{"action":"created","issue":{"url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/663","labels_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/663/labels{/name}","comments_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/663/comments","events_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/663/events","html_url":"https://github.com/neuropoly/spinalcordtoolbox/issues/663","id":116229479,"number":663,"title":"sct_process_segmentation: CSA averaging across vertebral levels is biased towards high values","user":{"login":"slevyrosetti","id":7769691,"avatar_url":"https://avatars.githubusercontent.com/u/7769691?v=3","gravatar_id":"","url":"https://api.github.com/users/slevyrosetti","html_url":"https://github.com/slevyrosetti","followers_url":"https://api.github.com/users/slevyrosetti/followers","following_url":"https://api.github.com/users/slevyrosetti/following{/other_user}","gists_url":"https://api.github.com/users/slevyrosetti/gists{/gist_id}","starred_url":"https://api.github.com/users/slevyrosetti/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/slevyrosetti/subscriptions","organizations_url":"https://api.github.com/users/slevyrosetti/orgs","repos_url":"https://api.github.com/users/slevyrosetti/repos","events_url":"https://api.github.com/users/slevyrosetti/events{/privacy}","received_events_url":"https://api.github.com/users/slevyrosetti/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/labels/priority:%20medium","name":"priority: medium","color":"eb6420"},{"url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/labels/sct_process_segmentation","name":"sct_process_segmentation","color":"d4c5f9"}],"state":"open","locked":false,"assignee":{"login":"slevyrosetti","id":7769691,"avatar_url":"https://avatars.githubusercontent.com/u/7769691?v=3","gravatar_id":"","url":"https://api.github.com/users/slevyrosetti","html_url":"https://github.com/slevyrosetti","followers_url":"https://api.github.com/users/slevyrosetti/followers","following_url":"https://api.github.com/users/slevyrosetti/following{/other_user}","gists_url":"https://api.github.com/users/slevyrosetti/gists{/gist_id}","starred_url":"https://api.github.com/users/slevyrosetti/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/slevyrosetti/subscriptions","organizations_url":"https://api.github.com/users/slevyrosetti/orgs","repos_url":"https://api.github.com/users/slevyrosetti/repos","events_url":"https://api.github.com/users/slevyrosetti/events{/privacy}","received_events_url":"https://api.github.com/users/slevyrosetti/received_events","type":"User","site_admin":false},"milestone":null,"comments":8,"created_at":"2015-11-10T23:51:59Z","updated_at":"2015-11-13T16:46:41Z","closed_at":null,"body":"Change the way to compute CSA across vertebral levels. Currently, an average of the voxels inside the segmentation mask over the CSA volume is performed. Hence, it includes more voxels of high CSA value (since slices of high CSA include more voxels) and less with lower values.\r\n\r\nSolution: find the slices corresponding to the selected vertebral levels in the output .txt file and perform an average of the CSA of these slices."},"comment":{"url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/comments/156484288","html_url":"https://github.com/neuropoly/spinalcordtoolbox/issues/663#issuecomment-156484288","issue_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/663","id":156484288,"user":{"login":"slevyrosetti","id":7769691,"avatar_url":"https://avatars.githubusercontent.com/u/7769691?v=3","gravatar_id":"","url":"https://api.github.com/users/slevyrosetti","html_url":"https://github.com/slevyrosetti","followers_url":"https://api.github.com/users/slevyrosetti/followers","following_url":"https://api.github.com/users/slevyrosetti/following{/other_user}","gists_url":"https://api.github.com/users/slevyrosetti/gists{/gist_id}","starred_url":"https://api.github.com/users/slevyrosetti/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/slevyrosetti/subscriptions","organizations_url":"https://api.github.com/users/slevyrosetti/orgs","repos_url":"https://api.github.com/users/slevyrosetti/repos","events_url":"https://api.github.com/users/slevyrosetti/events{/privacy}","received_events_url":"https://api.github.com/users/slevyrosetti/received_events","type":"User","site_admin":false},"created_at":"2015-11-13T16:46:41Z","updated_at":"2015-11-13T16:46:41Z","body":"To briefly sum up what I implemented:\r\n- if slices or vertebral levels were selected:\r\n   - if vertebral levels were selected, get the slices corresponding to the vertebral levels\r\n   - then, get the CSA estimated for each one of these slices based on the file csa.txt that was output before\r\n   - compute the mean (and std) across these values\r\n   - output the result and write it in a file\r\n"}}