{"action":"created","issue":{"url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/722","repository_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox","labels_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/722/labels{/name}","comments_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/722/comments","events_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/722/events","html_url":"https://github.com/neuropoly/spinalcordtoolbox/issues/722","id":130206116,"number":722,"title":"ERROR: no curved landmarks constructed...","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/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"},{"url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/labels/sct_straighten_spinalcord","name":"sct_straighten_spinalcord","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":32,"created_at":"2016-01-31T22:50:23Z","updated_at":"2016-02-04T01:35:46Z","closed_at":null,"body":"version: 2.2.2\r\n\r\ndata: sct_example_data\r\n\r\n~~~\r\nsct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l labels.nii.gz -param step=1,type=seg,algo=slicereg,metric=MeanSquares:step=2,type=seg,algo=bsplinesyn,iter=3,shrink=1,metric=MeanSquares:step=3,type=im,algo=syn,metric=CC,iter=1 -r 0\r\n\r\nCheck template files...\r\n  OK: /Users/julien/code/spinalcordtoolbox/data/template/MNI-Poly-AMU_T2.nii.gz\r\n  OK: /Users/julien/code/spinalcordtoolbox/data/template/landmarks_center.nii.gz\r\n  OK: /Users/julien/code/spinalcordtoolbox/data/template/MNI-Poly-AMU_cord.nii.gz\r\n\r\nCheck parameters:\r\n.. Data:                 t2.nii.gz\r\n.. Landmarks:            labels.nii.gz\r\n.. Segmentation:         t2_seg.nii.gz\r\n.. Path template:        /Users/julien/code/spinalcordtoolbox/data/template\r\n.. Path output:          \r\n.. Output type:          1\r\n.. Remove temp files:    0\r\n\r\nParameters for registration:\r\nStep #1\r\n.. Type #seg\r\n.. Algorithm................ slicereg\r\n.. Metric................... MeanSquares\r\n.. Number of iterations..... 10\r\n.. Shrink factor............ 1\r\n.. Smoothing factor......... 0\r\n.. Gradient step............ 0.5\r\n.. Degree of polynomial..... 3\r\nStep #2\r\n.. Type #seg\r\n.. Algorithm................ bsplinesyn\r\n.. Metric................... MeanSquares\r\n.. Number of iterations..... 3\r\n.. Shrink factor............ 1\r\n.. Smoothing factor......... 1\r\n.. Gradient step............ 0.5\r\n.. Degree of polynomial..... 3\r\nStep #3\r\n.. Type #im\r\n.. Algorithm................ syn\r\n.. Metric................... CC\r\n.. Number of iterations..... 1\r\n.. Shrink factor............ 1\r\n.. Smoothing factor......... 0\r\n.. Gradient step............ 0.5\r\n.. Degree of polynomial..... 3\r\n\r\nCheck input labels...\r\n\r\nCreate temporary folder...\r\nmkdir tmp.160131174836_949683/\r\n\r\nCopying input data to tmp folder and convert to nii...\r\nsct_convert -i t2.nii.gz -o tmp.160131174836_949683/data.nii\r\nsct_convert -i t2_seg.nii.gz -o tmp.160131174836_949683/seg.nii.gz\r\nsct_convert -i labels.nii.gz -o tmp.160131174836_949683/label.nii.gz\r\nsct_convert -i /Users/julien/code/spinalcordtoolbox/data/template/MNI-Poly-AMU_T2.nii.gz -o tmp.160131174836_949683/template.nii\r\nsct_convert -i /Users/julien/code/spinalcordtoolbox/data/template/MNI-Poly-AMU_cord.nii.gz -o tmp.160131174836_949683/template_seg.nii.gz\r\nsct_convert -i /Users/julien/code/spinalcordtoolbox/data/template/landmarks_center.nii.gz -o tmp.160131174836_949683/template_label.nii.gz\r\n\r\nSmooth segmentation...\r\nsct_maths -i seg.nii.gz -smooth 1.5 -o seg_smooth.nii.gz\r\n\r\nResample data to 1mm isotropic...\r\nsct_resample -i data.nii -mm 1.0x1.0x1.0 -x linear -o data_1mm.nii\r\nsct_resample -i seg_smooth.nii.gz -mm 1.0x1.0x1.0 -x linear -o seg_smooth_1mm.nii.gz\r\nPosition=(210,179,26) -- Value= 2\r\nPosition=(238,67,27) -- Value= 9\r\nUseful notation:\r\n210,179,26,2:238,67,27,9\r\nsct_label_utils -i data_1mm.nii -p create -coord 210,179,26,2:238,67,27,9 -v 1 -o label_1mm.nii.gz\r\n\r\nChange orientation of input images to RPI...\r\nsct_image -i data_1mm.nii -setorient RPI -o data_1mm_rpi.nii\r\nsct_image -i seg_smooth_1mm.nii.gz -setorient RPI -o seg_smooth_1mm_rpi.nii.gz\r\nsct_image -i label_1mm.nii.gz -setorient RPI -o label_1mm_rpi.nii.gz\r\nsct_crop_image -i seg_smooth_1mm_rpi.nii.gz -o seg_smooth_1mm_rpi_crop.nii.gz -dim 2 -bzmax\r\n\r\nStraighten the spinal cord using centerline/segmentation...\r\nsct_straighten_spinalcord -i seg_smooth_1mm_rpi_crop.nii.gz -s seg_smooth_1mm_rpi_crop.nii.gz -o seg_smooth_1mm_rpi_crop_straight.nii.gz -qc 0 -r 0 -v 1 \r\n/Users/julien/code/spinalcordtoolbox\r\n\r\nCheck input arguments:\r\n  Input volume ...................... seg_smooth_1mm_rpi_crop.nii.gz\r\n  Centerline ........................ seg_smooth_1mm_rpi_crop.nii.gz\r\n  Final interpolation ............... spline\r\n  Verbose ........................... 1\r\n\r\n\r\nCreate temporary folder...\r\nmkdir tmp.160131174846_778885/\r\n\r\nCopy files to tmp folder...\r\nsct_convert -i seg_smooth_1mm_rpi_crop.nii.gz -o tmp.160131174846_778885/data.nii\r\nsct_convert -i seg_smooth_1mm_rpi_crop.nii.gz -o tmp.160131174846_778885/centerline.nii.gz\r\ncp data.nii data_1mm.nii\r\ncp centerline.nii.gz centerline_1mm.nii.gz\r\n\r\nOrient centerline to RPI orientation...\r\nsct_image -i centerline_1mm.nii.gz -setorient RPI -o centerline_1mm_rpi.nii.gz\r\n\r\nGet dimensions...\r\n.. matrix size: 52 x 384 x 185\r\n.. voxel size:  1.0mm x 1.0mm x 1.0mm\r\n\r\nSmooth centerline/segmentation...\r\n.. Get center of mass of the centerline/segmentation...\r\n.. Smoothing algo = hanning\r\n.. Windows length = 50\r\n\r\nGet coordinates of landmarks along curved centerline...\r\nError during straightening on line 577\r\nERROR: no curved landmarks constructed...\r\n/Users/julien/code/spinalcordtoolbox/scripts/sct_utils.py, line 98\r\n~~~"},"comment":{"url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/comments/179566647","html_url":"https://github.com/neuropoly/spinalcordtoolbox/issues/722#issuecomment-179566647","issue_url":"https://api.github.com/repos/neuropoly/spinalcordtoolbox/issues/722","id":179566647,"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},"created_at":"2016-02-04T01:35:46Z","updated_at":"2016-02-04T01:35:46Z","body":"OK it solved the problem!!"}}