{"action":"created","issue":{"url":"https://api.github.com/repos/binarybottle/mindboggle/issues/65","labels_url":"https://api.github.com/repos/binarybottle/mindboggle/issues/65/labels{/name}","comments_url":"https://api.github.com/repos/binarybottle/mindboggle/issues/65/comments","events_url":"https://api.github.com/repos/binarybottle/mindboggle/issues/65/events","html_url":"https://github.com/binarybottle/mindboggle/issues/65","id":111293242,"number":65,"title":"could not run node: Mindboggle.Volume_labels.FreeSurfer_cerebellum_ANTs_cerebrum","user":{"login":"njhunsak","id":4333838,"avatar_url":"https://avatars.githubusercontent.com/u/4333838?v=3","gravatar_id":"","url":"https://api.github.com/users/njhunsak","html_url":"https://github.com/njhunsak","followers_url":"https://api.github.com/users/njhunsak/followers","following_url":"https://api.github.com/users/njhunsak/following{/other_user}","gists_url":"https://api.github.com/users/njhunsak/gists{/gist_id}","starred_url":"https://api.github.com/users/njhunsak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/njhunsak/subscriptions","organizations_url":"https://api.github.com/users/njhunsak/orgs","repos_url":"https://api.github.com/users/njhunsak/repos","events_url":"https://api.github.com/users/njhunsak/events{/privacy}","received_events_url":"https://api.github.com/users/njhunsak/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-10-13T23:34:26Z","updated_at":"2015-10-14T21:20:26Z","closed_at":null,"body":"Have you encountered this error before? Any help would be greatly appreciated. I'm so close and would really love to have this program run sans errors! Thanks. Naomi\r\n\r\n```\r\n{'node': Mindboggle.Volume_labels.FreeSurfer_cerebellum_ANTs_cerebrum, 'traceback': ['Traceback (most recent call last):\r\n', '  File \"/bluehome3/intj5/apps/miniconda/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py\", line 38, in run\r\n    node.run(updatehash=updatehash)\r\n', '  File \"/bluehome3/intj5/apps/miniconda/lib/python2.7/site-packages/nipype/pipeline/engine.py\", line 1428, in run\r\n    self._run_interface()\r\n', '  File \"/bluehome3/intj5/apps/miniconda/lib/python2.7/site-packages/nipype/pipeline/engine.py\", line 1538, in _run_interface\r\n    self._result = self._run_command(execute)\r\n', '  File \"/bluehome3/intj5/apps/miniconda/lib/python2.7/site-packages/nipype/pipeline/engine.py\", line 1664, in _run_command\r\n    result = self._interface.run()\r\n', '  File \"/bluehome3/intj5/apps/miniconda/lib/python2.7/site-packages/nipype/interfaces/base.py\", line 1033, in run\r\n    runtime = self._run_wrapper(runtime)\r\n', '  File \"/bluehome3/intj5/apps/miniconda/lib/python2.7/site-packages/nipype/interfaces/base.py\", line 983, in _run_wrapper\r\n    runtime = self._run_interface(runtime)\r\n', '  File \"/bluehome3/intj5/apps/miniconda/lib/python2.7/site-packages/nipype/interfaces/utility.py\", line 445, in _run_interface\r\n    out = function_handle(**args)\r\n', '  File \"<string>\", line 60, in overwrite_volume_labels\r\n', 'IOError: /bluehome3/intj5/mindboggle_working/1004--2014-08-15/Mindboggle/Volume_labels/Extract_FreeSurfer_cerebella/wmparc.mgz.nii.gz and /bluehome3/intj5/mindboggle_working/1004--2014-08-15/Mindboggle/Volume_labels/Combine_ANTs_cortex_noncortex_labels/ants_labels.nii.gz_to_ants_labels.nii.gz_through_combined_segmentations.nii.gz need to be the same shape.\r\nInterface Function failed to run. \r\n']}\r\n```"},"comment":{"url":"https://api.github.com/repos/binarybottle/mindboggle/issues/comments/148205178","html_url":"https://github.com/binarybottle/mindboggle/issues/65#issuecomment-148205178","issue_url":"https://api.github.com/repos/binarybottle/mindboggle/issues/65","id":148205178,"user":{"login":"njhunsak","id":4333838,"avatar_url":"https://avatars.githubusercontent.com/u/4333838?v=3","gravatar_id":"","url":"https://api.github.com/users/njhunsak","html_url":"https://github.com/njhunsak","followers_url":"https://api.github.com/users/njhunsak/followers","following_url":"https://api.github.com/users/njhunsak/following{/other_user}","gists_url":"https://api.github.com/users/njhunsak/gists{/gist_id}","starred_url":"https://api.github.com/users/njhunsak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/njhunsak/subscriptions","organizations_url":"https://api.github.com/users/njhunsak/orgs","repos_url":"https://api.github.com/users/njhunsak/repos","events_url":"https://api.github.com/users/njhunsak/events{/privacy}","received_events_url":"https://api.github.com/users/njhunsak/received_events","type":"User","site_admin":false},"created_at":"2015-10-14T21:20:26Z","updated_at":"2015-10-14T21:20:26Z","body":"Hum. Wasn't able to figure much out from the pklz files. But looking at the input images, the ants_labels.nii.gz_to_ants_labels.nii.gz_through_combined_segmentations.nii.gz file in the Combine_ANTs_cortex_noncortex_labels directory is totally blank where the wmparc.mgz.nii.gz file in the Extract_FreeSurfer_cerebella shows the right and left cerebellum. I'm guessing then something is going wrong when trying to extract the cerebellum label from the ANTs cortical thickness brain segmentation file. When I run antsCorticalThickness.sh, I am using the standard inputs. Am I using the correct file for mindboggle is the question? My output prefix for antscorticalthickness.sh is just a directory. I don't actually givd the files an additional prefix, so when I use mindboggle and I include the \"--ants\" option, the file I use is called \"BrainSegmentation.nii.gz\". It's the file that labels CSF as 1, GM as 2, WM as 3, subcortical as 4, brainstem as 5, and cerebellum as 6. Do you think I might be having a problem because I'm using the [NKI10andUnder template] (http://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436) instead of the OASIS template? Am I using the correct file for the mindboggle --ants option? The pipeline runs fine if I don't include the --ants option, so that's positive! Thanks for your help."}}