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

Worked very well and was easy to build by Jared Becksfort on 2017-09-19 16:03:36 for revision #4

expertise: 3 sensitivity: 5

Free comment :

Thank you!

Comment by Aaccajohn Holland:

Comment by Umcglaufllind Olivier:

Comment by Tsmccathedema Ken:

Comment by Aollwaymyrt Vigorda:

Comment by Tyamatriley Vigorda:

Comment by Mwangmajor Holland:

Comment by Aollwaymyrt Vigorda:

Comment by Rankeurensuan Ken:

Comment by Tsmccathedema Ken:

Comment by Pshopgolf Olivier:

Comment by Lheeralalkris Olivier:

Comment by Bridesmaidbride Ken:

Comment by Milbluemelsherr Ken:

Comment by Lheeralalkris Olivier:

Comment by Itezziodiss Holland:

Comment by Elissierdeon Olivier:

Comment by Pshopgolf Olivier:

Comment by Rnseremmi Vigorda:

Comment by Rsalbarrantravi Olivier:

Comment by Lheeralalkris Olivier:

Comment by Mwangmajor Holland:

Comment by Dfeedaro Ken:

Comment by Mwangmajor Holland:

Comment by Dfeedaro Ken:

Comment by Nhuskinsaran Ken:

Comment by Lheeralalkris Olivier:

Comment by Lithrailesmered Olivier:

Comment by Ekjamerkend Ken:

Comment by Ohnatowgabr Ken:

Comment by Tnorthfor Olivier:

Comment by Milbluemelsherr Ken:

Comment by Defeldanni Vigorda:

Comment by Elissierdeon Olivier:

Comment by Defeldanni Vigorda:

Comment by Tnorthfor Olivier:

Comment by Umcglaufllind Olivier:

Comment by Tsmccathedema Ken:

Comment by Aaccajohn Holland:

Comment by Tsmccathedema Ken:

Comment by Aollwaymyrt Vigorda:

Comment by Itezziodiss Holland:

Comment by Mwangmajor Holland:

Comment by Lheeralalkris Olivier:

Comment by Dfeedaro Ken:

Comment by Aollwaymyrt Vigorda:

Comment by Dsfordthad Holland:

Comment by Elissierdeon Olivier:

Comment by Adennamajor Vigorda:

Comment by Aaccajohn Holland:

Comment by Bridesmaidbride Ken:

Comment by Dfeedaro Ken:

Comment by Ntlnoel Holland:

Comment by Itezziodiss Holland:

Comment by Umcglaufllind Olivier:

Comment by Itezziodiss Holland:

Comment by Mwangmajor Holland:

Comment by Rankeurensuan Ken:

Comment by Pshopgolf Olivier:

Comment by Itezziodiss Holland:

Comment by Acavarand Holland:

Comment by Tsmccathedema Ken:

Comment by Elissierdeon Olivier:

Comment by Lheeralalkris Olivier:

Comment by Ekjamerkend Ken:

Comment by Bridesmaidbride Ken:

Comment by Elissierdeon Olivier:

Comment by Itezziodiss Holland:

Comment by Ntlnoel Holland:

Comment by Aollwaymyrt Vigorda:

Comment by Pshopgolf Olivier:

Comment by Ntlnoel Holland:

Comment by Bridesmaidbride Ken:

Comment by Mwangmajor Holland:

Comment by Lheeralalkris Olivier:

Comment by Defeldanni Vigorda:

Comment by Lheeralalkris Olivier:

Comment by Aaccajohn Holland:

Comment by Milbluemelsherr Ken:

Comment by Umcglaufllind Olivier:

Comment by Mwangmajor Holland:

Comment by Itezziodiss Holland:

Comment by Mwangmajor Holland:

Comment by Bridesmaidbride Ken:

Comment by Mwangmajor Holland:

Comment by Ekjamerkend Ken:

Comment by Elissierdeon Olivier:

Comment by Dfeedaro Ken:

Comment by Aollwaymyrt Vigorda:

Comment by Bridesmaidbride Ken:

Comment by Rankeurensuan Ken:

Comment by Ekjamerkend Ken:

Comment by Milbluemelsherr Ken:

Comment by Rankeurensuan Ken:

Comment by Tyamatriley Vigorda:

Comment by Rankeurensuan Ken:

Comment by Lheeralalkris Olivier:

Comment by Rankeurensuan Ken:

Comment by Tsmccathedema Ken:

Comment by Milbluemelsherr Ken:

Comment by Rnseremmi Vigorda:

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 Elissierdeon Olivier:

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:	37687
Downloads:	7691
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


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.
Diffeomorphic Demons Using ITK's Finite Difference Solver Hierarchy by Vercauteren T., Pennec X., Perchant A., Ayache N.
A Label Geometry Image Filter for Multiple Object Measurement by Padfield D., Miller J.
Mattes’ Mutual Information Metric for Multimodality Registration of DESS and T2 Mapped Knee... by Urish K.
An OpenCL implementation of the Gaussian pyramid and the resampler by Shamonin D., Staring M.
Next Generation of the JAVA Image Science Toolkit (JIST) Visualization and Validation by Li B., Bryan F., Landman B.
An implementation of the minimization of region-scalable fitting energy levelsets by Tang H., Hameeteman R., Gelas A., Van Walsum T.
Importing Contours from DICOM-RT Structure Sets by Dowling J., Malaterre M., Greer P.B., Salvado O.
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.
Incremental Delaunay Triangulation by Rigaud S., Gouaillard A.

View license

Loading license...

Send a message to the author