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[WIP] - Free water elimination algorithm for single-shell DTI #1603
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...).
Hello @mvgolub, Thank you for submitting the Pull Request !
Do see the DIPY coding Style guideline
@@ 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