{"action":"created","issue":{"url":"https://api.github.com/repos/CobraLab/atlases/issues/6","repository_url":"https://api.github.com/repos/CobraLab/atlases","labels_url":"https://api.github.com/repos/CobraLab/atlases/issues/6/labels{/name}","comments_url":"https://api.github.com/repos/CobraLab/atlases/issues/6/comments","events_url":"https://api.github.com/repos/CobraLab/atlases/issues/6/events","html_url":"https://github.com/CobraLab/atlases/issues/6","id":174840191,"number":6,"title":"for your consideration: support other formats","user":{"login":"fedorov","id":313942,"avatar_url":"https://avatars.githubusercontent.com/u/313942?v=3","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},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":22,"created_at":"2016-09-02T20:19:20Z","updated_at":"2016-09-13T18:58:21Z","closed_at":null,"body":"It is not very trivial to convert .mnc to other formats. There are many questions about going from mnc to other formats if one googles (and I did), but there are no binary tools for conversion. Perhaps the reason is that [MINC software has LGPL license](http://slicer-devel.65872.n3.nabble.com/Reading-MINC-files-tp2505809p2505844.html) Anyway, I've just been through the exercise to help a colleague of mine with this task, and it took much longer than I thought, so I decided to spend this extra bit of time to document and report to you.\r\n\r\nI think your atlas might be more useable to the community if you provided labels in formats other than mnc. I attach the file I converted for my colleague so you can use it for your purposes.\r\n\r\nThe recipe I used to convert:\r\n1. have a build of [3D Slicer](https://github.com/slicer/slicer) handy\r\n2. In the ITKv4-build directory in Slicer super-build change the variable `Module_ITKIOMINC` to on\r\n3. Run `make` from the Slicer superbuild directory - this will rebuild ITK and SimpleITK\r\n4. The MINC reader will still not be available in the Slicer \"Add data\" dialog to load MINC files, but you can do it via the python console: Ctrl+3 will show the python console, then you can do the following\r\n```\r\n>>> import SimpleITK as sitk\r\n>>> i=sitk.ReadImage(\"your_file.mnc\")\r\n>>> sitk.WriteImage(i,\"your_compressed_file.nrrd\",True)\r\n```\r\n\r\nResulting file: [thalamus_subdivisions.nrrd.zip](https://github.com/CobraLab/atlases/files/452844/thalamus_subdivisions.nrrd.zip)\r\n\r\nHopefully this is helpful to you, or other people who would have the same issue."},"comment":{"url":"https://api.github.com/repos/CobraLab/atlases/issues/comments/246787217","html_url":"https://github.com/CobraLab/atlases/issues/6#issuecomment-246787217","issue_url":"https://api.github.com/repos/CobraLab/atlases/issues/6","id":246787217,"user":{"login":"lassoan","id":307929,"avatar_url":"https://avatars.githubusercontent.com/u/307929?v=3","gravatar_id":"","url":"https://api.github.com/users/lassoan","html_url":"https://github.com/lassoan","followers_url":"https://api.github.com/users/lassoan/followers","following_url":"https://api.github.com/users/lassoan/following{/other_user}","gists_url":"https://api.github.com/users/lassoan/gists{/gist_id}","starred_url":"https://api.github.com/users/lassoan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lassoan/subscriptions","organizations_url":"https://api.github.com/users/lassoan/orgs","repos_url":"https://api.github.com/users/lassoan/repos","events_url":"https://api.github.com/users/lassoan/events{/privacy}","received_events_url":"https://api.github.com/users/lassoan/received_events","type":"User","site_admin":false},"created_at":"2016-09-13T18:58:21Z","updated_at":"2016-09-13T18:58:21Z","body":"If you have a patch then let me know and I can test it.\r\n\r\nYou would need to set up a nightly Windows build or convince some ITK build machine developers to enable MINC so that you can see when something breaks."}}
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