{"action":"created","issue":{"url":"https://api.github.com/repos/BIC-MNI/minc-tools/issues/42","repository_url":"https://api.github.com/repos/BIC-MNI/minc-tools","labels_url":"https://api.github.com/repos/BIC-MNI/minc-tools/issues/42/labels{/name}","comments_url":"https://api.github.com/repos/BIC-MNI/minc-tools/issues/42/comments","events_url":"https://api.github.com/repos/BIC-MNI/minc-tools/issues/42/events","html_url":"https://github.com/BIC-MNI/minc-tools/issues/42","id":160249305,"number":42,"title":"Feature Idea: Allow mnc2nii to use transform from a nifti file","user":{"login":"gdevenyi","id":3001850,"avatar_url":"https://avatars.githubusercontent.com/u/3001850?v=3","gravatar_id":"","url":"https://api.github.com/users/gdevenyi","html_url":"https://github.com/gdevenyi","followers_url":"https://api.github.com/users/gdevenyi/followers","following_url":"https://api.github.com/users/gdevenyi/following{/other_user}","gists_url":"https://api.github.com/users/gdevenyi/gists{/gist_id}","starred_url":"https://api.github.com/users/gdevenyi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gdevenyi/subscriptions","organizations_url":"https://api.github.com/users/gdevenyi/orgs","repos_url":"https://api.github.com/users/gdevenyi/repos","events_url":"https://api.github.com/users/gdevenyi/events{/privacy}","received_events_url":"https://api.github.com/users/gdevenyi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"rdvincent","id":1395526,"avatar_url":"https://avatars.githubusercontent.com/u/1395526?v=3","gravatar_id":"","url":"https://api.github.com/users/rdvincent","html_url":"https://github.com/rdvincent","followers_url":"https://api.github.com/users/rdvincent/followers","following_url":"https://api.github.com/users/rdvincent/following{/other_user}","gists_url":"https://api.github.com/users/rdvincent/gists{/gist_id}","starred_url":"https://api.github.com/users/rdvincent/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rdvincent/subscriptions","organizations_url":"https://api.github.com/users/rdvincent/orgs","repos_url":"https://api.github.com/users/rdvincent/repos","events_url":"https://api.github.com/users/rdvincent/events{/privacy}","received_events_url":"https://api.github.com/users/rdvincent/received_events","type":"User","site_admin":false},"milestone":null,"comments":4,"created_at":"2016-06-14T18:18:49Z","updated_at":"2016-06-15T13:44:18Z","closed_at":null,"body":"I have run into the following problem on many occasions:\r\n\r\n1) Receive from collaborator some kind of nifti file, which has been \"processed\" by SPM or FSL (aka has sform/qform data)\r\n2) Convert said file to minc using ``nii2mnc`` which properly handles sform/qform and provides me with a reasonably oriented minc file\r\n3) Process said file (for example, produce label files for it using magetbrain)\r\n4) Convert label files back to nifti using ``mnc2nii``\r\n5) Problem arises -> resulting nifti file is not in the space of the original nifti file, due to not having any transforms applied.\r\n\r\nProposed solution:\r\nProvide an option for ``mnc2nii`` which reads from a given \"reference\" NIFTI file the sform/qform information, and applies it during conversion so that the resulting file is in the right space."},"comment":{"url":"https://api.github.com/repos/BIC-MNI/minc-tools/issues/comments/226191099","html_url":"https://github.com/BIC-MNI/minc-tools/issues/42#issuecomment-226191099","issue_url":"https://api.github.com/repos/BIC-MNI/minc-tools/issues/42","id":226191099,"user":{"login":"gdevenyi","id":3001850,"avatar_url":"https://avatars.githubusercontent.com/u/3001850?v=3","gravatar_id":"","url":"https://api.github.com/users/gdevenyi","html_url":"https://github.com/gdevenyi","followers_url":"https://api.github.com/users/gdevenyi/followers","following_url":"https://api.github.com/users/gdevenyi/following{/other_user}","gists_url":"https://api.github.com/users/gdevenyi/gists{/gist_id}","starred_url":"https://api.github.com/users/gdevenyi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gdevenyi/subscriptions","organizations_url":"https://api.github.com/users/gdevenyi/orgs","repos_url":"https://api.github.com/users/gdevenyi/repos","events_url":"https://api.github.com/users/gdevenyi/events{/privacy}","received_events_url":"https://api.github.com/users/gdevenyi/received_events","type":"User","site_admin":false},"created_at":"2016-06-15T13:44:18Z","updated_at":"2016-06-15T13:44:18Z","body":"@andrewjanke I've played around with ana2mnc and related, I found I don't fully understand the NIFTI sform/qform maddness (maybe there's some docs somewhere that describe everything coherently?) Additionally, this dataset didn't have .mat, it had headers in the NIFTI file, which I don't think ana2mnc handles?\r\n\r\nMy major goal is a workflow that goes from/to NIFTI without special casing every dataset I get, I was hoping this might accomplish this."}}
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