{"action":"created","issue":{"url":"https://api.github.com/repos/poldracklab/fitlins/issues/56","repository_url":"https://api.github.com/repos/poldracklab/fitlins","labels_url":"https://api.github.com/repos/poldracklab/fitlins/issues/56/labels{/name}","comments_url":"https://api.github.com/repos/poldracklab/fitlins/issues/56/comments","events_url":"https://api.github.com/repos/poldracklab/fitlins/issues/56/events","html_url":"https://github.com/poldracklab/fitlins/issues/56","id":345300274,"node_id":"MDU6SXNzdWUzNDUzMDAyNzQ=","number":56,"title":"Missing values for confounds result in incorrect number of volumes","user":{"login":"adelavega","id":2774448,"node_id":"MDQ6VXNlcjI3NzQ0NDg=","avatar_url":"https://avatars0.githubusercontent.com/u/2774448?v=4","gravatar_id":"","url":"https://api.github.com/users/adelavega","html_url":"https://github.com/adelavega","followers_url":"https://api.github.com/users/adelavega/followers","following_url":"https://api.github.com/users/adelavega/following{/other_user}","gists_url":"https://api.github.com/users/adelavega/gists{/gist_id}","starred_url":"https://api.github.com/users/adelavega/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adelavega/subscriptions","organizations_url":"https://api.github.com/users/adelavega/orgs","repos_url":"https://api.github.com/users/adelavega/repos","events_url":"https://api.github.com/users/adelavega/events{/privacy}","received_events_url":"https://api.github.com/users/adelavega/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2018-07-27T17:05:34Z","updated_at":"2018-07-27T19:10:04Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"Occasionally, confounds have missing values\r\n\r\nFor example, for `SherlockMerlin` sub-28 `MerlinMovie` task, the first volume for `FrameWiseDisplacement` is `n/a`. \r\n\r\nRegardless of the reason, we should be prepared to deal with such values.\r\n\r\nCurrently, the `n/a` value will be skipped (by pybids), and result in an incorrect number of volumes in the confounds file passed to nistats. Resulting in this error: \r\n\r\n```\r\n  File \"/opt/conda/envs/neuro/lib/python3.6/site-packages/nistats/design_matrix.py\", line 351, in make_design_matrix\r\n    'time-frames: %d' % (add_regs.shape[0], np.size(frame_times)))\r\nAssertionError: Incorrect specification of additional regressors: length of regressors provided: 1026, number of time-frames: 1027\r\n```\r\n\r\nThe \"proper\" BIDS model solution would be the replace n/as with the mean value using  a transformation, but that seems too cumbersome. Probably best if fitlins does this if any n/as are detected in confounds."},"comment":{"url":"https://api.github.com/repos/poldracklab/fitlins/issues/comments/408512762","html_url":"https://github.com/poldracklab/fitlins/issues/56#issuecomment-408512762","issue_url":"https://api.github.com/repos/poldracklab/fitlins/issues/56","id":408512762,"node_id":"MDEyOklzc3VlQ29tbWVudDQwODUxMjc2Mg==","user":{"login":"adelavega","id":2774448,"node_id":"MDQ6VXNlcjI3NzQ0NDg=","avatar_url":"https://avatars0.githubusercontent.com/u/2774448?v=4","gravatar_id":"","url":"https://api.github.com/users/adelavega","html_url":"https://github.com/adelavega","followers_url":"https://api.github.com/users/adelavega/followers","following_url":"https://api.github.com/users/adelavega/following{/other_user}","gists_url":"https://api.github.com/users/adelavega/gists{/gist_id}","starred_url":"https://api.github.com/users/adelavega/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adelavega/subscriptions","organizations_url":"https://api.github.com/users/adelavega/orgs","repos_url":"https://api.github.com/users/adelavega/repos","events_url":"https://api.github.com/users/adelavega/events{/privacy}","received_events_url":"https://api.github.com/users/adelavega/received_events","type":"User","site_admin":false},"created_at":"2018-07-27T19:10:04Z","updated_at":"2018-07-27T19:10:04Z","author_association":"CONTRIBUTOR","body":"Ah, that makes sense, and yes we should zero fill. I guess the larger question of which component should handle this, and in which way (silently? by default? for which variables?)"}}
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