{"action":"created","issue":{"url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/989","repository_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox","labels_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/989/labels{/name}","comments_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/989/comments","events_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/989/events","html_url":"https://github.com/neuropoly/spinalcordtoolbox/issues/989","id":175113472,"number":989,"title":"sct_process_segmentation: Bug using '-vert' flag","user":{"login":"charleygros","id":14353425,"avatar_url":"https://avatars.githubusercontent.com/u/14353425?v=3","gravatar_id":"","url":"https://api.github.com/users/charleygros","html_url":"https://github.com/charleygros","followers_url":"https://api.github.com/users/charleygros/followers","following_url":"https://api.github.com/users/charleygros/following{/other_user}","gists_url":"https://api.github.com/users/charleygros/gists{/gist_id}","starred_url":"https://api.github.com/users/charleygros/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/charleygros/subscriptions","organizations_url":"https://api.github.com/users/charleygros/orgs","repos_url":"https://api.github.com/users/charleygros/repos","events_url":"https://api.github.com/users/charleygros/events{/privacy}","received_events_url":"https://api.github.com/users/charleygros/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_process_segmentation","name":"sct_process_segmentation","color":"d4c5f9"}],"state":"closed","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},"assignees":[{"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":5,"created_at":"2016-09-05T18:18:13Z","updated_at":"2016-09-09T21:04:26Z","closed_at":"2016-09-09T20:50:44Z","body":"Command:\r\n```\r\nsct_process_segmentation -i /Volumes/folder_shared/als_gm_atrophy/test_benjamin/143/t2/t2_seg.nii.gz -p csa -output-type txt -vert 2:13 -vertfile /Volumes/folder_shared/als_gm_atrophy/test_benjamin/143/t2/label/template/PAM50_levels.nii.gz \r\n```\r\n\r\nError:\r\n```\r\nSelected vertebral levels... 2:13\r\n  OK: /Volumes/folder_shared/als_gm_atrophy/test_benjamin/143/t2/label/template/PAM50_levels.nii.gz\r\n    Find slices corresponding to vertebral levels based on the centerline...\r\n/Users/chgroc/code/spinalcordtoolbox/scripts/sct_process_segmentation.py:915: VisibleDeprecationWarning: using a non-integer number instead of an integer will result in an error in the future\r\n  if vertebral_labeling_data[np.round(x_centerline_fit[i_z]), np.round(y_centerline_fit[i_z]), z_centerline[i_z]] in range(vert_levels_list[0], vert_levels_list[1]+1):\r\nTraceback (most recent call last):\r\n  File \"/Users/chgroc/code/spinalcordtoolbox/scripts/sct_process_segmentation.py\", line 1035, in <module>\r\n    main(sys.argv[1:])\r\n  File \"/Users/chgroc/code/spinalcordtoolbox/scripts/sct_process_segmentation.py\", line 262, in main\r\n    compute_csa(fname_segmentation, output_prefix, param_default.suffix_csa_output_files, output_type, overwrite, verbose, remove_temp_files, step, smoothing_param, figure_fit, slices, vert_lev, fname_vertebral_labeling, algo_fitting = param.algo_fitting, type_window= param.type_window, window_length=param.window_length, angle_correction=angle_correction)\r\n  File \"/Users/chgroc/code/spinalcordtoolbox/scripts/sct_process_segmentation.py\", line 647, in compute_csa\r\n    slices, vert_levels_list, warning = get_slices_matching_with_vertebral_levels_based_centerline(vert_levels, im_vertebral_labeling.data, x_centerline_fit, y_centerline_fit, z_centerline)\r\n  File \"/Users/chgroc/code/spinalcordtoolbox/scripts/sct_process_segmentation.py\", line 919, in get_slices_matching_with_vertebral_levels_based_centerline\r\n    slices = str(min(matching_slices_centerline_vert_labeling))+':'+str(max(matching_slices_centerline_vert_labeling))\r\nValueError: min() arg is an empty sequence\r\n```"},"comment":{"url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/comments/246039401","html_url":"https://github.com/neuropoly/spinalcordtoolbox/issues/989#issuecomment-246039401","issue_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/989","id":246039401,"user":{"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},"created_at":"2016-09-09T21:04:26Z","updated_at":"2016-09-09T21:04:26Z","body":"The issue is fixed. `sct_testing` works, as well as the `batch_processing`.\r\n\r\nNote that the bug affected the computation of CSA. Therefore, all study computing cord CSA need to be done again."}}
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