carpentries-incubator / SDC-BIDS-dMRI

Introduction to dMRI
https://carpentries-incubator.github.io/SDC-BIDS-dMRI/
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ENH: Add exercises to tractography episodes #105

Open kaitj opened 3 years ago

kaitj commented 3 years ago

Similar to #30 , should add one or several exercises to both probabilistic and deterministic tractography episodes.

jhlegarreta commented 3 years ago

A few candidates

  1. Use a different stopping criterion to perform the tracking process.

Not sure about the result it would yield, and learners might not know how to estimate the WM tissue using other methods (e.g. partial volume maps). So it might be difficult.

  1. Plot the streamlines with a colormap that indicates their FA value. You will need to modify the arguments for the actor.line call and have a look at the actor.scalar_bar method to visualize the values that correspond to the used colormap. You might also explore with different colormap LUTs.

This one should be easy, but I grant that this is more a visualization exercise, rather than a tracking one, and requires them to look into the documentation (which is explicitly said). However, the point of looking at the documentation might be an interesting exercise to allow them to "see beyond the notebooks". Also it allows to make a link with both the DTI espisode and the tractometry discussion in the extras.

jhlegarreta commented 3 years ago

Other candidates:

kaitj commented 3 years ago

105 adds exercises in for deterministic tractography. Probablistic tractography exercises to be added at a later time