[DOC] add interactive bundle viz to OR example #861
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A couple of thoughts here:
Also, noticed that the ORs in this subject also have the additional more anterior section:
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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): | |||
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| 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
examples/plot_optic_radiations.py
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| 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.
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@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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@36000 : when you get a chance, could you please rebase this on top of current master? |
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Looks like it works now! |
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