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.

Comment by Aollwaymyrt Vigorda:

Comment by Ekjamerkend Ken:

Comment by Rankeurensuan Ken:

Comment by Elissierdeon Olivier:

Comment by Nndnilandraymo Ken:

Comment by Htonhung Ken:

Comment by Redbergaaro Ken:

Comment by Rnseremmi Vigorda:

Comment by Pshopgolf Olivier:

Comment by Redbergaaro Ken:

Comment by Ntlawrencetheos Ken:

Comment by Cbuycheap Holland:

Comment by Zbularzstacy Holland:

Comment by Nhuskinsaran Ken:

Comment by Ekjamerkend Ken:

Comment by Ohnatowgabr Ken:

Comment by Pshopgolf Olivier:

Comment by Defeldanni Vigorda:

Comment by Rnseremmi Vigorda:

Comment by Pshopgolf Olivier:

Comment by Rankeurensuan Ken:

Comment by Lithrailesmered Olivier:

Comment by Aaccajohn Holland:

Comment by Elissierdeon Olivier:

Comment by Aollwaymyrt Vigorda:

Comment by Nhuskinsaran Ken:

Comment by Pshopgolf Olivier:

Comment by Rsalbarrantravi Olivier:

Comment by Defeldanni Vigorda:

Comment by Ntlnoel Holland:

Comment by Conecoyn Vigorda:

Comment by Nhuskinsaran Ken:

Comment by Lbbellquin Holland:

Comment by Mwangmajor Holland:

Comment by Nhuskinsaran Ken:

Comment by Tbootsbuy Vigorda:

Comment by Defeldanni Vigorda:

Comment by Lcyleot Ken:

Comment by Lheeralalkris Olivier:

Comment by Itezziodiss Holland:

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

expertise: 5 sensitivity: 3

Add a new review

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.

Resources


Download All
Download Paper , View Paper
Download Source code
Source code repository

Statistics more


Global rating:
Review rating:	[review]
Code rating:
Views:	28400
Downloads:	5928
Paper Quality:
1 comment

Information more


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

Share

Linked Publications more


An implementation of the minimization of region-scalable fitting energy levelsets by Tang H., Hameeteman R., Gelas A., Van Walsum T.
Diffeomorphic Demons Using ITK's Finite Difference Solver Hierarchy by Vercauteren T., Pennec X., Perchant A., Ayache N.
Primal/Dual Mesh with Application to Triangular/Simplex Mesh and Delaunay/Voronoi by Irshad H., Rigaud S., Gouaillard A.
Importing Contours from DICOM-RT Structure Sets by Dowling J., Malaterre M., Greer P.B., Salvado O.
Mattes’ Mutual Information Metric for Multimodality Registration of DESS and T2 Mapped Knee... by Urish K.
Statismo - A framework for PCA based statistical models by Lüthi M., Blanc R., Albrecht T., Gass T., Goksel O., Büchler P., Kistler M., Bousleiman H., Reyes M., Cattin P., Vetter T.
A Label Geometry Image Filter for Multiple Object Measurement by Padfield D., Miller J.
An ITK Implementation of Physics-based Non-rigid Registration Method by Liu Y., Kot A., Drakopoulos F., Fedorov A., Enquobahrie A., Clatz O., Chrisochoides N.
Robust Scattered Data Points Approximation Using Finite Element Biomechanical Model by Liu Y., Chrisochoides N.
An OpenCL implementation of the Gaussian pyramid and the resampler by Shamonin D., Staring M.

View license

Loading license...

Send a message to the author