{"action":"created","issue":{"url":"https://api.github.com/repos/neuropoly/template/issues/6","repository_url":"https://api.github.com/repos/neuropoly/template","labels_url":"https://api.github.com/repos/neuropoly/template/issues/6/labels{/name}","comments_url":"https://api.github.com/repos/neuropoly/template/issues/6/comments","events_url":"https://api.github.com/repos/neuropoly/template/issues/6/events","html_url":"https://github.com/neuropoly/template/issues/6","id":384933434,"node_id":"MDU6SXNzdWUzODQ5MzM0MzQ=","number":6,"title":"msct_image does not exist in the newer versions of SCT","user":{"login":"armaneshaghi","id":4290297,"node_id":"MDQ6VXNlcjQyOTAyOTc=","avatar_url":"https://avatars2.githubusercontent.com/u/4290297?v=4","gravatar_id":"","url":"https://api.github.com/users/armaneshaghi","html_url":"https://github.com/armaneshaghi","followers_url":"https://api.github.com/users/armaneshaghi/followers","following_url":"https://api.github.com/users/armaneshaghi/following{/other_user}","gists_url":"https://api.github.com/users/armaneshaghi/gists{/gist_id}","starred_url":"https://api.github.com/users/armaneshaghi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/armaneshaghi/subscriptions","organizations_url":"https://api.github.com/users/armaneshaghi/orgs","repos_url":"https://api.github.com/users/armaneshaghi/repos","events_url":"https://api.github.com/users/armaneshaghi/events{/privacy}","received_events_url":"https://api.github.com/users/armaneshaghi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-11-27T18:42:08Z","updated_at":"2018-11-29T18:46:35Z","closed_at":null,"author_association":"NONE","body":"@jcohenadad @benjamindeleener\r\nHas anyone managed to run the template scripts with the latest SCT? I get import error for `msct_image` which I think has been removed from SCT. \r\n\r\nAlternatively, does anyone know what version of SCT was used in the De Leneer et al (PAM 50) paper so I can probably get the template creation running with that (presumably old) version .\r\n\r\nThank you. "},"comment":{"url":"https://api.github.com/repos/neuropoly/template/issues/comments/442947712","html_url":"https://github.com/neuropoly/template/issues/6#issuecomment-442947712","issue_url":"https://api.github.com/repos/neuropoly/template/issues/6","id":442947712,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0Mjk0NzcxMg==","user":{"login":"armaneshaghi","id":4290297,"node_id":"MDQ6VXNlcjQyOTAyOTc=","avatar_url":"https://avatars2.githubusercontent.com/u/4290297?v=4","gravatar_id":"","url":"https://api.github.com/users/armaneshaghi","html_url":"https://github.com/armaneshaghi","followers_url":"https://api.github.com/users/armaneshaghi/followers","following_url":"https://api.github.com/users/armaneshaghi/following{/other_user}","gists_url":"https://api.github.com/users/armaneshaghi/gists{/gist_id}","starred_url":"https://api.github.com/users/armaneshaghi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/armaneshaghi/subscriptions","organizations_url":"https://api.github.com/users/armaneshaghi/orgs","repos_url":"https://api.github.com/users/armaneshaghi/repos","events_url":"https://api.github.com/users/armaneshaghi/events{/privacy}","received_events_url":"https://api.github.com/users/armaneshaghi/received_events","type":"User","site_admin":false},"created_at":"2018-11-29T18:46:35Z","updated_at":"2018-11-29T18:46:35Z","author_association":"NONE","body":"Thank you @charleygros. It has improved significantly. \r\n\r\nWhen I try to run the `pipeline.py` with SCT's Python. \r\n\r\n```\r\nStatus:  20%|####################8                                                                                   | 1.00/5.00 [00:21<01:26, 21.6s/B]\r\nStatus: 100%|########################################################################################################| 5.00/5.00 [01:45<00:00, 21.0s/B]\r\nStatus: 100%|#########################################################################################################| 5.00/5.00 [15:38<00:00, 187s/B]\r\nStatus:   0%|                                                                                                               | 0.00/5.00 [00:00<?, ?B/s]\r\n/mounts/auto/ipmsa/supertemplate/template/preprocessing.py:660: RuntimeWarning: divide by zero encountered in double_scalars\r\n  image_image_new.data[:, :, i] *= average_intensity / intensity_profiles[subject_name][i]\r\n/mounts/auto/ipmsa/supertemplate/template/preprocessing.py:660: RuntimeWarning: invalid value encountered in multiply\r\n  image_image_new.data[:, :, i] *= average_intensity / intensity_profiles[subject_name][i]\r\n\r\nTraceback (most recent call last):                                                                                   | 1.00/5.00 [00:01<00:07, 1.97s/B]\r\n  File \"template/pipeline.py\", line 41, in <module>##################################################################| 5.00/5.00 [00:10<00:00, 2.13s/B]\r\n    convert_data2mnc(dataset_info, contrast='t1')\r\n  File \"/mounts/auto/ipmsa/supertemplate/template/preprocessing.py\", line 688, in convert_data2mnc\r\n    path_template_mask = create_mask_template(dataset_info, contrast)\r\n  File \"/mounts/auto/ipmsa/supertemplate/template/preprocessing.py\", line 679, in create_mask_template\r\n    sct.run('nii2mnc ' + path_template + 'template_mask.nii.gz ' + ' ' + path_template + 'template_mask.mnc')\r\n  File \"/data/ipmsa/ipmsa/sct/scripts/sct_utils.py\", line 476, in run\r\n    raise RunError(output)\r\nsct_utils.RunError: ** ERROR: nifti_image_read(/mounts/auto/ipmsa/supertemplate/data/template/template_mask.nii.gz): bad dim[0]\r\nSegmentation fault (core dumped)\r\n```\r\n\r\nAny idea what to check next? I thought might be minc toolkit issue but that seems to have been installed."}}
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