Comments (5)
😍 😍 😍 Looks awesome!
Q1: Maybe the Talaraich atlases can be removed from the default atlases so that users who want them can add them but they're not included for those who don't know better? I agree that we shouldn't be responsible for normalizing the atlas, ourselves.
Q2: Maybe we can include a select few that are "representative" (e.g., AAL, DK, and Harvard Oxford) rather than all of them? They're very pretty (thanks, nilearn
!).
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A1: I agree, Talairach should be removed.
A2: I think it's a good idea to have only a few as default. So, would you create an additional parameter default
where only 3-4 are specified or would you overwrite all
(which would be wrong, no?).
Q1 for everyone:
- Ross proposes AAL, DK and HarvardOxford as default atlases.
- I've never heard/seen the Aicha and Neuromorphometrics and never used Talairach. And I don't have a strong preference for DK or Destrieux. I've used Juelich but think I will be happier with AAL. Therefore, I'm all happy with Ross' proposal.
What do others think?
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I like the idea of AAL, DK, and HarvardOxford. Having just used atlasreader
for a project, I found those to be the most reliable and helpful. Just to be clear, are we talking about atlas defaults in general (how I interpreted this), or if the atlases will be plotted by default?
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@danjgale, we're talking about atlas defaults. The plots were just to bring the topic to our attention.
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I actually initially meant for the atlas plots, but I do like the idea of having only a few as defaults, too! I'm happy with those three 👍 It might be good to show those three plots in the writeup, as well, to explain that they're the defaults 🙂
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Related Issues (20)
- JOSS REVIEW: paper wording suggestion HOT 2
- JOSS REVIEW: scipy and sklearn missing DOIs HOT 2
- JOSS REVIEW: checksum unit test failing HOT 5
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- Using mask as input image? HOT 6
- read_atlas_peak with "pip install" HOT 1
- White matter atlases HOT 1
- python dependency ? HOT 2
- Desikan Killiany Atlas HOT 2
- A way to name cluster plots based on atlas label?
- Question: does AtlasReader reslice statistical maps?
- AttributeError: module 'matplotlib.cm' has no attribute 'revcmap'
- /Users/abernal/opt/anaconda3/envs/atlasreader/lib/python3.7/site-packages/nilearn/plotting/displays/_slicers.py:382: UserWarning: empty mask get_mask_bounds(new_img_like(img, not_mask, affine))
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- run tests on github action instead of travis HOT 1
- run flake8 via github action instead of travis HOT 2
- replace zenodo.json by citation.cff HOT 1
- update packaging HOT 10
- fix broken badge in readme HOT 1
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