{"action":"created","issue":{"url":"https://api.github.com/repos/miykael/atlasreader/issues/72","repository_url":"https://api.github.com/repos/miykael/atlasreader","labels_url":"https://api.github.com/repos/miykael/atlasreader/issues/72/labels{/name}","comments_url":"https://api.github.com/repos/miykael/atlasreader/issues/72/comments","events_url":"https://api.github.com/repos/miykael/atlasreader/issues/72/events","html_url":"https://github.com/miykael/atlasreader/issues/72","id":365385607,"node_id":"MDU6SXNzdWUzNjUzODU2MDc=","number":72,"title":"MNI152 overlay of atlases","user":{"login":"miykael","id":950321,"node_id":"MDQ6VXNlcjk1MDMyMQ==","avatar_url":"https://avatars0.githubusercontent.com/u/950321?v=4","gravatar_id":"","url":"https://api.github.com/users/miykael","html_url":"https://github.com/miykael","followers_url":"https://api.github.com/users/miykael/followers","following_url":"https://api.github.com/users/miykael/following{/other_user}","gists_url":"https://api.github.com/users/miykael/gists{/gist_id}","starred_url":"https://api.github.com/users/miykael/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/miykael/subscriptions","organizations_url":"https://api.github.com/users/miykael/orgs","repos_url":"https://api.github.com/users/miykael/repos","events_url":"https://api.github.com/users/miykael/events{/privacy}","received_events_url":"https://api.github.com/users/miykael/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-10-01T09:50:45Z","updated_at":"2018-10-01T17:48:23Z","closed_at":null,"author_association":"OWNER","body":"## Preparation for the question\r\n\r\nI've plotted all atlases on the MNI template with the following command:\r\n\r\n```python\r\nfrom nilearn import plotting\r\nfrom glob import glob\r\nimport nibabel as nb\r\n\r\natlases = glob('atlases/*gz')\r\ntemplate = 'templates/MNI152_T1_1mm_brain.nii.gz'\r\n\r\nfor a in atlases:\r\n    atlas_dim = len(nb.load(a).shape)\r\n\r\n    if atlas_dim == 4:\r\n        plotting.plot_prob_atlas(a, bg_img=template, title=a[8:-7],\r\n                                 cut_coords=[0,0,0], threshold=0.25, draw_cross=False,\r\n                                 output_file=a[8:-7]+'.png');\r\n    else:\r\n        plotting.plot_roi(a, bg_img=template, title=a[8:-7],\r\n                                 cut_coords=[10,0,0], draw_cross=False,\r\n                                 output_file=a[8:-7]+'.png');\r\n```\r\n\r\nGenerating the following figures:\r\n\r\n### Atlas AAL\r\n![atlas_aal](https://user-images.githubusercontent.com/950321/46281711-be53ba00-c56f-11e8-9c64-c4002a54ce72.png)\r\n\r\n### Atlas Aicha\r\n![atlas_aicha](https://user-images.githubusercontent.com/950321/46281712-be53ba00-c56f-11e8-8914-a66adef31787.png)\r\n\r\n### Atlas Desikan-Killiany\r\n![atlas_desikan_killiany](https://user-images.githubusercontent.com/950321/46281713-be53ba00-c56f-11e8-80d4-d4f2484269ac.png)\r\n\r\n### Atlas Destrieux\r\n![atlas_destrieux](https://user-images.githubusercontent.com/950321/46281714-be53ba00-c56f-11e8-84e4-5c69b9e2c082.png)\r\n\r\n### Atlas Harvard-Oxford\r\n![atlas_harvard_oxford](https://user-images.githubusercontent.com/950321/46281715-be53ba00-c56f-11e8-976c-99327784aaac.png)\r\n\r\n### Atlas Juelich\r\n![atlas_juelich](https://user-images.githubusercontent.com/950321/46281716-be53ba00-c56f-11e8-8221-5428f1b9e1f4.png)\r\n\r\n### Atlas Neuromorphometrics\r\n![atlas_neuromorphometrics](https://user-images.githubusercontent.com/950321/46281717-beec5080-c56f-11e8-94a2-0bad01b89d88.png)\r\n\r\n### Atlas Talairach BA (Brodmann)\r\n![atlas_talairach_ba](https://user-images.githubusercontent.com/950321/46281718-beec5080-c56f-11e8-8643-09dbf277e0a9.png)\r\n\r\n### Atlas Talairach Gyrus\r\n![atlas_talairach_gyrus](https://user-images.githubusercontent.com/950321/46281719-beec5080-c56f-11e8-8e8b-e2f8180effca.png)\r\n\r\n## Question\r\n\r\n1. Do you think that we need to point out in the code, that not all atlases are perfectly aligned to the MNI atlas? See for example the FSL's Talairach atlases.\r\n2. Should we include such figures in the JOSS paper?\r\n\r\nPersonally, I don't think that we should put effort into better normalizing Talairach (and similar atlases) to the MNI template. People who use a particular atlas should be aware of their defaults. What do you think?"},"comment":{"url":"https://api.github.com/repos/miykael/atlasreader/issues/comments/425999635","html_url":"https://github.com/miykael/atlasreader/issues/72#issuecomment-425999635","issue_url":"https://api.github.com/repos/miykael/atlasreader/issues/72","id":425999635,"node_id":"MDEyOklzc3VlQ29tbWVudDQyNTk5OTYzNQ==","user":{"login":"rmarkello","id":14265705,"node_id":"MDQ6VXNlcjE0MjY1NzA1","avatar_url":"https://avatars0.githubusercontent.com/u/14265705?v=4","gravatar_id":"","url":"https://api.github.com/users/rmarkello","html_url":"https://github.com/rmarkello","followers_url":"https://api.github.com/users/rmarkello/followers","following_url":"https://api.github.com/users/rmarkello/following{/other_user}","gists_url":"https://api.github.com/users/rmarkello/gists{/gist_id}","starred_url":"https://api.github.com/users/rmarkello/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rmarkello/subscriptions","organizations_url":"https://api.github.com/users/rmarkello/orgs","repos_url":"https://api.github.com/users/rmarkello/repos","events_url":"https://api.github.com/users/rmarkello/events{/privacy}","received_events_url":"https://api.github.com/users/rmarkello/received_events","type":"User","site_admin":false},"created_at":"2018-10-01T17:48:23Z","updated_at":"2018-10-01T17:48:23Z","author_association":"COLLABORATOR","body":":heart_eyes: :heart_eyes: :heart_eyes: Looks awesome!\r\n\r\n**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.\r\n**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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