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NF - Add PMF Threshold to Tractography #1041
This PR adds pmf_threshold parameter to ProbabilisticDirectionGetter, which set to 0 all directions with probability mass function value < pmf_threshold.. It is common to remove low CSD-ODF value (e.g. mrtrix) from the probability mass function used in probabilistic tractography. Increasing pmf_threshold tends to reduce erroneous streamlines by following 'less noisy' directions of the CSD-ODF.
I set the default to 0.1 as suggested by [Tournier et al. 2012, Girard et al. 2014]. However, this will change probabilistic streamline output of current scripts.
changed the title from
NF - add PMF Threshold for tractography
NF - Add PMF Threshold to Tractography
May 3, 2016
referenced this pull request
May 4, 2016
This looks great to me. What are your thoughts on absorbing the inevitable changes to previous behavior? I think it'll probably be alright (that's what happens when you upgrade software...), but if someone has any ideas on how to not surprise users with this, that would be good.
Either way, a note in the API changes doc needs to be made.
Thanks for your comments.
With pmf_threshold = 0.1, changes in the reconstruction are small, but I would prefer having it at 0.1 by default that 0.0. My only concern is reproducibility of previous results, with previous code.
How should this note be made? In the documentation of the class
In here: https://github.com/nipy/dipy/blob/master/doc/api_changes.rst, under a new 0.12 heading.