{"action":"created","issue":{"url":"https://api.github.com/repos/poldracklab/fmriprep/issues/913","repository_url":"https://api.github.com/repos/poldracklab/fmriprep","labels_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/913/labels{/name}","comments_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/913/comments","events_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/913/events","html_url":"https://github.com/poldracklab/fmriprep/issues/913","id":285188058,"node_id":"MDU6SXNzdWUyODUxODgwNTg=","number":913,"title":"MP2RAGE skull-stripping","user":{"login":"oesteban","id":598470,"node_id":"MDQ6VXNlcjU5ODQ3MA==","avatar_url":"https://avatars2.githubusercontent.com/u/598470?v=4","gravatar_id":"","url":"https://api.github.com/users/oesteban","html_url":"https://github.com/oesteban","followers_url":"https://api.github.com/users/oesteban/followers","following_url":"https://api.github.com/users/oesteban/following{/other_user}","gists_url":"https://api.github.com/users/oesteban/gists{/gist_id}","starred_url":"https://api.github.com/users/oesteban/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/oesteban/subscriptions","organizations_url":"https://api.github.com/users/oesteban/orgs","repos_url":"https://api.github.com/users/oesteban/repos","events_url":"https://api.github.com/users/oesteban/events{/privacy}","received_events_url":"https://api.github.com/users/oesteban/received_events","type":"User","site_admin":false},"labels":[{"id":645743847,"node_id":"MDU6TGFiZWw2NDU3NDM4NDc=","url":"https://api.github.com/repos/poldracklab/fmriprep/labels/help%20wanted","name":"help wanted","color":"0e8a16","default":true},{"id":538829709,"node_id":"MDU6TGFiZWw1Mzg4Mjk3MDk=","url":"https://api.github.com/repos/poldracklab/fmriprep/labels/potential%20hackathon%20project","name":"potential hackathon project","color":"006b75","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-12-30T06:55:47Z","updated_at":"2018-07-13T12:05:46Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"Make MP2RAGE amenable to `antsBrainExtraction.sh`. One possibility, as @chrisfilo mentioned in #431 is using the inversion echoes https://github.com/poldracklab/pydeface/pull/15.\r\n"},"comment":{"url":"https://api.github.com/repos/poldracklab/fmriprep/issues/comments/404813943","html_url":"https://github.com/poldracklab/fmriprep/issues/913#issuecomment-404813943","issue_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/913","id":404813943,"node_id":"MDEyOklzc3VlQ29tbWVudDQwNDgxMzk0Mw==","user":{"login":"tknapen","id":436593,"node_id":"MDQ6VXNlcjQzNjU5Mw==","avatar_url":"https://avatars0.githubusercontent.com/u/436593?v=4","gravatar_id":"","url":"https://api.github.com/users/tknapen","html_url":"https://github.com/tknapen","followers_url":"https://api.github.com/users/tknapen/followers","following_url":"https://api.github.com/users/tknapen/following{/other_user}","gists_url":"https://api.github.com/users/tknapen/gists{/gist_id}","starred_url":"https://api.github.com/users/tknapen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tknapen/subscriptions","organizations_url":"https://api.github.com/users/tknapen/orgs","repos_url":"https://api.github.com/users/tknapen/repos","events_url":"https://api.github.com/users/tknapen/events{/privacy}","received_events_url":"https://api.github.com/users/tknapen/received_events","type":"User","site_admin":false},"created_at":"2018-07-13T12:05:46Z","updated_at":"2018-07-13T12:05:46Z","author_association":"NONE","body":"I'm working on this for a 7T dataset we have, for which the only anatomicals are MP2RAGE images. My workflow is to take the magnitude image of the second inversion, and thresholding that after running it through ANTS' `N4BiasFieldCorrection`. This creates a mask that I apply to the `_T1w.nii.gz` image. For now, I'm determining the threshold by eye, but it should be trivial to automate that (http://nilearn.github.io/modules/generated/nilearn.masking.compute_background_mask.html#nilearn-masking-compute-background-mask for example). Should I work on a pull request, working from the BIDS MP2RAGE extension proposal (https://groups.google.com/forum/#!topic/bids-discussion/wtolT5qPjy0), or are you already working on a similar feature (as this issue is from 7 months ago)?  "}}
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