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[DOC] add interactive bundle viz to OR example #861

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merged 5 commits into from
Nov 9, 2022

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36000
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@36000 36000 commented Jul 20, 2022

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@arokem
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arokem commented Jul 20, 2022

A couple of thoughts here:

  1. For some reason, the plotly plot appears at the very top of this example, unlike the other examples where it appears in the end. I couldn't really find the code reason for it, though.
  2. Should we do only the OR in this example? I think that the visualization will be a bit clearer in that case.
  3. I see that the code also generates a montage. Maybe we should pull in the montage to display, instead of the standard html visualization? It's not interactive, but it would at least demonstrate this functionality. We could also do both.

Also, noticed that the ORs in this subject also have the additional more anterior section:

Screen Shot 2022-07-20 at 9 27 10 AM

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36000 commented Jul 20, 2022

I think putting the montage only is a good idea. The cropped endpoint ROIs would fix the anterior section problem

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A couple of comments here.

I didn't realize that this also involves a new set of OR ROIs! We should ask @SendyCaffarra and @jyeatman for some feedback on this new definition of the anterior portion of the OR, which should help get rid of the anterior branch that we have been seeing in some subjects.

@@ -593,9 +593,9 @@ def read_templates(as_img=True, resample_to=False):
]

or_remote_fnames = [
"26831630",
"36514170",
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Just making sure I understand this: These are the new edited ROIs for thalamus?

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Yes and this works well in test datasets

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Do we have a way to refer to different versions of this data on figshare?

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I am not sure what you mean by this. Note that the new OR ROIs are on my figshare but the old ones are not.

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Oh! Gotcha. I think that means we are good to go here.

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I mean up to the sphinx stuff, which I can sort out. Let me pull this rebased thing down and fiddle with that.

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Oh - I see you are sorting that out too in a8a12a1

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I still need to test that

my_afq.combine_bundle("L_OR")
display(Image(filename=montages[0]))
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This call to display does not embed this in the html that sphinx generates. I think that we need the sphinx rst to encode the figure. Something like this code: https://github.com/yeatmanlab/pyAFQ/blob/master/examples/plot_afq_api.py#L181-L184 should do it.

@36000 36000 changed the title [DOC] add interactive bundle viz to OR example WIP: [DOC] add interactive bundle viz to OR example Aug 17, 2022
@36000 36000 changed the title WIP: [DOC] add interactive bundle viz to OR example [DOC] add interactive bundle viz to OR example Nov 2, 2022
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36000 commented Nov 2, 2022

@arokem I am not sure if the sphinx integration is good to go, but otherwise this is good. for example the new thalamus ROI is tested on hbn, hcp, and hardi, and it gets rid of the anterior endpoint problem.

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arokem commented Nov 7, 2022

@36000 : when you get a chance, could you please rebase this on top of current master?

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arokem commented Nov 9, 2022

Looks like it works now!

@arokem arokem merged commit bc07b62 into yeatmanlab:master Nov 9, 2022
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2 participants