{"action":"created","issue":{"url":"https://api.github.com/repos/FCP-INDI/C-PAC/issues/447","repository_url":"https://api.github.com/repos/FCP-INDI/C-PAC","labels_url":"https://api.github.com/repos/FCP-INDI/C-PAC/issues/447/labels{/name}","comments_url":"https://api.github.com/repos/FCP-INDI/C-PAC/issues/447/comments","events_url":"https://api.github.com/repos/FCP-INDI/C-PAC/issues/447/events","html_url":"https://github.com/FCP-INDI/C-PAC/issues/447","id":59563938,"number":447,"title":"C-PAC's workflow construction will fail if given an incorrect string for the regOption","user":{"login":"jpellman","id":5000591,"avatar_url":"https://avatars.githubusercontent.com/u/5000591?v=3","gravatar_id":"","url":"https://api.github.com/users/jpellman","html_url":"https://github.com/jpellman","followers_url":"https://api.github.com/users/jpellman/followers","following_url":"https://api.github.com/users/jpellman/following{/other_user}","gists_url":"https://api.github.com/users/jpellman/gists{/gist_id}","starred_url":"https://api.github.com/users/jpellman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jpellman/subscriptions","organizations_url":"https://api.github.com/users/jpellman/orgs","repos_url":"https://api.github.com/users/jpellman/repos","events_url":"https://api.github.com/users/jpellman/events{/privacy}","received_events_url":"https://api.github.com/users/jpellman/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/FCP-INDI/C-PAC/labels/bug","name":"bug","color":"e11d21"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2015-03-02T22:41:21Z","updated_at":"2016-08-31T22:35:46Z","closed_at":null,"body":"If you write 'FNIRT' instead of 'FSL' in the config file for the 'regOption' field, the construction of the segmentation workflow will fail.  Specifically, there is an issue with the 'create_seg_preproc' function in seg_preproc.py (probably due to an issue with the 'use_ants' boolean).  It looks like C-PAC doesn't know how to deal with incorrect input to that field.  Here is the error:\r\n\r\n>ERROR: Invalid Connection: Segmentation Preprocessing: 0, resource_pool: {'anatomical_reorient': (resting_preproc_2014113_session_1.anat_preproc_0, 'outputspec.reorient'), 'anatomical_brain': (resting_preproc_2014113_session_1.anat_preproc_0, 'outputspec.brain')}\r\n>\r\n>Error name: cpac_pipeline_0004\r\n>\r\n>This is a pipeline creation error - the workflows have not started yet.\r\n>\r\n>\r\n>Process Process-1:\r\n>Traceback (most recent call last):\r\n>  File \"/usr/lib/python2.7/multiprocessing/process.py\", line 258, in _bootstrap\r\n>    self.run()\r\n>  File \"/usr/lib/python2.7/multiprocessing/process.py\", line 114, in run\r\n>    self._target(*self._args, **self._kwargs)\r\n>  File \"/usr/local/lib/python2.7/dist-packages/CPAC/pipeline/cpac_pipeline.py\", line 640, in prep_workflow\r\n>    seg_preproc, 'inputspec.brain')\r\n>UnboundLocalError: local variable 'seg_preproc' referenced before assignment"},"comment":{"url":"https://api.github.com/repos/FCP-INDI/C-PAC/issues/comments/243923691","html_url":"https://github.com/FCP-INDI/C-PAC/issues/447#issuecomment-243923691","issue_url":"https://api.github.com/repos/FCP-INDI/C-PAC/issues/447","id":243923691,"user":{"login":"adonayn","id":17873774,"avatar_url":"https://avatars.githubusercontent.com/u/17873774?v=3","gravatar_id":"","url":"https://api.github.com/users/adonayn","html_url":"https://github.com/adonayn","followers_url":"https://api.github.com/users/adonayn/followers","following_url":"https://api.github.com/users/adonayn/following{/other_user}","gists_url":"https://api.github.com/users/adonayn/gists{/gist_id}","starred_url":"https://api.github.com/users/adonayn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adonayn/subscriptions","organizations_url":"https://api.github.com/users/adonayn/orgs","repos_url":"https://api.github.com/users/adonayn/repos","events_url":"https://api.github.com/users/adonayn/events{/privacy}","received_events_url":"https://api.github.com/users/adonayn/received_events","type":"User","site_admin":false},"created_at":"2016-08-31T22:35:45Z","updated_at":"2016-08-31T22:35:45Z","body":"Hi,\n\nIt worked! Also If I turn off the anatomical registration the error\nreoccurs, I guess it needs anatomical to mni registration.\n\nThanks for your help,\nAdonay\n\nSent from my HTC One\nOn 31 Aug 2016 14:50, \"John Pellman\" <notifications@github.com> wrote:\n\n> What happens if you change *runRegistrationPreprocessing : [1, 0]* to\n> just *runRegistrationPreprocessing : [1]*? Does the error persist?\n>\n> —\n> You are receiving this because you commented.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/FCP-INDI/C-PAC/issues/447#issuecomment-243913668>, or mute\n> the thread\n> <https://github.com/notifications/unsubscribe-auth/ARC7bh_dmJ9AEQ7h1f1oyF_JonuYjmwEks5qlfcRgaJpZM4DoYAC>\n> .\n>\n"}}
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