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ENH: Add exercises to tractography episodes #105

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kaitj opened this issue Mar 28, 2021 · 3 comments
Open

ENH: Add exercises to tractography episodes #105

kaitj opened this issue Mar 28, 2021 · 3 comments
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help wanted Looking for Contributors type:enhancement Propose enhancement to the lesson

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@kaitj
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kaitj commented Mar 28, 2021

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

@jhlegarreta
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jhlegarreta commented Mar 28, 2021

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.

@kaitj kaitj added the type:enhancement Propose enhancement to the lesson label Mar 30, 2021
@kaitj kaitj changed the title Add exercises to tractography episodes ENH: Add exercises to tractography episodes Apr 2, 2021
@jhlegarreta
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Other candidates:

  • Changing the parameters of the tracking objects when instantiating them (e.g. angles, relative peak threshold, etc.).
  • Returning the seeds and visualizing them.

@kaitj kaitj added the status:in progress Contributor working on issue label Apr 5, 2021
@kaitj kaitj self-assigned this Apr 5, 2021
@kaitj
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kaitj commented Apr 6, 2021

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

@kaitj kaitj removed the status:in progress Contributor working on issue label Apr 6, 2021
@kaitj kaitj removed their assignment Apr 6, 2021
@jhlegarreta jhlegarreta added the help wanted Looking for Contributors label Nov 6, 2021
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