{"action":"closed","issue":{"url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/833","repository_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox","labels_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/833/labels{/name}","comments_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/833/comments","events_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/833/events","html_url":"https://github.com/neuropoly/spinalcordtoolbox/issues/833","id":150454995,"number":833,"title":"Error: make sure vert.txt is an image","user":{"login":"jcohenadad","id":2482071,"avatar_url":"https://avatars.githubusercontent.com/u/2482071?v=3","gravatar_id":"","url":"https://api.github.com/users/jcohenadad","html_url":"https://github.com/jcohenadad","followers_url":"https://api.github.com/users/jcohenadad/followers","following_url":"https://api.github.com/users/jcohenadad/following{/other_user}","gists_url":"https://api.github.com/users/jcohenadad/gists{/gist_id}","starred_url":"https://api.github.com/users/jcohenadad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jcohenadad/subscriptions","organizations_url":"https://api.github.com/users/jcohenadad/orgs","repos_url":"https://api.github.com/users/jcohenadad/repos","events_url":"https://api.github.com/users/jcohenadad/events{/privacy}","received_events_url":"https://api.github.com/users/jcohenadad/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/sct_segment_graymatter","name":"sct_segment_graymatter","color":"d4c5f9"}],"state":"closed","locked":false,"assignee":{"login":"SaraDupont","id":5857909,"avatar_url":"https://avatars.githubusercontent.com/u/5857909?v=3","gravatar_id":"","url":"https://api.github.com/users/SaraDupont","html_url":"https://github.com/SaraDupont","followers_url":"https://api.github.com/users/SaraDupont/followers","following_url":"https://api.github.com/users/SaraDupont/following{/other_user}","gists_url":"https://api.github.com/users/SaraDupont/gists{/gist_id}","starred_url":"https://api.github.com/users/SaraDupont/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SaraDupont/subscriptions","organizations_url":"https://api.github.com/users/SaraDupont/orgs","repos_url":"https://api.github.com/users/SaraDupont/repos","events_url":"https://api.github.com/users/SaraDupont/events{/privacy}","received_events_url":"https://api.github.com/users/SaraDupont/received_events","type":"User","site_admin":false},"milestone":null,"comments":0,"created_at":"2016-04-22T19:42:38Z","updated_at":"2016-04-25T14:34:22Z","closed_at":"2016-04-25T14:34:22Z","body":"i've created this file:\r\nvert.txt:\r\n~~~\r\n0,3\r\n1,3\r\n2,3\r\n3,3\r\n4,3\r\n5,2\r\n6,2\r\n7,2\r\n8,2\r\n9,2\r\n~~~\r\n\r\nbut it gave this error:\r\n~~~\r\nsct_segment_graymatter -i data19_mean.nii.gz -s data19_mean_seg.nii.gz -use-levels int -vertfile vert.txt \r\n\r\nSpinal Cord Toolbox (version dev)\r\nRunning /Users/julien/code/spinalcordtoolbox/scripts/sct_segment_graymatter.py -i data19_mean.nii.gz -s data19_mean_seg.nii.gz -use-levels int -vertfile vert.txt\r\n  OK: vert.txt\r\n\r\nBuilding the appearance model...\r\n\r\nLoading a reduced common space (using a PCA) ...\r\n\r\n ---> sum of eigenvalues : 25601230.092\r\nkept eigenvalues (PCA space dimension)  : 47\r\n\r\n\r\n-------> IN PCA : \r\n\r\n-> kept_modes:[[  2.39757031e-16  -8.21900381e-17   2.93683807e-17 ...,   4.24317548e-17\r\n   -3.89564413e-17  -9.12340398e-17]\r\n [ -3.79002146e-16   3.60424298e-16  -3.35096744e-16 ...,  -2.00513278e-16\r\n   -6.37809817e-16  -7.37722667e-16]\r\n [  8.81995193e-17  -1.86772023e-17  -4.35252228e-17 ...,  -1.35261546e-16\r\n   -5.47676640e-16  -6.75053168e-16]\r\n ..., \r\n [  2.74755125e-41  -3.70707367e-41  -1.68272897e-41 ...,   4.54141770e-42\r\n   -7.48202727e-41   4.22570827e-41]\r\n [  1.75581766e-41  -3.29436870e-41   2.66076533e-41 ...,  -5.07662462e-41\r\n    2.05743668e-40   1.53877001e-40]\r\n [ -1.10186724e-44   3.10061910e-42  -4.61501418e-43 ...,   9.75283339e-42\r\n    3.05073686e-42   8.30540278e-42]]\r\n\r\n-> kept_eigenval:47\r\nmkdir tmp_data19_mean_160422154120_639188/\r\n\r\nDoing target pre-processing ...\r\ncp vert.txt tmp_data19_mean_160422154120_639188//vert.txt\r\ncp data19_mean.nii.gz tmp_data19_mean_160422154120_639188//target.nii.gz\r\ncp data19_mean_seg.nii.gz tmp_data19_mean_160422154120_639188//target_sc_seg.nii.gz\r\nError: make sure vert.txt is an image.\r\n/Users/julien/code/spinalcordtoolbox/scripts/msct_image.py, line 99\r\n~~~"}}