{"action":"created","issue":{"url":"https://api.github.com/repos/Mouse-Imaging-Centre/pydpiper/issues/285","repository_url":"https://api.github.com/repos/Mouse-Imaging-Centre/pydpiper","labels_url":"https://api.github.com/repos/Mouse-Imaging-Centre/pydpiper/issues/285/labels{/name}","comments_url":"https://api.github.com/repos/Mouse-Imaging-Centre/pydpiper/issues/285/comments","events_url":"https://api.github.com/repos/Mouse-Imaging-Centre/pydpiper/issues/285/events","html_url":"https://github.com/Mouse-Imaging-Centre/pydpiper/issues/285","id":189207397,"number":285,"title":"twolevel_model_building protocols","user":{"login":"DJFernandes","id":17433141,"avatar_url":"https://avatars.githubusercontent.com/u/17433141?v=3","gravatar_id":"","url":"https://api.github.com/users/DJFernandes","html_url":"https://github.com/DJFernandes","followers_url":"https://api.github.com/users/DJFernandes/followers","following_url":"https://api.github.com/users/DJFernandes/following{/other_user}","gists_url":"https://api.github.com/users/DJFernandes/gists{/gist_id}","starred_url":"https://api.github.com/users/DJFernandes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DJFernandes/subscriptions","organizations_url":"https://api.github.com/users/DJFernandes/orgs","repos_url":"https://api.github.com/users/DJFernandes/repos","events_url":"https://api.github.com/users/DJFernandes/events{/privacy}","received_events_url":"https://api.github.com/users/DJFernandes/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-11-14T19:47:41Z","updated_at":"2016-11-14T20:26:30Z","closed_at":null,"body":"I seem to be having issues with protocols:\r\nFirst, I ran...\r\n`twolevel_model_building.py --pipeline-name=exp1 --num-executors=40 --init-model=/hpf/largeprojects/MICe/tools/initial-models/Pydpiper-pride-of-models/p36/p36_MEMRI_mouse_brain.mnc --registration-method=mincANTS  --csv-file files.csv`\r\n\r\nand got the following error:\r\n\r\n`NotImplementedError: ('You need to supply a protocol at the moment.  Sorry!', 'occurred at index 0')`\r\n\r\nI then ran...\r\n`twolevel_model_building.py --pipeline-name=exp1 --num-executors=40 --init-model=/hpf/largeprojects/MICe/tools/initial-models/Pydpiper-pride-of-models/p36/p36_MEMRI_mouse_brain.mnc --registration-method=mincANTS --lsq6-protocol /hpf/largeprojects/MICe/tools/protocols/linear/Pydpiper_in_vivo_scans_minctracc_center_estimation.csv --lsq12-protocol /hpf/largeprojects/MICe/tools/protocols/linear/Pydpiper_testing_default_lsq12.csv --nlin-protocol /hpf/largeprojects/MICe/tools/protocols/nonlinear/Pydpiper_mincANTS_standard_90_micron.pl --csv-file files.csv`\r\n\r\nand \r\n\r\n`twolevel_model_building.py --pipeline-name=exp1 --num-executors=40 --init-model=/hpf/largeprojects/MICe/tools/initial-models/Pydpiper-pride-of-models/p36/p36_MEMRI_mouse_brain.mnc --registration-method=mincANTS --lsq6-protocol /hpf/largeprojects/MICe/tools/protocols/linear/Pydpiper_in_vivo_scans_minctracc_center_estimation.csv --lsq12-protocol /hpf/largeprojects/MICe/tools/protocols/linear/Pydpiper_testing_default_lsq12.csv --csv-file files.csv`\r\n\r\nand\r\n\r\n`twolevel_model_building.py --pipeline-name=exp1 --num-executors=40 --init-model=/hpf/largeprojects/MICe/tools/initial-models/Pydpiper-pride-of-models/p36/p36_MEMRI_mouse_brain.mnc --registration-method=mincANTS --lsq12-protocol /hpf/largeprojects/MICe/tools/protocols/linear/Pydpiper_testing_default_lsq12.csv --csv-file files.csv`\r\n\r\nAll of which gave me a different error:\r\n`ValueError: I'd use the MAGeT nlin protocol for masking as well but different programs are specified`\r\n\r\nWhich protocols should I be using?\r\n\r\nDirectory to replicate my commands is here:\r\n/hpf/largeprojects/MICe/dfernandes/social_behaviour_study/exp1/registration/two_level_pydpyper"},"comment":{"url":"https://api.github.com/repos/Mouse-Imaging-Centre/pydpiper/issues/comments/260452219","html_url":"https://github.com/Mouse-Imaging-Centre/pydpiper/issues/285#issuecomment-260452219","issue_url":"https://api.github.com/repos/Mouse-Imaging-Centre/pydpiper/issues/285","id":260452219,"user":{"login":"bcdarwin","id":164148,"avatar_url":"https://avatars.githubusercontent.com/u/164148?v=3","gravatar_id":"","url":"https://api.github.com/users/bcdarwin","html_url":"https://github.com/bcdarwin","followers_url":"https://api.github.com/users/bcdarwin/followers","following_url":"https://api.github.com/users/bcdarwin/following{/other_user}","gists_url":"https://api.github.com/users/bcdarwin/gists{/gist_id}","starred_url":"https://api.github.com/users/bcdarwin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bcdarwin/subscriptions","organizations_url":"https://api.github.com/users/bcdarwin/orgs","repos_url":"https://api.github.com/users/bcdarwin/repos","events_url":"https://api.github.com/users/bcdarwin/events{/privacy}","received_events_url":"https://api.github.com/users/bcdarwin/received_events","type":"User","site_admin":false},"created_at":"2016-11-14T20:26:30Z","updated_at":"2016-11-14T20:26:30Z","body":"--lsq12-protocol, --nlin-protocol, and --maget-nlin-protocol (or to use the same mincANTS protocol as for the nonlinear part of the build model, set --maget-registration-method=mincANTS, but this probably isn't what you want)"}}
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