[Insight-users] [Community] ITK, Random Forests, and OpenCV

Fri Oct 18 11:53:37 EDT 2013

Just to throw another option out there---

Brian Avants and I recently did pretty well at the 
MICCAI 2013 brain tumor segmentation challenge

http://www.virtualskeleton.ch

using random forests.  We used the R random forest
implementation and the ANTsR package

http://github.com/stnava/ANTsR

The code for the algorithm (including the 4-page abstract
and a fully-functioning 2-D example) is also available on
github.

https://github.com/ntustison/BRATS2013

Nick

 18, 2013, at 11:02 AM, Xiaoxiao Liu <xiaoxiao.liu at kitware.com> wrote:

> It's great to see more activities that engage both the computer vision and medical image analysis fronts.
> The Video bridge modules in ITK were made to facilitate those activities.
> Looking forward to see some exciting contributions in deloying random forest ideas to medical images!
> 
> 
> On Fri, Oct 18, 2013 at 10:49 AM, Becksfort, Jared <Jared.Becksfort at stjude.org> wrote:
> Julien,
> 
> Excellent.  Thank you.
> 
> Jared
> 
> -----Original Message-----
> From: Julien Malik [mailto:julien.malik at c-s.fr]
> Sent: Friday, October 18, 2013 3:33 AM
> To: Becksfort, Jared; Matt McCormick
> Cc: Insight Users
> Subject: Re: [Insight-users] ITK, Random Forests, and OpenCV
> 
> Hi Jared,
> 
> You may look into what we have in Orfeo Toolbox, where we have wrapped the OpenCV machine learning framework in an ITK-compatible way [1].
> 
> There is :
> - generic ListSample/CvMat conversion
> - MachineLearningModel abstract class with derivated classes for each machine learning model algorithm, which can be trained from ListSample, and results can be saved to file and loaded. Once trained or loaded from file, it predicts classes from input sample.
> - an I/O mechanism inspired from the ImageIO framework, capable of loading an arbitrary machine learning model file and returning a MachineLearningModel object.
> - a generic classification filter working on an abstract MachineLearningModel and classifying VectorImage.
> 
> Hope this helps,
> Julien
> 
> [1]
> http://www.orfeo-toolbox.org/SoftwareGuide/SoftwareGuidech19.html#x45-29300019.3.3
> 
> 
> On 10/18/2013 12:42 AM, Becksfort, Jared wrote:
> > Matt,
> >
> > Wow, you'd think I might have googled "convert itk to opencv" at least once in the several hours I looked into this.  The bridge is on the first page of the results.  I guess I spent all my time looking at comparisons between ITK and OpenCV rather than conversions.
> >
> > Thanks for the help.  I'll see what I can do with it.
> >
> > Jared
> >
> > -----Original Message-----
> > From: Matt McCormick [mailto:matt.mccormick at kitware.com]
> > Sent: Thursday, October 17, 2013 5:22 PM
> > To: Becksfort, Jared
> > Cc: Insight Users
> > Subject: Re: [Insight-users] ITK, Random Forests, and OpenCV
> >
> > Hi Jared,
> >
> > There is a bridge [1] to/from ITK and OpenCV.
> >
> > I understand your frustration of articles without code!  If you get something going, please consider submitting it to the Insight Journal [2].
> >
> > Thanks,
> > Matt
> >
> > [1]
> > http://itk.org/ITKExamples/src/Video/BridgeOpenCV/ConvertAnITKGrayScal
> > eImageToCVMat/Documentation.html?highlight=opencv
> > [2] http://insight-journal.org/
> >
> > On Thu, Oct 17, 2013 at 9:19 PM, Becksfort, Jared <Jared.Becksfort at stjude.org> wrote:
> >> Hello,
> >>
> >> I am trying to use random forests on medical images.  I am converting a Java Weka program I wrote to C++.  I want to use ITK for its medical imaging tools and file format support, but it doesn't seem like there is a random forest package in ITK.  Am I wrong?
> >>
> >> If there is not a random forest package, I had planned to use the machine learning component of OpenCV, but it does not support the file types I have to support, such as nii, dicom, and mhd/mha and isn't really designed for medical imaging.  It also seems like I am making it much more difficult than I need to.  I have seen papers published that used ITK with random forests, but the code is not available.
> >>
> >> Does anyone have any suggestions for using a random forest package with or within ITK?  Or using OpenCV for medical images (yes, I know I should ask that on the OpenCV mailing list)?
> >>
> >> Thanks,
> >> Jared
> >>
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> -- 
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> 
> ---------------------------------------------
> Xiaoxiao Liu, Ph.D.
> R & D Engineer
> Kitware Inc.
> Clifton Park, NY
> Phone: (518) 881-4924  or  (518) 371-3971 x124
> 
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