{"action":"created","issue":{"url":"https://api.github.com/repos/TIGRLab/admin/issues/581","repository_url":"https://api.github.com/repos/TIGRLab/admin","labels_url":"https://api.github.com/repos/TIGRLab/admin/issues/581/labels{/name}","comments_url":"https://api.github.com/repos/TIGRLab/admin/issues/581/comments","events_url":"https://api.github.com/repos/TIGRLab/admin/issues/581/events","html_url":"https://github.com/TIGRLab/admin/issues/581","id":159977792,"number":581,"title":"DTIprep","user":{"login":"arash-n","id":11356980,"avatar_url":"https://avatars.githubusercontent.com/u/11356980?v=3","gravatar_id":"","url":"https://api.github.com/users/arash-n","html_url":"https://github.com/arash-n","followers_url":"https://api.github.com/users/arash-n/followers","following_url":"https://api.github.com/users/arash-n/following{/other_user}","gists_url":"https://api.github.com/users/arash-n/gists{/gist_id}","starred_url":"https://api.github.com/users/arash-n/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arash-n/subscriptions","organizations_url":"https://api.github.com/users/arash-n/orgs","repos_url":"https://api.github.com/users/arash-n/repos","events_url":"https://api.github.com/users/arash-n/events{/privacy}","received_events_url":"https://api.github.com/users/arash-n/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"navonacalarco","id":13733654,"avatar_url":"https://avatars.githubusercontent.com/u/13733654?v=3","gravatar_id":"","url":"https://api.github.com/users/navonacalarco","html_url":"https://github.com/navonacalarco","followers_url":"https://api.github.com/users/navonacalarco/followers","following_url":"https://api.github.com/users/navonacalarco/following{/other_user}","gists_url":"https://api.github.com/users/navonacalarco/gists{/gist_id}","starred_url":"https://api.github.com/users/navonacalarco/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/navonacalarco/subscriptions","organizations_url":"https://api.github.com/users/navonacalarco/orgs","repos_url":"https://api.github.com/users/navonacalarco/repos","events_url":"https://api.github.com/users/navonacalarco/events{/privacy}","received_events_url":"https://api.github.com/users/navonacalarco/received_events","type":"User","site_admin":false},"assignees":[{"login":"navonacalarco","id":13733654,"avatar_url":"https://avatars.githubusercontent.com/u/13733654?v=3","gravatar_id":"","url":"https://api.github.com/users/navonacalarco","html_url":"https://github.com/navonacalarco","followers_url":"https://api.github.com/users/navonacalarco/followers","following_url":"https://api.github.com/users/navonacalarco/following{/other_user}","gists_url":"https://api.github.com/users/navonacalarco/gists{/gist_id}","starred_url":"https://api.github.com/users/navonacalarco/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/navonacalarco/subscriptions","organizations_url":"https://api.github.com/users/navonacalarco/orgs","repos_url":"https://api.github.com/users/navonacalarco/repos","events_url":"https://api.github.com/users/navonacalarco/events{/privacy}","received_events_url":"https://api.github.com/users/navonacalarco/received_events","type":"User","site_admin":false}],"milestone":null,"comments":12,"created_at":"2016-06-13T15:26:44Z","updated_at":"2016-06-27T22:56:37Z","closed_at":null,"body":"Hey guys,\r\n\r\nI will be using DTIprep to preprocess PACTMD which requires nrrd files. I was wondering if you can convert the DICOMs for multi-shell data to nrrd. In addition, please let me know how we generally use DTIprep (e.g. a protocol, GUI vs. command line, etc.). \r\n\r\nCheers,\r\nArash "},"comment":{"url":"https://api.github.com/repos/TIGRLab/admin/issues/comments/228900650","html_url":"https://github.com/TIGRLab/admin/issues/581#issuecomment-228900650","issue_url":"https://api.github.com/repos/TIGRLab/admin/issues/581","id":228900650,"user":{"login":"josephdviviano","id":4142570,"avatar_url":"https://avatars.githubusercontent.com/u/4142570?v=3","gravatar_id":"","url":"https://api.github.com/users/josephdviviano","html_url":"https://github.com/josephdviviano","followers_url":"https://api.github.com/users/josephdviviano/followers","following_url":"https://api.github.com/users/josephdviviano/following{/other_user}","gists_url":"https://api.github.com/users/josephdviviano/gists{/gist_id}","starred_url":"https://api.github.com/users/josephdviviano/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/josephdviviano/subscriptions","organizations_url":"https://api.github.com/users/josephdviviano/orgs","repos_url":"https://api.github.com/users/josephdviviano/repos","events_url":"https://api.github.com/users/josephdviviano/events{/privacy}","received_events_url":"https://api.github.com/users/josephdviviano/received_events","type":"User","site_admin":false},"created_at":"2016-06-27T22:56:37Z","updated_at":"2016-06-27T22:56:37Z","body":"@arash-n see this file: /archive/data-2.0/DTI/CMH/README.md\r\n\r\nWe've been through this already and we're pretty sure the data isn't appropriate for data-2.0. You're welcome to work with the DICOMs if you want.\r\n\r\n- Thu May  7 16:44:43 EDT 2015\r\n\r\n  After discussion with @djrotenberg and @josephdviviano I think I can\r\n  summarize the DTI situation as this:\r\n\r\n  - Some subjects have 32 direction + 3 B0 DTI images which are the standard GE\r\n    DTI acquisition, and these are a problem for us; they are mistakenly\r\n    acquired after service to the scanner reset the configuration for our\r\n    protocol.\r\n\r\n  - The b=1000 33 direction + 2 B0 DTI images are what we should be acquiring\r\n    as part of the DTIG protocol. This is according to Yogesh Rathi'ss\r\n    specifications for doing multi-shell DTI properly.\r\n\r\n  Therefore, all images that have 32 directions are probably garbage (since the\r\n  60 direction DTI scan covers the same information, at least for b=1000). I've\r\n  replaced the DTI/CMH gold standard with subject scan DTI_CMH_H011_02_01 since\r\n  this was the first scan acquired correctly with 33 directions. All other 33\r\n  direction DTI scans conform header/bvec/bval-wise to this scan (which is\r\n  great news).\r\n\r\n  I've also blacklisted all of the 32 direction scans, and removed them from\r\n  the data folder.\r\n\r\n  See also: https://github.com/TIGRLab/data/issues/28\r\n\r\n  @jp\r\n\r\n\r\n"}}
{"actor":{"display_login":"josephdviviano"}}