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[WIP] - Free water elimination algorithm for single-shell DTI #1603

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@mvgolub
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commented Jul 30, 2018

This is my attempt at implementing a free water elimination algorithm for single-shell DTI based on a Beltrami framework described in the work of Pasternak et al. 2009 (https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.22055), it is still a work in progress and not ready to be merged. I have not yet created classes to integrate this with the dipy architecture. I have put this as a separate reconst module, but eventually we could integrate this in the existing fwdti.py module, I look forward on some suggestions on the best way to integrate this code.

This work is part of my thesis in biomedical engineering, one of my supervisors is Rafael Neto Henriques @RafaelNH , who worked on the multi-shell fwDTI already implemented in dipy.

I apologize for the comments in my code not being very detailed, but I will be responding to the original issue #827 where this feature was requested and provide some documents where I explain the algorithm in more detail and show some results. I appreciate any suggestions to make the code more efficient and solve some numerical problems (overflows, underflows...).

Marc Golub

@pep8speaks

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commented Jul 30, 2018

Hello @mvgolub, Thank you for submitting the Pull Request !

Line 882:81: E501 line too long (90 > 80 characters)
Line 885:81: E501 line too long (90 > 80 characters)
Line 1000:81: E501 line too long (82 > 80 characters)
Line 1041:81: E501 line too long (83 > 80 characters)

Do see the DIPY coding Style guideline

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commented Jul 30, 2018

Codecov Report

Merging #1603 into master will decrease coverage by 1.16%.
The diff coverage is 7.21%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1603      +/-   ##
==========================================
- Coverage   87.33%   86.17%   -1.17%     
==========================================
  Files         246      247       +1     
  Lines       31814    32285     +471     
  Branches     3451     3452       +1     
==========================================
+ Hits        27786    27821      +35     
- Misses       3205     3642     +437     
+ Partials      823      822       -1
Impacted Files Coverage Δ
dipy/reconst/beltrami_fwdti.py 7.21% <7.21%> (ø)
dipy/core/graph.py 75% <0%> (+1.19%) ⬆️

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@jottino

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commented Aug 6, 2018

Hi @mvgolub sorry to use this section but I tried to find a way to reach you to ask if you could help me to apply your code to my single-shell data. Could you reach me at jottino(at)ub.edu? Thanks!!

@arokem

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commented Mar 15, 2019

This seems to be superseded by #1744. I'll close this one.

@arokem arokem closed this Mar 15, 2019
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