Insight Journal - A Skull-Stripping Filter for ITK

A Skull-Stripping Filter for ITK

Institute for Surgical Technology and Biomechanics, University of Bern

Please use this identifier to cite or link to this publication: http://hdl.handle.net/10380/3353

Published in The Insight Journal - 2012 January-December.

Submitted by Stefan Bauer on 04-30-2012.

Skull-stripping (or brain extraction) is an important pre-processing step in neuroimage analysis. This document describes a skull-stripping filter implemented using the Insight Toolkit ITK, which we named itk::StripTsImageFilter. It is a composite filter based on existing ITK classes. The filter has been implemented with usability, robustness, speed and versatility in mind, rather than accuracy. This makes it useful for many pre-processing tasks in neuroimage analysis. This paper is accompanied by the source code, input data and a testing environment.

Code

Automatic Testing Results by Insight-Journal Dashboard on Tue Jan 29 16:07:52 2013 for revision #3

expertise: 5 sensitivity: 3

Automatic Testing Results by Insight-Journal Dashboard on Tue Jan 29 15:58:47 2013 for revision #1

expertise: 5 sensitivity: 5

Reviews

Simple interface by Todd Jensen on 2016-05-30 08:00:15 for revision #4

expertise: 4 sensitivity: 5

Summary:

This filter provides a simple interface for handling a number of semi-complex steps to generate a brain mask from an MR image. I found it easy to incorporate into my own code.

Open Science:

Everything was available in the source code and files. I would suggest adding a README or some other file in the source code describing the source of the atlas data and the license for its use as it is not the same as the skull strip code.

Reproducibility:

I was able to compile the code as a remote module within ITK v4 and incorporate it into my own code.

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Quick, robust skull stripper by Bill Lorensen on 2013-01-03 06:32:06 for revision #3

expertise: 5 sensitivity: 3

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Quick Comments

Comment by Stefan Bauer

The current version (revision #4) is also working as a remote module for ITKv4 now, thanks to Bill Lorensen for his help in setting this up.

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Paper Id:	859
Categories:	Atlas-based segmentation, Level sets, Segmentation
Keywords:	brain extraction, skull-stripping
Toolkits:	ITK, CMake
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Status:	Open for public review

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