{"action":"created","issue":{"url":"https://api.github.com/repos/Radiomics/pyradiomics/issues/360","repository_url":"https://api.github.com/repos/Radiomics/pyradiomics","labels_url":"https://api.github.com/repos/Radiomics/pyradiomics/issues/360/labels{/name}","comments_url":"https://api.github.com/repos/Radiomics/pyradiomics/issues/360/comments","events_url":"https://api.github.com/repos/Radiomics/pyradiomics/issues/360/events","html_url":"https://github.com/Radiomics/pyradiomics/issues/360","id":305490892,"number":360,"title":"Image extraction, segmentation, 2D, MRI cardiac images","user":{"login":"tommydino93","id":37182324,"avatar_url":"https://avatars2.githubusercontent.com/u/37182324?v=4","gravatar_id":"","url":"https://api.github.com/users/tommydino93","html_url":"https://github.com/tommydino93","followers_url":"https://api.github.com/users/tommydino93/followers","following_url":"https://api.github.com/users/tommydino93/following{/other_user}","gists_url":"https://api.github.com/users/tommydino93/gists{/gist_id}","starred_url":"https://api.github.com/users/tommydino93/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tommydino93/subscriptions","organizations_url":"https://api.github.com/users/tommydino93/orgs","repos_url":"https://api.github.com/users/tommydino93/repos","events_url":"https://api.github.com/users/tommydino93/events{/privacy}","received_events_url":"https://api.github.com/users/tommydino93/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":37,"created_at":"2018-03-15T10:21:21Z","updated_at":"2018-04-09T14:54:03Z","closed_at":null,"author_association":"NONE","body":"Hi everyone!\r\nSince I am about to begin a radiomic study ex novo, I just wanted to ask some questions so as to avoid annoying future problems. We will extract images and masks of interest next week from cardiac MRI with the intent of performing a future binary classification.\r\n\r\n1) Should I necessarily extract images in .nrrd format or the .dcm (DICOM) format is fine and easy to convert into .nrrd?\r\n\r\n2) Should the mask simply be an image with ones in the ROI and zeros outside of it?\r\n\r\n3) Since we will probably work with single slices (we will select the most significant 2D slice for each patient), how should I set my third dimension since pyradiomics wants volumes as input? Moreover, which are the features that I will be able to extract? (meaning...are there some features that are only applicable in 3D?)\r\n\r\n4) This is a strange question: one of the two ground truths of the final binary classification is myocarditis and this has the problem that it often doesn't appear as a single concentrated region in the image. As a matter of fact, since it is an inflammatory phenomenon, it often appears as sparse sub regions on the image. How should we deal with masks in this case? Should we just select the biggest region of inflammation? Should we somehow average the inflamed regions?\r\n\r\nThank you very much in advance,\r\nTommaso\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/Radiomics/pyradiomics/issues/comments/379780592","html_url":"https://github.com/Radiomics/pyradiomics/issues/360#issuecomment-379780592","issue_url":"https://api.github.com/repos/Radiomics/pyradiomics/issues/360","id":379780592,"user":{"login":"fedorov","id":313942,"avatar_url":"https://avatars1.githubusercontent.com/u/313942?v=4","gravatar_id":"","url":"https://api.github.com/users/fedorov","html_url":"https://github.com/fedorov","followers_url":"https://api.github.com/users/fedorov/followers","following_url":"https://api.github.com/users/fedorov/following{/other_user}","gists_url":"https://api.github.com/users/fedorov/gists{/gist_id}","starred_url":"https://api.github.com/users/fedorov/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fedorov/subscriptions","organizations_url":"https://api.github.com/users/fedorov/orgs","repos_url":"https://api.github.com/users/fedorov/repos","events_url":"https://api.github.com/users/fedorov/events{/privacy}","received_events_url":"https://api.github.com/users/fedorov/received_events","type":"User","site_admin":false},"created_at":"2018-04-09T14:54:03Z","updated_at":"2018-04-09T14:54:03Z","author_association":"OWNER","body":"I am not an NRRD expert, but it looks to me like an invalid header. Indeed, it looks inconsistent to have 3 components for the direction vectors, but only 2 vectors, and only 2 dimensions of the image.\r\n\r\nIs your dataset volumetric, or is it a single slice? If it is supposed to be volumetric, I would really recommend you go back and try other converters. It maye well be that ImageJ NRRD writing may have issues. You could also ask ImageJ support.\r\n\r\nIf you want to just try something, you can maybe manually modify this line\r\n```\r\nspace directions: (0.89843749,0,0) (0,0.89843749,0)\r\n```\r\n\r\nto this:\r\n```\r\nspace directions: (0.89843749,0) (0,0.89843749)\r\n```\r\nMaybe it will fix the ITK issue ..."}}
{"actor":{"display_login":"fedorov"}}