{"action":"created","issue":{"url":"https://api.github.com/repos/ME-ICA/tedana/issues/163","repository_url":"https://api.github.com/repos/ME-ICA/tedana","labels_url":"https://api.github.com/repos/ME-ICA/tedana/issues/163/labels{/name}","comments_url":"https://api.github.com/repos/ME-ICA/tedana/issues/163/comments","events_url":"https://api.github.com/repos/ME-ICA/tedana/issues/163/events","html_url":"https://github.com/ME-ICA/tedana/pull/163","id":386004913,"node_id":"MDExOlB1bGxSZXF1ZXN0MjM0ODQ3NDQ3","number":163,"title":"[REF] Remove unused arguments and simplify CLI","user":{"login":"tsalo","id":8228902,"node_id":"MDQ6VXNlcjgyMjg5MDI=","avatar_url":"https://avatars3.githubusercontent.com/u/8228902?v=4","gravatar_id":"","url":"https://api.github.com/users/tsalo","html_url":"https://github.com/tsalo","followers_url":"https://api.github.com/users/tsalo/followers","following_url":"https://api.github.com/users/tsalo/following{/other_user}","gists_url":"https://api.github.com/users/tsalo/gists{/gist_id}","starred_url":"https://api.github.com/users/tsalo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tsalo/subscriptions","organizations_url":"https://api.github.com/users/tsalo/orgs","repos_url":"https://api.github.com/users/tsalo/repos","events_url":"https://api.github.com/users/tsalo/events{/privacy}","received_events_url":"https://api.github.com/users/tsalo/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-11-30T02:00:39Z","updated_at":"2018-12-03T16:37:05Z","closed_at":null,"author_association":"MEMBER","pull_request":{"url":"https://api.github.com/repos/ME-ICA/tedana/pulls/163","html_url":"https://github.com/ME-ICA/tedana/pull/163","diff_url":"https://github.com/ME-ICA/tedana/pull/163.diff","patch_url":"https://github.com/ME-ICA/tedana/pull/163.patch"},"body":"<!---\r\nThis is a suggested pull request template for tedana.\r\nIt's designed to capture information we've found to be useful in reviewing pull requests.\r\n\r\nIf there is other information that would be helpful to include, please don't hesitate to add it!\r\n\r\nPlease also label your pull request with the relevant tags.\r\nSee here for more information and a list of available options:\r\nhttps://github.com/ME-ICA/tedana/blob/master/CONTRIBUTING.md#pull-requests\r\n-->\r\n\r\n<!-- Please indicate after the # which issue you're closing with this PR.\r\nThis is helpful for the maintainers AND will magically close the issue when this\r\npull request is merged!\r\nhttps://help.github.com/articles/closing-issues-using-keywords -->\r\nRef. #161, #162.\r\n\r\n<!-- Please give a brief overview of what has changed in the PR.\r\nIf you're not sure what to write, consider it a note to the maintainers to indicate\r\nwhat they should be looking for when they review the pull request. -->\r\nChanges proposed in this pull request:\r\n\r\n- Change maximum number of iterations for `tedica` from 200 to 5000.\r\n- Remove `conv` argument from `tedica` and workflow, to use FastICA's default tolerance.\r\n- Change argument `denoiseTEs` to `verbose`, which will be expanded to toggle output of many intermediate and less-used files, as discussed in #17.\r\n- Change argument `no_gscontrol` to `gscontrol` and change default behavior from performing GSR to _not_ performing GSR.\r\n- Remove arguments `filecsdata` and `strict`.\r\n- Add `global_denoise` argument that (currently) toggles minimum image regression, but which will ultimately set a number of processes, including GODEC, GSR, and T1c-GSR."},"comment":{"url":"https://api.github.com/repos/ME-ICA/tedana/issues/comments/443776337","html_url":"https://github.com/ME-ICA/tedana/pull/163#issuecomment-443776337","issue_url":"https://api.github.com/repos/ME-ICA/tedana/issues/163","id":443776337,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0Mzc3NjMzNw==","user":{"login":"tsalo","id":8228902,"node_id":"MDQ6VXNlcjgyMjg5MDI=","avatar_url":"https://avatars3.githubusercontent.com/u/8228902?v=4","gravatar_id":"","url":"https://api.github.com/users/tsalo","html_url":"https://github.com/tsalo","followers_url":"https://api.github.com/users/tsalo/followers","following_url":"https://api.github.com/users/tsalo/following{/other_user}","gists_url":"https://api.github.com/users/tsalo/gists{/gist_id}","starred_url":"https://api.github.com/users/tsalo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tsalo/subscriptions","organizations_url":"https://api.github.com/users/tsalo/orgs","repos_url":"https://api.github.com/users/tsalo/repos","events_url":"https://api.github.com/users/tsalo/events{/privacy}","received_events_url":"https://api.github.com/users/tsalo/received_events","type":"User","site_admin":false},"created_at":"2018-12-03T16:37:05Z","updated_at":"2018-12-03T16:37:05Z","author_association":"MEMBER","body":"That's from moving `--denoiseTEs` into `--verbose`. It's unrelated to the binder stuff."}}
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