and used to compute the height of the added surface. They define the consideration of the calculated value and there aggregation to the final additional height.The parameters serve as divisors, so the lower they are set the more they are considered. The surface parameter defines the distance of a surface point to the border of the image, the middle value the distance from the point to the center of the z-axis and the median value the distance between the point and the median of all surface values of the current slice. Furthermore every value can be en- or disabled by the respective check box.
 
:These parameters are calculated and used to compute the height of the added surface. They define the consideration of the calculated value and there aggregation to the final additional height.The parameters serve as divisors, so the lower they are set the more they are considered. The surface parameter defines the distance of a surface point to the border of the image, the middle value the distance from the point to the center of the z-axis and the median value the distance between the point and the median of all surface values of the current slice. Furthermore every value can be en- or disabled by the respective check box.
  
 
+
* '''''Enable overflow cut'''''
* '''Enable overflow cut'''
 
 
:By checking the overflow cut box every value above the created additional surface is set to zero. This improves the fuzzy effect because especially values which are not detected by the Otsu Threhold Preprocessing like especially skin which wouldn't be influenced otherwise can be removed. But this also means that all information above the created surface will be lost.
 
:By checking the overflow cut box every value above the created additional surface is set to zero. This improves the fuzzy effect because especially values which are not detected by the Otsu Threhold Preprocessing like especially skin which wouldn't be influenced otherwise can be removed. But this also means that all information above the created surface will be lost.
  
 
* '''''Infiltration Depth'''''
 
* '''''Infiltration Depth'''''
 +
:The infiltration depth defines the number of voxels the algorithm goes into the detected surface structure to overlap original voxels with the new created ones. The deeper the algorithm goes into the object the more information will be lost.
 +
 +
* '''''Infilling random range'''''
 +
:For the intensity of the added voxels an average value of the underneath voxels (5 by default) from the surface value is determined. For adding the new surface this value including a random created value is used for intensity estimation. The random range parameter defines the range for the random created value.
 +
 
===Examples, Use Cases & Tutorials===
 
===Examples, Use Cases & Tutorials===
  

Revision as of 14:25, 4 September 2008

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Fuzzy Surface Creation

The panel for this module
Before
After

General Information

Data sharing became a big issue in the last few years. Unfortunately for research data sharing is a difficult undertaking because of patient privacy protection. This constricts the exchange of patient secific data between different research groups and faculties.

MRI and CT data itself wouldn't be that delicate since the identification of a patient isn't obvious. But the rendering of the data into a 3D view reveals a lot of information about the skin and skull structure of a patient and therefore makes a patient easily identifiable.

The aim of this module is therefore to hide as much surface information of the patient as possible but also to keep internal structures untouched.

Module Type & Category

Type: CLI

Category: Privacy Protection

Authors, Collaborators & Contact

  • Author: Bernhard Pflug, University for medical informatics and technology, Tyrol, Austria
  • Contact: Bernhard Pflug, bernhard.pflug@gmail.com

Module Description

The purpose of this module is to hide as much surface details of a patient as possible. Therefore it adds an additional surface to the front of the object in the image depending on different calulated parameters.

As a first step the module detects the object in the image. Subsequent it adds additional data on the detected surface depending on several calculated parameters. As a result it creates an additional surface on the object which hides skin and skull details so that patient identification isn't obvious any more.

Usage

This module is a CLI Module for Slicer. It is mainly seperated into two parts:

  • Preprocessing
  • Fuzzy Surface Creation

Preprocessing

The first step is meant to be the pre-processing step. The Otsu - Threshold - Filter is used as it provides quite good segmentation results on the object in the image and is considerably robust against noise, especially if it is not connected to the object.

The pre-processing task defines the following parameters:

  • bright objects
  • number of histogram bins
  • face connected
  • minimum object size

For further information about these parameters check the Otsu - Threhold - Filter in Slicer3.

Fuzzy Surface Creation

The second step is the actual creation of the fuzzy surface. Important to mention is that this algorithm works local, so it creates the additional surface for each voxel without considering the environment!

It defines the following parameters:

  • Surface value
    • Enable surface value
    • Surface value divisor
  • Middle value
    • Enable middle value
    • Middle value divisor
  • Median value
    • Enable median value
    • Median value divisor
  • Enable overflow cut
  • Infiltration depth
  • Infilling random range


  • Surface-, Middle-, Median value
These parameters are calculated and used to compute the height of the added surface. They define the consideration of the calculated value and there aggregation to the final additional height.The parameters serve as divisors, so the lower they are set the more they are considered. The surface parameter defines the distance of a surface point to the border of the image, the middle value the distance from the point to the center of the z-axis and the median value the distance between the point and the median of all surface values of the current slice. Furthermore every value can be en- or disabled by the respective check box.
  • Enable overflow cut
By checking the overflow cut box every value above the created additional surface is set to zero. This improves the fuzzy effect because especially values which are not detected by the Otsu Threhold Preprocessing like especially skin which wouldn't be influenced otherwise can be removed. But this also means that all information above the created surface will be lost.
  • Infiltration Depth
The infiltration depth defines the number of voxels the algorithm goes into the detected surface structure to overlap original voxels with the new created ones. The deeper the algorithm goes into the object the more information will be lost.
  • Infilling random range
For the intensity of the added voxels an average value of the underneath voxels (5 by default) from the surface value is determined. For adding the new surface this value including a random created value is used for intensity estimation. The random range parameter defines the range for the random created value.

Examples, Use Cases & Tutorials

Best results without median

  • Note use cases for which this module is especially appropriate, and/or link to examples.
  • Link to examples of the module's use
  • Link to any existing tutorials

Quick Tour of Features and Use

List all the panels in your interface, their features, what they mean, and how to use them. For instance:

  • Input panel:
  • Parameters panel:
  • Output panel:
  • Viewing panel:

Development

This module can be splitted in two generic parts:

  • Image preprocessing
  • Fuzzy surface creation

Dependencies

Other modules or packages that are required for this module's use.

Known bugs

Follow this link to the Slicer3 bug tracker.


Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

Source code & documentation

Customize following links for your module.

Links to documentation generated by doxygen.


More Information

Acknowledgment

Include funding and other support here.

References

Publications related to this module go here. Links to pdfs would be useful.