{"action":"closed","issue":{"url":"https://api.github.com/repos/gallantlab/pycortex/issues/126","labels_url":"https://api.github.com/repos/gallantlab/pycortex/issues/126/labels{/name}","comments_url":"https://api.github.com/repos/gallantlab/pycortex/issues/126/comments","events_url":"https://api.github.com/repos/gallantlab/pycortex/issues/126/events","html_url":"https://github.com/gallantlab/pycortex/issues/126","id":91100682,"number":126,"title":"align.automatic and freesurfer.import_subj integration","user":{"login":"rfarouni","id":9895004,"avatar_url":"https://avatars.githubusercontent.com/u/9895004?v=3","gravatar_id":"","url":"https://api.github.com/users/rfarouni","html_url":"https://github.com/rfarouni","followers_url":"https://api.github.com/users/rfarouni/followers","following_url":"https://api.github.com/users/rfarouni/following{/other_user}","gists_url":"https://api.github.com/users/rfarouni/gists{/gist_id}","starred_url":"https://api.github.com/users/rfarouni/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rfarouni/subscriptions","organizations_url":"https://api.github.com/users/rfarouni/orgs","repos_url":"https://api.github.com/users/rfarouni/repos","events_url":"https://api.github.com/users/rfarouni/events{/privacy}","received_events_url":"https://api.github.com/users/rfarouni/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-06-25T23:14:03Z","updated_at":"2015-07-09T22:50:13Z","closed_at":"2015-07-09T22:50:13Z","body":"When I run align.automatic after I import a subject from Freesurfer, pycortex  runs FSL to generate a brain mask, a white matter mask, and a segemented brain. But are these steps needed If Freesurfer has generated the required files already, namely, brainmask.mgz (or brain.mgz), wm.mgz, and  filled.mgz  according to [this]( https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.3) list. Is there a reason they are not imported by import_subj function?\r\n\r\nThanks"}}