{"action":"created","issue":{"url":"https://api.github.com/repos/poldracklab/fmriprep/issues/1341","repository_url":"https://api.github.com/repos/poldracklab/fmriprep","labels_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/1341/labels{/name}","comments_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/1341/comments","events_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/1341/events","html_url":"https://github.com/poldracklab/fmriprep/issues/1341","id":373047654,"node_id":"MDU6SXNzdWUzNzMwNDc2NTQ=","number":1341,"title":"parts of skull missing from T1w image during acquisition","user":{"login":"bababen","id":21152566,"node_id":"MDQ6VXNlcjIxMTUyNTY2","avatar_url":"https://avatars1.githubusercontent.com/u/21152566?v=4","gravatar_id":"","url":"https://api.github.com/users/bababen","html_url":"https://github.com/bababen","followers_url":"https://api.github.com/users/bababen/followers","following_url":"https://api.github.com/users/bababen/following{/other_user}","gists_url":"https://api.github.com/users/bababen/gists{/gist_id}","starred_url":"https://api.github.com/users/bababen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bababen/subscriptions","organizations_url":"https://api.github.com/users/bababen/orgs","repos_url":"https://api.github.com/users/bababen/repos","events_url":"https://api.github.com/users/bababen/events{/privacy}","received_events_url":"https://api.github.com/users/bababen/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-10-23T14:59:56Z","updated_at":"2018-10-23T16:01:51Z","closed_at":"2018-10-23T16:01:51Z","author_association":"NONE","body":"I had a subject with a large head and the T1w image includes the brain but not all of the skull.  I tried running the subject through fmriprep as usual with the following command:\r\n\r\ndocker run --rm -it -v /home/ben/license.txt:/opt/freesurfer/license.txt:ro -v /mnt/barracuda/utmc_pilot2_processed:/data:ro -v /mnt/barracuda/utmc_pilot2_processed/fmriprep_output:/out poldracklab/fmriprep:1.1.0 /data /out participant --ignore slicetiming --use-syn-sdc --use-aroma --output-space T1w template fsaverage fsnative --participant_label 203\r\n\r\nHere is the error that pops up before it stops:\r\n\r\n[Node] Error on \"fmriprep_wf.single_subject_203_wf.summary\" (/root/src/fmriprep/work/fmriprep_wf/single_subject_203_wf/summary)\r\n\r\nMy best guess it is having trouble with the T1w image (see below).  But I'm not sure how to salvage this subject.\r\n\r\n![screenshot](https://user-images.githubusercontent.com/21152566/47369647-28183d00-d6b2-11e8-92c2-66e4880ec496.png)\r\n\r\nI'm not sure how best to handle "},"comment":{"url":"https://api.github.com/repos/poldracklab/fmriprep/issues/comments/432309937","html_url":"https://github.com/poldracklab/fmriprep/issues/1341#issuecomment-432309937","issue_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/1341","id":432309937,"node_id":"MDEyOklzc3VlQ29tbWVudDQzMjMwOTkzNw==","user":{"login":"bababen","id":21152566,"node_id":"MDQ6VXNlcjIxMTUyNTY2","avatar_url":"https://avatars1.githubusercontent.com/u/21152566?v=4","gravatar_id":"","url":"https://api.github.com/users/bababen","html_url":"https://github.com/bababen","followers_url":"https://api.github.com/users/bababen/followers","following_url":"https://api.github.com/users/bababen/following{/other_user}","gists_url":"https://api.github.com/users/bababen/gists{/gist_id}","starred_url":"https://api.github.com/users/bababen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bababen/subscriptions","organizations_url":"https://api.github.com/users/bababen/orgs","repos_url":"https://api.github.com/users/bababen/repos","events_url":"https://api.github.com/users/bababen/events{/privacy}","received_events_url":"https://api.github.com/users/bababen/received_events","type":"User","site_admin":false},"created_at":"2018-10-23T16:01:51Z","updated_at":"2018-10-23T16:01:51Z","author_association":"NONE","body":"Ah, I had a double underscore in the filename for the BOLD images.  It is running now.  I am still concerned the T1w image quality might cause some trouble with the recon-all, but we'll see I suppose.\r\n\r\nSorry for the simple error but thanks for the help!"}}
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