{"action":"created","issue":{"url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/569","labels_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/569/labels{/name}","comments_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/569/comments","events_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/569/events","html_url":"https://github.com/neuropoly/spinalcordtoolbox/issues/569","id":110561976,"number":569,"title":"BUG during sct_register_to_template: bad registration of the labels","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/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/labels/priority:%20high","name":"priority: high","color":"e11d21"},{"url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/labels/sct_register_to_template","name":"sct_register_to_template","color":"d4c5f9"}],"state":"open","locked":false,"assignee":{"login":"benjamindeleener","id":7757117,"avatar_url":"https://avatars.githubusercontent.com/u/7757117?v=3","gravatar_id":"","url":"https://api.github.com/users/benjamindeleener","html_url":"https://github.com/benjamindeleener","followers_url":"https://api.github.com/users/benjamindeleener/followers","following_url":"https://api.github.com/users/benjamindeleener/following{/other_user}","gists_url":"https://api.github.com/users/benjamindeleener/gists{/gist_id}","starred_url":"https://api.github.com/users/benjamindeleener/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/benjamindeleener/subscriptions","organizations_url":"https://api.github.com/users/benjamindeleener/orgs","repos_url":"https://api.github.com/users/benjamindeleener/repos","events_url":"https://api.github.com/users/benjamindeleener/events{/privacy}","received_events_url":"https://api.github.com/users/benjamindeleener/received_events","type":"User","site_admin":false},"milestone":null,"comments":1,"created_at":"2015-10-08T23:39:50Z","updated_at":"2015-10-09T15:46:30Z","closed_at":null,"body":"Data available here: /Volumes/folder_shared/sct_issues/20151008_london_sub2\r\n\r\nCommand line: `sct_register_to_template -i t2.nii.gz -l labels.nii.gz -s t2_seg.nii.gz -p step=1,type=seg,algo=slicereg:step=2,type=seg,algo=bsplinesyn,iter=5,shrink=2:step=3,type=seg,algo=syn,iter=3,shrink=1`\r\n\r\n-----------------------\r\n\r\nThe bug seems to occur during registration of labels template <--> straigth2templateAffine at this step:\r\n[...]\r\n`Remove labels that do not correspond with each others.\r\nsct_label_utils -t remove-symm -i landmarks_rpi_cross3x3_straight.nii.gz -o landmarks_rpi_cross3x3_straight.nii.gz,template_label_cross.nii.gz -r template_label_cross.nii.gz`\r\n\r\n`Estimate affine transfo: straight anat --> template (landmark-based)...`\r\n\r\n`Computing rigid transformation (algo=translation-scaling-z) ...`\r\n[..]\r\n\r\n\r\n![screen shot 2015-10-08 at 7 22 18 pm](https://cloud.githubusercontent.com/assets/7769691/10382601/a6e446c2-6df3-11e5-8e52-ae2985063e71.png)\r\n![screen shot 2015-10-08 at 7 27 08 pm](https://cloud.githubusercontent.com/assets/7769691/10382603/a6e4ab1c-6df3-11e5-85e8-5288afb330d3.png)\r\n![screen shot 2015-10-08 at 7 28 23 pm](https://cloud.githubusercontent.com/assets/7769691/10382602/a6e45888-6df3-11e5-921a-b443f9ae657c.png)\r\n"},"comment":{"url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/comments/146907894","html_url":"https://github.com/neuropoly/spinalcordtoolbox/issues/569#issuecomment-146907894","issue_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/569","id":146907894,"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":"2015-10-09T15:46:30Z","updated_at":"2015-10-09T15:46:30Z","body":"The bug seems to be the same with subject 3 from London, see result on screenshots below. (Ask me if you need the data).\r\n![screen shot 2015-10-09 at 11 43 36 am](https://cloud.githubusercontent.com/assets/7769691/10398486/51aa1a0a-6e7b-11e5-8e97-1a103b5ae9a2.png)\r\n![screen shot 2015-10-09 at 11 43 41 am](https://cloud.githubusercontent.com/assets/7769691/10398487/51ab37be-6e7b-11e5-9a7b-d8c097f3e9d9.png)\r\n\r\n"}}