Re: Probabilistic Tractography Module in SlicerDMRI

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Re: Probabilistic Tractography Module in SlicerDMRI

O'Donnell, Lauren J., Ph.D.
Hi again Nandikashore. The UKF method is deterministic, as is the SlicerDMRI default method. We recommend Slicer 4.6 for diffusion MRI because we have updated and improved the diffusion functionality in the SlicerDMRI and UKFTractography extensions.

I hope this helps.
Best regards,

Lauren J. O’Donnell, Ph.D.
Assistant Professor, Harvard Medical School
1249 Boylston St., Room #210
Boston, Massachusetts 02215
[hidden email]

On Dec 2, 2016, at 3:08 PM, Nandakishore Puttashamachar <[hidden email]> wrote:

Thank you, Lauren.

I learned about Slicer tractography from various tutorials available online such as Neurosurgical Planning tutorial.

As I understand, In slicer 4.5 version - 

The DTI tractography algorithm used is "Deterministic", right? 

The SlicerDMRI available at is also a "deterministic" algorithm, right?

The only available Stochastic/Probabilistic tractography module is the UKF method, right?

Kindly correct me if I am wrong with these questions.

Thank you,

From: O'Donnell, Lauren J., Ph.D. <[hidden email]>
Sent: Saturday, December 3, 2016 1:16:52 AM
To: Nandakishore Puttashamachar; Steve Pieper; Norton, Isaiah; SPL Slicer Users
Subject: Re: FW: Probabilistic Tractography Module in SlicerDMRI

Hi Nandikashore.

The closest to probabilistic tractography in Slicer is the sensitive UKF method, which due to the multi fiber model seeding at random points has some probabilistic aspect. SlicerDMRI currently supports traditional DTI and also UKF deterministic tractography methods. There may be other options included in current and past Slicer extensions. Where did you find information about Slicer tractography?


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On Fri, Dec 2, 2016 at 2:05 PM -0500, "Nandakishore Puttashamachar" <[hidden email]> wrote:

Hi Steve,

Thank you for the quick response. 

I have visited the SlicerDMRI website multiple times, but I could not find out which paper/authors work has been implemented in Probabilistic Tractography. 

could you kindly refer me to the original article?

Thank you,

From: Steve Pieper <[hidden email]>
Sent: Saturday, December 3, 2016 12:25:04 AM
To: Nandakishore Puttashamachar; Norton, Isaiah; Lauren O'Donnell; [hidden email]
Subject: Re: FW: Probabilistic Tractography Module in SlicerDMRI
Hi Nandakishore -

Probably everything you need is on this site:

Also, be sure to email [hidden email] and not [hidden email] (the later is only for admin purposes).


On Fri, Dec 2, 2016 at 1:42 PM, Pieper, Steven D. <[hidden email]> wrote:

From: slicer-devel <[hidden email]> on behalf of Nandakishore Puttashamachar <[hidden email]>
Date: Thursday, December 1, 2016 at 11:09 PM
To: SPL Slicer Devel Owner <[hidden email]>
Subject: Probabilistic Tractography Module in SlicerDMRI
Resent-From: <[hidden email]>
Resent-Date: Thursday, December 1, 2016 at 11:09 PM

Hi Team,

Hope you are doing good.

I am writing to discuss upon the SlicerDMRI module. I need to reproduce the results of SlicerDMRI Probabilistic Tractography for evaluation. However, I am unable to find a suitable resource on SlicerDMRI Source code.

I did notice the GitHub repo for SlicerDMRI, but was not successful in building the module. 

* Do you have specific documentation toward building and using SlicerDMRI module?

* Also, I would like to know which paper/research work is being used currently by Slicer Probabilistic Tractography?

Kindly help out on my questions.

Your help is much appreciated.

Thank you,
University of Central Florida

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