{"action":"created","issue":{"url":"https://api.github.com/repos/mwaskom/lyman/issues/87","repository_url":"https://api.github.com/repos/mwaskom/lyman","labels_url":"https://api.github.com/repos/mwaskom/lyman/issues/87/labels{/name}","comments_url":"https://api.github.com/repos/mwaskom/lyman/issues/87/comments","events_url":"https://api.github.com/repos/mwaskom/lyman/issues/87/events","html_url":"https://github.com/mwaskom/lyman/issues/87","id":152674431,"number":87,"title":"lyman .08 issue","user":{"login":"iancballard","id":5826949,"avatar_url":"https://avatars.githubusercontent.com/u/5826949?v=3","gravatar_id":"","url":"https://api.github.com/users/iancballard","html_url":"https://github.com/iancballard","followers_url":"https://api.github.com/users/iancballard/followers","following_url":"https://api.github.com/users/iancballard/following{/other_user}","gists_url":"https://api.github.com/users/iancballard/gists{/gist_id}","starred_url":"https://api.github.com/users/iancballard/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/iancballard/subscriptions","organizations_url":"https://api.github.com/users/iancballard/orgs","repos_url":"https://api.github.com/users/iancballard/repos","events_url":"https://api.github.com/users/iancballard/events{/privacy}","received_events_url":"https://api.github.com/users/iancballard/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-05-03T00:17:57Z","updated_at":"2016-05-03T03:57:35Z","closed_at":null,"body":"Recently updated to the latest version from git and am running into an error when running the preproc workflow. I can't recreate it outside of the lyman workflow: nib.load works fine on the functional_mask.nii.gz file produced by convertmask. I tried uninstalling nibabel and updating to the most recent version, and also reset permissions on all the relevant folders. Any ideas?\r\n\r\nS'Traceback (most recent call last):\\n'\r\np207\r\naS'  File \"/home/iballard/anaconda/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py\", line 18, in run_node\\n    result[\\'result\\'] = node.run(updatehash=updatehash)\\n'\r\np208\r\naS'  File \"/home/iballard/anaconda/lib/python2.7/site-packages/nipype/pipeline/engine.py\", line 1428, in run\\n    self._run_interface()\\n'\r\np209\r\naS'  File \"/home/iballard/anaconda/lib/python2.7/site-packages/nipype/pipeline/engine.py\", line 1538, in _run_interface\\n    self._result = self._run_command(execute)\\n'\r\np210\r\naS'  File \"/home/iballard/anaconda/lib/python2.7/site-packages/nipype/pipeline/engine.py\", line 1664, in _run_command\\n    result = self._interface.run()\\n'\r\np211\r\naS'  File \"/home/iballard/anaconda/lib/python2.7/site-packages/nipype/interfaces/base.py\", line 1033, in run\\n    runtime = self._run_wrapper(runtime)\\n'\r\np212\r\naS'  File \"/home/iballard/anaconda/lib/python2.7/site-packages/nipype/interfaces/base.py\", line 983, in _run_wrapper\\n    runtime = self._run_interface(runtime)\\n'\r\np213\r\naS'  File \"/home/iballard/anaconda/lib/python2.7/site-packages/lyman/workflows/preproc.py\", line 916, in _run_interface\\n    self.plot_mean_image()\\n'\r\np214\r\naS'  File \"/home/iballard/anaconda/lib/python2.7/site-packages/lyman/workflows/preproc.py\", line 926, in plot_mean_image\\n    self.inputs.mask_file, step=1)\\n'\r\np215\r\naS'  File \"/home/iballard/.local/lib/python2.7/site-packages/moss/mosaic.py\", line 86, in __init__\\n    mask_img = nib.load(mask)\\n'\r\np216\r\naS'  File \"/home/iballard/anaconda/lib/python2.7/site-packages/nibabel/loadsave.py\", line 44, in load\\n    return guessed_image_type(filename).from_filename(filename, **kwargs)\\n'\r\np217\r\naS'  File \"/home/iballard/anaconda/lib/python2.7/site-packages/nibabel/keywordonly.py\", line 16, in wrapper\\n    return func(*args, **kwargs)\\n'\r\np218\r\naS'  File \"/home/iballard/anaconda/lib/python2.7/site-packages/nibabel/freesurfer/mghformat.py\", line 528, in from_filename\\n    return klass.from_file_map(file_map, mmap=mmap)\\n'\r\np219\r\naS'  File \"/home/iballard/anaconda/lib/python2.7/site-packages/nibabel/keywordonly.py\", line 16, in wrapper\\n    return func(*args, **kwargs)\\n'\r\np220\r\naS'  File \"/home/iballard/anaconda/lib/python2.7/site-packages/nibabel/freesurfer/mghformat.py\", line 494, in from_file_map\\n    header = klass.header_class.from_fileobj(mghf)\\n'\r\np221\r\naS'  File \"/home/iballard/anaconda/lib/python2.7/site-packages/nibabel/freesurfer/mghformat.py\", line 192, in from_fileobj\\n    return klass(hdr_str + ftr_str, check)\\n'\r\np222\r\naS'  File \"/home/iballard/anaconda/lib/python2.7/site-packages/nibabel/freesurfer/mghformat.py\", line 110, in __init__\\n    hdr = self._set_affine_default(hdr)\\n'\r\np223\r\naS'  File \"/home/iballard/anaconda/lib/python2.7/site-packages/nibabel/freesurfer/mghformat.py\", line 409, in _set_affine_default\\n    hdr[\\'delta\\'][:] = np.array([1, 1, 1])\\n'\r\np224\r\naS'ValueError: assignment destination is read-only\\nInterface MaskReport failed to run. \\n'"},"comment":{"url":"https://api.github.com/repos/mwaskom/lyman/issues/comments/216429944","html_url":"https://github.com/mwaskom/lyman/issues/87#issuecomment-216429944","issue_url":"https://api.github.com/repos/mwaskom/lyman/issues/87","id":216429944,"user":{"login":"mwaskom","id":315810,"avatar_url":"https://avatars.githubusercontent.com/u/315810?v=3","gravatar_id":"","url":"https://api.github.com/users/mwaskom","html_url":"https://github.com/mwaskom","followers_url":"https://api.github.com/users/mwaskom/followers","following_url":"https://api.github.com/users/mwaskom/following{/other_user}","gists_url":"https://api.github.com/users/mwaskom/gists{/gist_id}","starred_url":"https://api.github.com/users/mwaskom/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mwaskom/subscriptions","organizations_url":"https://api.github.com/users/mwaskom/orgs","repos_url":"https://api.github.com/users/mwaskom/repos","events_url":"https://api.github.com/users/mwaskom/events{/privacy}","received_events_url":"https://api.github.com/users/mwaskom/received_events","type":"User","site_admin":false},"created_at":"2016-05-03T03:57:35Z","updated_at":"2016-05-03T03:57:35Z","body":"haven't seen it. what version nibabel "}}