{"action":"created","issue":{"url":"https://api.github.com/repos/Mouse-Imaging-Centre/pydpiper/issues/177","labels_url":"https://api.github.com/repos/Mouse-Imaging-Centre/pydpiper/issues/177/labels{/name}","comments_url":"https://api.github.com/repos/Mouse-Imaging-Centre/pydpiper/issues/177/comments","events_url":"https://api.github.com/repos/Mouse-Imaging-Centre/pydpiper/issues/177/events","html_url":"https://github.com/Mouse-Imaging-Centre/pydpiper/issues/177","id":57233784,"number":177,"title":"MBM.py registration with model mask fails where unmasked run succeeds","user":{"login":"gdevenyi","id":3001850,"avatar_url":"https://avatars.githubusercontent.com/u/3001850?v=3","gravatar_id":"","url":"https://api.github.com/users/gdevenyi","html_url":"https://github.com/gdevenyi","followers_url":"https://api.github.com/users/gdevenyi/followers","following_url":"https://api.github.com/users/gdevenyi/following{/other_user}","gists_url":"https://api.github.com/users/gdevenyi/gists{/gist_id}","starred_url":"https://api.github.com/users/gdevenyi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gdevenyi/subscriptions","organizations_url":"https://api.github.com/users/gdevenyi/orgs","repos_url":"https://api.github.com/users/gdevenyi/repos","events_url":"https://api.github.com/users/gdevenyi/events{/privacy}","received_events_url":"https://api.github.com/users/gdevenyi/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":14,"created_at":"2015-02-10T20:44:15Z","updated_at":"2015-04-08T20:48:36Z","closed_at":"2015-04-08T20:48:36Z","body":"I ran an initial MBM.py with my raw input files to bootstrap a model, it ran file and the resulting average looked good. I then created a rough brain mask for the model and I'm attempting to re-run the MBM.py against the model with mask:\r\n```\r\nMBM.py --queue-type=sge --num-executors=120 --proc=1 --mem=3 \\\r\n    --verbose --pipeline-name=male-and-female-raw-masked \\\r\n    --lsq6-large-rotations --registration-method=mincANTS --calc-stats \\\r\n    --init-model=/data/chamal/projects/gabriel/rat-atlas/model/raw-model.mnc \\\r\n    --max-failed-executors 10 \\\r\n    --no-monitor-heartbeats \\\r\n    /data/chamal/projects/gabriel/rat-atlas/subjects/*.mnc\r\n```\r\n\r\nThe resulting registrations are terrible with no sensible average produced\r\n\r\nI've also tried the run with ``--lsq6-centre-estimation``(fails, can't find center) and ``--lsq6-simple`` (same result as large rotations.\r\n\r\nAm I doing something wrong? Perhaps the --lsq6-large-rotations step should be done without a mask?\r\n"},"comment":{"url":"https://api.github.com/repos/Mouse-Imaging-Centre/pydpiper/issues/comments/91032901","html_url":"https://github.com/Mouse-Imaging-Centre/pydpiper/issues/177#issuecomment-91032901","issue_url":"https://api.github.com/repos/Mouse-Imaging-Centre/pydpiper/issues/177","id":91032901,"user":{"login":"gdevenyi","id":3001850,"avatar_url":"https://avatars.githubusercontent.com/u/3001850?v=3","gravatar_id":"","url":"https://api.github.com/users/gdevenyi","html_url":"https://github.com/gdevenyi","followers_url":"https://api.github.com/users/gdevenyi/followers","following_url":"https://api.github.com/users/gdevenyi/following{/other_user}","gists_url":"https://api.github.com/users/gdevenyi/gists{/gist_id}","starred_url":"https://api.github.com/users/gdevenyi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gdevenyi/subscriptions","organizations_url":"https://api.github.com/users/gdevenyi/orgs","repos_url":"https://api.github.com/users/gdevenyi/repos","events_url":"https://api.github.com/users/gdevenyi/events{/privacy}","received_events_url":"https://api.github.com/users/gdevenyi/received_events","type":"User","site_admin":false},"created_at":"2015-04-08T20:48:36Z","updated_at":"2015-04-08T20:48:36Z","body":"Resolved as being an issue with \"large rotations\" not being large enough."}}