[Insight-users] suggestions for ITK-based projects for a graduate image analysis class?

Wed Sep 26 12:11:10 EDT 2012

Hello Michel,

1. My code from my paper, creates 32 single simplex meshes at the same time and and deform them individually (i.e, running 32 deformable model classes simultaneously) and uses binary masks (32 of them) created (also code I contributes to itk, TrignaleMeshToBinaryImage) to avoid collision between them, so I am not sure what you mean by "old v3 Simplex classes were not completely functional", all the functionality (create simplex sphere --> convert to and from Triangle to Simplex and deform Simplex mesh) that I used was there, I can not remember if I changed any of the simplex classes code but its easy to check the code.

2. sorry can not comment on Dr Gilles' work as I really do not know much about it,

Leila

----- Original Message -----
From: "Audette, Michel A." <maudette at odu.edu>
Sent: Wed, 9/26/2012 11:53am
To: Leila Baghdadi <baghdadi at phenogenomics.ca> ; insight-users at itk.org
Subject: RE: [Insight-users] suggestions for ITK-based projects for a graduate image analysis class?

Hi Leila, 

I'm familiar with Dr Delingette's work of course. I was referring to Dr Gilles' work on multi-surface Simplex, which builds on Delingette's single-surface, as well as provides new topological operators. 

My understanding about the old Simplex classes were that they did not completely implement the original Delingette model, which is why I'm working on a new Delingette Simplex implementation with the ITK Mesh class contributors (Alex Gouaillard and his colleagues), but this is separate from, and serves as a starting point for, my student's planned project. I may be wrong, or my understanding might not be up-to-date as it relates to v4, but my recollection based on my time at Kitware was that the old v3 Simplex classes were not completely functional; I'm surprised that you were able to build on them for your multi-surface code.  Please confirm. 

Best wishes,

Michel

Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
________________________________________
From: Leila Baghdadi [baghdadi at phenogenomics.ca]
Sent: Wednesday, September 26, 2012 11:40 AM
To: Audette, Michel A.; insight-users at itk.org
Subject: RE: [Insight-users] suggestions for ITK-based projects for a graduate image analysis class?

regarding number 2, to my knowledge most of the simplex deformable code in ITK is related to the work of Herve Delingette (also from INRIA), so my code just uses that concept and elaborates on it for multi object segmentation,

one other note regarding subdivision of mesh for segmentation of high curvature areas, the paper I published uses vtk linear subdivision method which I do not think its the right thing but later I heard about
root 3 subdivision by Leif Kobbelt, I think its a great addition to the ITK deformable model segmentation which I hope to implement and submit it to ITK, so I will wait and see what changes you guys do to the original models,

anyhow, I am all in for it, I can provide you with my code or help develop some of it, i.e the above

Leila

----- Original Message -----
From: "Audette, Michel A." <maudette at odu.edu>
Sent: Wed, 9/26/2012 11:17am
To: Leila Baghdadi <baghdadi at phenogenomics.ca> ; insight-users at itk.org
Subject: RE: [Insight-users] suggestions for ITK-based projects for a graduate image analysis class?

Hi Leila,

I'm familiar with both topics.

I became interested in FSL through my interest in FIRST, for deep brain stimulation applications.

The kind of multi-surface simplex modeling that you describe is related to the work of Benjamin Gilles of INRIA, and Dr Gilles is helping my group with our applications of multi-surface simplex. I can tell you that I have an on-going collaboration that is looking at reimplementing the ITK Simplex implementation, and it may be of interest to use code that does multi-surface, in the manner suggested by Dr Gilles.

If you have code that relates to either area  that is ITK-friendly, I think that we could use it, and it would be great to make a contribution via Insight Journal.

Cheers,

Michel

Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
________________________________________
From: Leila Baghdadi [baghdadi at phenogenomics.ca]
Sent: Wednesday, September 26, 2012 10:58 AM
To: Audette, Michel A.; insight-users at itk.org
Subject: RE: [Insight-users] suggestions for ITK-based projects for a graduate image analysis class?

Hi Michel,

I was actually looking at a few of the ITK projects I have done in the past and wondering if I could find some free time to rewrite some of them for ITK4 and submit them to the journal,
so not sure if this is exactly the right thing for your students but I am gonna give it a shot anyways,

1. BET (brain segmentation algorithm) http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/
I wrote the code for ITK 3.2 sometime ago and found it very useful, infact I think it was used to segment preterm baby brains. not sure if this is in ITK yet

2. simplex deformable model segmentation (multi-object) --> I added extra code for multi-object and collision detection of multi-mouse embryo segmentation, also in ITK3.2
published last year http://www.ncbi.nlm.nih.gov/pubmed/21679425

Leila

----- Original Message -----
From: "Audette, Michel A." <maudette at odu.edu>
Sent: Wed, 9/26/2012 10:42am
To: insight-users at itk.org
Subject: [Insight-users] suggestions for ITK-based projects for a graduate image analysis class?

Dear ITK users,

I am teaching a graduate class in medical image analysis, and I would like to provide my students with a list of possible projects based on ITK that could implement recent algorithms, which possibly could then be submitted to Insight Journal and meet some needs of the ITK community. This class is based on the Toennies textbook from 2012, and will feature a number of registration and segmentation techniques, including graph cuts and level sets, as well as meshing methods not in the textbook. These projects will be for two students on which to collaborate, typically.

If the community has any suggestions on how ITKv4 might be extended, based on recent papers in MICCAI, MedIA, or IEEE TMI, please let me know as soon as possible. Thanks for your kind consideration.

Cheers,

Michel

Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
_____________________________________
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