open source, neuro, learning, collaboration, sound theory, solid results

Uncategorized

ANTs and ANTsR

http://stnava.github.io/ANTs/

http://stnava.github.io/ANTsR/

If you have comments or questions on this software, please refer to the “issues” links available via the above sites.


New ants documentation

To accompany a new release:

http://stnava.github.io/ANTsDoc/


ANTs leads in open competition / evaluation

The SyN Paper is one of the most cited in Medical Image Analysis since 2008

http://www.journals.elsevier.com/medical-image-analysis/most-cited-articles/

Advanced Normalization Tools finished first overall in three different competitions that test the reliability, reproducibility and accuracy of our image registration and segmentation methods.   This is joint work with Nick Tustison, Gang Song, Paul Yushkevich, Hongzhi Wang and Hans Johnson.

Each of these was conducted in a blinded fashion and judged impartially on hidden data.  These types of open competitions provide a more accurate window into the rigor and reliability of methods in real world scenarios.

1)  Klein 2009 brain mapping competition http://www.ncbi.nlm.nih.gov/pubmed/19195496

2) Murphy 2011 http://www.ncbi.nlm.nih.gov/pubmed/21632295

3) Multi-atlas challenge MICCAI 2012 https://masi.vuse.vanderbilt.edu/workshop2012/index.php/Workshop_Program

The conclusion of this workshop was that the registration tool strongly impacts performance ( all the top finishers used ANTs ) and that, in future workshops , everyone should use ANTs (or another equally good tool). This would allow pure testing of the multi-atlas labeling approach.

challenge_results_miccai_2012


updated ANTs compile instructions: ITKv4

latest ants binaries are here:   ANTs-Binaries

instructions for linux / osx type installation.   windows works too ( via cmake ) but i dont have specifics.

to compile ants from the source code, you first need: git, cmake and a c++ compiler

then in a terminal, do:

>  git clone git://github.com/stnava/ANTs.git

>  mkdir antsbin

> cd antsbin

>  ccmake ../ANTs

then go into cmake and type “c” and then “g”  then exit back to the
terminal.   then:

>  make -j 4

and wait a while.

to update an existing ANTs install, go to the ANTs directory and type “git pull origin master”

Don’t forget to toggle to advanced and turn off

SuperBuild_ANTS_USE_GIT_PROTOC if behind firewall


Networks


Welcome!

January 13, 2011—-Philadelphia, PA.

I hope to keep this pig fed with software updates, publications and heavily filtered details from my life.