{"action":"created","issue":{"url":"https://api.github.com/repos/nipy/nipype/issues/2340","repository_url":"https://api.github.com/repos/nipy/nipype","labels_url":"https://api.github.com/repos/nipy/nipype/issues/2340/labels{/name}","comments_url":"https://api.github.com/repos/nipy/nipype/issues/2340/comments","events_url":"https://api.github.com/repos/nipy/nipype/issues/2340/events","html_url":"https://github.com/nipy/nipype/issues/2340","id":281749443,"number":2340,"title":"spm.EstimateModel & spm.EstimateContrast give error although completing","user":{"login":"SebastianSpeer","id":29842476,"avatar_url":"https://avatars0.githubusercontent.com/u/29842476?v=4","gravatar_id":"","url":"https://api.github.com/users/SebastianSpeer","html_url":"https://github.com/SebastianSpeer","followers_url":"https://api.github.com/users/SebastianSpeer/followers","following_url":"https://api.github.com/users/SebastianSpeer/following{/other_user}","gists_url":"https://api.github.com/users/SebastianSpeer/gists{/gist_id}","starred_url":"https://api.github.com/users/SebastianSpeer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SebastianSpeer/subscriptions","organizations_url":"https://api.github.com/users/SebastianSpeer/orgs","repos_url":"https://api.github.com/users/SebastianSpeer/repos","events_url":"https://api.github.com/users/SebastianSpeer/events{/privacy}","received_events_url":"https://api.github.com/users/SebastianSpeer/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":17,"created_at":"2017-12-13T13:28:28Z","updated_at":"2018-04-02T16:55:31Z","closed_at":"2018-02-02T23:24:47Z","author_association":"NONE","body":"### Summary\r\nWhen running spm.EstimateModel & spm.EstimateContrast:\r\n```\r\nprint \"- Estimate\",\r\nlevel1estimate = spm.EstimateModel()\r\nlevel1estimate.inputs.estimation_method = {'Classical': 1}\r\nlevel1estimate.inputs.spm_mat_file = '/data/sebastian/SPD/Firstlevel/unvariate/SPM.mat'\r\nlevel1estimate.inputs.use_mcr=True\r\nlevel1estimate.inputs.mfile=False\r\nout = level1estimate.run()\r\n```\r\n```\r\nprint \"- Contrast\",\r\nlevel1contrast = spm.EstimateContrast()\r\nlevel1contrast.inputs.spm_mat_file = '/data/sebastian/SPD/Firstlevel/unvariate/SPM.mat'\r\nlevel1contrast.inputs.beta_images = glob('/data/sebastian/SPD/Firstlevel/unvariate/beta*')\r\nlevel1contrast.inputs.residual_image =glob('/data/sebastian/SPD/Firstlevel/unvariate/Res*')[0]\r\n# Condition names DID\r\ncondition_names = ['Disg', 'Neutral']\r\n\r\ncont01=['Disgusting>Baseline','T', condition_names,[1,0]]\r\ncont02=['Neutral>Baseline','T', condition_names,[0,1]]\r\ncont03=['Disgusting>Neutral','T',condition_names,[1,-1]]\r\ncont04=['Neutral>Disgusting','T', condition_names,[-1,1]]\r\n#cont05=['fd>Baseline','T',['FD'],[1]]\r\ncontrast_list = [cont01, cont02, cont03, cont04]\r\nlevel1contrast.inputs.contrasts = contrast_list\r\nout=level1contrast.run()\r\n```\r\n\r\n I get the following error:\r\n\r\n`AttributeError: 'NoneType' object has no attribute 'split'`\r\n\r\n\r\n### How to replicate the behavior\r\n\r\n### Script/Workflow details\r\n\r\nPlease put URL to code or code here (if not too long).\r\n\r\n### Platform details:\r\n\r\nPlease paste the output of: `python -c \"import nipype; print(nipype.get_info()); print(nipype.__version__)\"`\r\n```\r\nimport nipype\r\nnipype.get_info()\r\nprint(nipype.get_info(),nipype.__version__)\r\n```\r\n`({'nibabel_version': '2.2.1', 'sys_executable': '/home/sebastian/anaconda2/bin/python', 'networkx_version': '2.0', 'numpy_version': '1.13.3', 'sys_platform': 'linux2', 'sys_version': '2.7.12 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:42:40) \\n[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]', 'commit_source': 'installation', 'commit_hash': 'ac1412ff', 'pkg_path': '/home/sebastian/anaconda2/lib/python2.7/site-packages/nipype', 'nipype_version': '0.14.0-rc1', 'traits_version': '4.6.0', 'scipy_version': '1.0.0'}, u'0.14.0-rc1')\r\n`\r\n\r\n### Execution environment\r\n\r\nI'm running in a Jupyter notebook on a VM running on  ubuntu 14.04\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/nipy/nipype/issues/comments/377977210","html_url":"https://github.com/nipy/nipype/issues/2340#issuecomment-377977210","issue_url":"https://api.github.com/repos/nipy/nipype/issues/2340","id":377977210,"user":{"login":"SebastianSpeer","id":29842476,"avatar_url":"https://avatars0.githubusercontent.com/u/29842476?v=4","gravatar_id":"","url":"https://api.github.com/users/SebastianSpeer","html_url":"https://github.com/SebastianSpeer","followers_url":"https://api.github.com/users/SebastianSpeer/followers","following_url":"https://api.github.com/users/SebastianSpeer/following{/other_user}","gists_url":"https://api.github.com/users/SebastianSpeer/gists{/gist_id}","starred_url":"https://api.github.com/users/SebastianSpeer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SebastianSpeer/subscriptions","organizations_url":"https://api.github.com/users/SebastianSpeer/orgs","repos_url":"https://api.github.com/users/SebastianSpeer/repos","events_url":"https://api.github.com/users/SebastianSpeer/events{/privacy}","received_events_url":"https://api.github.com/users/SebastianSpeer/received_events","type":"User","site_admin":false},"created_at":"2018-04-02T16:55:31Z","updated_at":"2018-04-02T16:55:31Z","author_association":"NONE","body":"Hi, I am sorry for the delayed response I have been on holidays for some time.\r\nThe issue still has not been resolved.\r\n\r\nThe suggestion regarding the paths did not help.\r\n\r\nfor the `os.environ` in the Jupyter notebook I get the following output:\r\n`{'FSLDIR': '/usr/share/fsl/5.0', 'POSSUMDIR': '/usr/share/fsl/5.0', 'UPSTART_EVENTS': 'runlevel', 'FSLREMOTECALL': '', 'USER': 'sebastian', 'HOME': '/home/sebastian', 'PATH': '/home/sebastian/anaconda2/bin:/usr/lib/fsl/5.0:/data/sebastian/ICA-AROMA:/sbin:/usr/sbin:/bin:/usr/bin:/usr/lib/afni/bin', 'LD_LIBRARY_PATH': '/usr/lib/fsl/5.0', 'previous': 'N', 'LANG': 'en_US.UTF-8', 'FSLLOCKDIR': '', 'TERM': 'xterm-color', 'SHELL': '/bin/bash', 'FSLBROWSER': '/etc/alternatives/x-www-browser', 'SHLVL': '1', 'PREVLEVEL': 'N', 'FREESURFER_HOME': '/data/freesurfer', 'UPSTART_INSTANCE': '', 'runlevel': '2', 'LOGNAME': 'sebastian', 'FSLWISH': '/usr/bin/wish', 'XDG_RUNTIME_DIR': '/run/user/1002', 'JPY_PARENT_PID': '1459', 'UPSTART_JOB': 'rc', 'GIT_PAGER': 'cat', 'XDG_SESSION_ID': 'c2', '_': '/home/sebastian/anaconda2/bin/jupyter', 'FSLOUTPUTTYPE': 'NIFTI_GZ', 'MPLBACKEND': 'module://ipykernel.pylab.backend_inline', 'FSLMACHINELIST': '', 'FSLMULTIFILEQUIT': 'TRUE', 'OLDPWD': '/', 'FSLTCLSH': '/usr/bin/tclsh', 'CLICOLOR': '1', 'PWD': '/data', 'RUNLEVEL': '2', 'MAIL': '/var/mail/sebastian', 'PAGER': 'cat', 'XDG_SEAT': 'seat0'}`\r\n\r\nfrom the python interpreter I get:\r\n`{'FSLDIR': '/usr/local/fsl', 'GLADE_PIXMAP_PATH': ':', 'XDG_GREETER_DATA_DIR': '/var/lib/lightdm-data/sebastian', 'UPSTART_EVENTS': 'started xsession', 'XDG_RUNTIME_DIR': '/run/user/1002', 'LESSOPEN': '| /usr/bin/lesspipe %s', 'LOGNAME': 'sebastian', 'USER': 'sebastian', 'HOME': '/home/sebastian', 'XDG_VTNR': '7', 'PATH': '/home/sebastian/anaconda2/bin:/usr/local/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games', 'DISPLAY': ':0.0', 'SSH_AGENT_PID': '1685', 'LANG': 'en_US.UTF-8', 'TERM': 'xterm', 'SHELL': '/bin/bash', 'XDG_SESSION_PATH': '/org/freedesktop/DisplayManager/Session0', 'XAUTHORITY': '/home/sebastian/.Xauthority', 'LANGUAGE': 'en_US', 'SESSION_MANAGER': 'local/145:@/tmp/.ICE-unix/1792,unix/145:/tmp/.ICE-unix/1792', 'SHLVL': '1', 'MANDATORY_PATH': '/usr/share/gconf/xubuntu.mandatory.path', 'TEXTDOMAIN': 'im-config', 'UPSTART_INSTANCE': '', 'JOB': 'dbus', 'WINDOWID': '38249172', 'SESSIONTYPE': '', 'IM_CONFIG_PHASE': '1', 'GLADE_CATALOG_PATH': ':', 'SELINUX_INIT': 'YES', 'GLADE_MODULE_PATH': ':', 'INSTANCE': '', 'SSH_AUTH_SOCK': '/tmp/ssh-hOXYcGBUNdR8/agent.1683', 'GDMSESSION': 'xubuntu', 'UPSTART_JOB': 'startxfce4', 'TEXTDOMAINDIR': '/usr/share/locale/', 'XDG_SEAT_PATH': '/org/freedesktop/DisplayManager/Seat0', 'LESSCLOSE': '/usr/bin/lesspipe %s %s', 'XDG_CURRENT_DESKTOP': 'XFCE', 'XDG_SESSION_ID': 'c5', 'DBUS_SESSION_BUS_ADDRESS': 'unix:abstract=/tmp/dbus-eI5ho5lDdm', '_': '/home/sebastian/anaconda2/bin/python', 'SESSION': 'xubuntu', 'DESKTOP_SESSION': 'xubuntu', 'UPSTART_SESSION': 'unix:abstract=/com/ubuntu/upstart-session/1002/1518', 'XDG_CONFIG_DIRS': '/etc/xdg/xdg-xubuntu:/usr/share/upstart/xdg:/etc/xdg:/etc/xdg', 'DEFAULTS_PATH': '/usr/share/gconf/xubuntu.default.path', 'GDM_LANG': 'en_US', 'XDG_DATA_DIRS': '/usr/share/xubuntu:/usr/share/xfce4:/usr/local/share/:/usr/share/:/usr/share', 'PWD': '/home/sebastian/Desktop', 'SSH_AGENT_LAUNCHER': 'upstart', 'COLORTERM': 'xfce4-terminal', 'XDG_MENU_PREFIX': 'xfce-', 'LS_COLORS': 'rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:', 'XDG_SEAT': 'seat0'}`"}}
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