deleteorientation bug

[darya-chyzhyk]

When "deleteorient = True" there is an error:

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/usr/lib/python2.7/dist-packages/IPython/init.py in start_ipython(argv=None, *_kwargs={})
113 kwargs : various, optional
114 Any other kwargs will be passed to the Application constructor,
115 such as config.
116 """
117 from IPython.terminal.ipapp import launch_new_instance
--> 118 return launch_new_instance(argv=argv, *_kwargs)
launch_new_instance = <bound method MetaHasTraits.launch_instance of <class 'IPython.terminal.ipapp.TerminalIPythonApp'>>
argv = None
kwargs = {}
119
120 def start_kernel(argv=None, **kwargs):
121 """Launch a normal IPython kernel instance (as opposed to embedded)
122

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/usr/lib/python2.7/dist-packages/IPython/config/application.py in launch_instance(cls=<class 'IPython.terminal.ipapp.TerminalIPythonApp'>, argv=None, **kwargs={})
541 If a global instance already exists, this reinitializes and starts it
542 """
543 try:
544 app = cls.instance(**kwargs)
545 app.initialize(argv)
--> 546 app.start()
app.start = <bound method TerminalIPythonApp.start of <IPython.terminal.ipapp.TerminalIPythonApp object>>
547 except ImportError as e:
548 from IPython.utils import py3compat
549 ipy = "ipython3" if py3compat.PY3 else "ipython"
550 if "IPython.qt" in str(e) or "qt.console.qtconsoleapp" in str(e):

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/usr/lib/python2.7/dist-packages/IPython/terminal/ipapp.py in start(self=<IPython.terminal.ipapp.TerminalIPythonApp object>)
357 if self.subapp is not None:
358 return self.subapp.start()
359 # perform any prexec steps:
360 if self.interact:
361 self.log.debug("Starting IPython's mainloop...")
--> 362 self.shell.mainloop()
self.shell.mainloop = <bound method TerminalInteractiveShell.mainloop ...nteractiveshell.TerminalInteractiveShell object>>
363 else:
364 self.log.debug("IPython not interactive...")
365
366

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/usr/lib/python2.7/dist-packages/IPython/terminal/interactiveshell.py in mainloop(self=<IPython.terminal.interactiveshell.TerminalInteractiveShell object>, display_banner=None)
431
432 with nested(self.builtin_trap, self.display_trap):
433
434 while 1:
435 try:
--> 436 self.interact(display_banner=display_banner)
self.interact = <bound method TerminalInteractiveShell.interact ...nteractiveshell.TerminalInteractiveShell object>>
display_banner = None
437 #self.interact_with_readline()
438 # XXX for testing of a readline-decoupled repl loop, call
439 # interact_with_readline above
440 break

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/usr/lib/python2.7/dist-packages/IPython/terminal/interactiveshell.py in interact(self=<IPython.terminal.interactiveshell.TerminalInteractiveShell object>, display_banner=False)
550 if (self.SyntaxTB.last_syntax_error and
551 self.autoedit_syntax):
552 self.edit_syntax_error()
553 if not more:
554 source_raw = self.input_splitter.source_raw_reset()[1]
--> 555 self.run_cell(source_raw, store_history=True)
self.run_cell = <bound method TerminalInteractiveShell.run_cell ...nteractiveshell.TerminalInteractiveShell object>>
source_raw = u'run preprocess.py\n'
556 hlen_b4_cell =
557 self._replace_rlhist_multiline(source_raw, hlen_b4_cell)
558
559 # Turn off the exit flag, so the mainloop can be restarted if desired

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/usr/lib/python2.7/dist-packages/IPython/core/interactiveshell.py in run_cell(self=<IPython.terminal.interactiveshell.TerminalInteractiveShell object>, raw_cell=u'run preprocess.py\n', store_history=True, silent=False, shell_futures=True)
2655
2656 code_ast = self.transform_ast(code_ast)
2657
2658 interactivity = "none" if silent else self.ast_node_interactivity
2659 self.run_ast_nodes(code_ast.body, cell_name,
-> 2660 interactivity=interactivity, compiler=compiler)
interactivity = 'last_expr'
compiler = <IPython.core.compilerop.CachingCompiler instance>
2661
2662 # Execute any registered post-execution functions.
2663 # unless we are silent
2664 post_exec = [] if silent else self._post_execute.iteritems()

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/usr/lib/python2.7/dist-packages/IPython/core/interactiveshell.py in run_ast_nodes(self=<IPython.terminal.interactiveshell.TerminalInteractiveShell object>, nodelist=[<_ast.Expr object>], cell_name='', interactivity='last', compiler=<IPython.core.compilerop.CachingCompiler instance>)
2765 return True
2766
2767 for i, node in enumerate(to_run_interactive):
2768 mod = ast.Interactive([node])
2769 code = compiler(mod, cell_name, "single")
-> 2770 if self.run_code(code):
self.run_code = <bound method TerminalInteractiveShell.run_code ...nteractiveshell.TerminalInteractiveShell object>>
code = <code object at 0x7f5363f280b0, file "", line 1>
2771 return True
2772
2773 # Flush softspace
2774 if softspace(sys.stdout, 0):

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/usr/lib/python2.7/dist-packages/IPython/core/interactiveshell.py in run_code(self=<IPython.terminal.interactiveshell.TerminalInteractiveShell object>, code_obj=<code object at 0x7f5363f280b0, file "", line 1>)
2815 outflag = 1 # happens in more places, so it's easier as default
2816 try:
2817 try:
2818 self.hooks.pre_run_code_hook()
2819 #rprint('Running code', repr(code_obj)) # dbg
-> 2820 exec code_obj in self.user_global_ns, self.user_ns
code_obj = <code object at 0x7f5363f280b0, file "", line 1>
self.user_global_ns = {'BASE_DIR': '/volatile/darya/Documents/experiments/preprocessing_adnidod/data_2_subj', 'In': ['', u"get_ipython().magic(u'run preprocess.py')", u"get_ipython().magic(u'run preprocess.py')", u'import nibabel', u'nibabel.version', u"get_ipython().magic(u'run preprocess.py')", u"get_ipython().magic(u'run preprocess.py')", u"get_ipython().magic(u'run preprocess.py')"], 'Out': {4: '1.3.0'}, '': '1.3.0', '4': '1.3.0', '': '', '': '', 'builtin': <module 'builtin' (built-in)>, 'builtins': <module 'builtin' (built-in)>, 'doc': 'Automatically created module for IPython interactive environment', ...}
self.user_ns = {'BASE_DIR': '/volatile/darya/Documents/experiments/preprocessing_adnidod/data_2_subj', 'In': ['', u"get_ipython().magic(u'run preprocess.py')", u"get_ipython().magic(u'run preprocess.py')", u'import nibabel', u'nibabel.version', u"get_ipython().magic(u'run preprocess.py')", u"get_ipython().magic(u'run preprocess.py')", u"get_ipython().magic(u'run preprocess.py')"], 'Out': {4: '1.3.0'}, '': '1.3.0', '4': '1.3.0', '': '', '': '', 'builtin': <module 'builtin' (built-in)>, 'builtins': <module 'builtin' (built-in)>, 'doc': 'Automatically created module for IPython interactive environment', ...}
2821 finally:
2822 # Reset our crash handler in place
2823 sys.excepthook = old_excepthook
2824 except SystemExit:

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/volatile/darya/Documents/experiments/preprocessing_adnidod/ in ()
----> 1
2
3
4
5
6 get_ipython().magic(u'run preprocess.py')
7
8
9
10

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/usr/lib/python2.7/dist-packages/IPython/core/interactiveshell.py in magic(self=<IPython.terminal.interactiveshell.TerminalInteractiveShell object>, arg_s=u'run preprocess.py')
2160 compound statements.
2161 """
2162 # TODO: should we issue a loud deprecation warning here?
2163 magic_name, _, magic_arg_s = arg_s.partition(' ')
2164 magic_name = magic_name.lstrip(prefilter.ESC_MAGIC)
-> 2165 return self.run_line_magic(magic_name, magic_arg_s)
self.run_line_magic = >
magic_name = u'run'
magic_arg_s = u'preprocess.py'
2166
2167 #-------------------------------------------------------------------------
2168 # Things related to macros
2169 #-------------------------------------------------------------------------

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/usr/lib/python2.7/dist-packages/IPython/core/interactiveshell.py in run_line_magic(self=<IPython.terminal.interactiveshell.TerminalInteractiveShell object>, magic_name=u'run', line=u'preprocess.py')
2081 kwargs = {}
2082 # Grab local namespace if we need it:
2083 if getattr(fn, "needs_local_scope", False):
2084 kwargs['local_ns'] = sys._getframe(stack_depth).f_locals
2085 with self.builtin_trap:
-> 2086 result = fn(args,*kwargs)
result = undefined
fn = <bound method ExecutionMagics.run of <IPython.core.magics.execution.ExecutionMagics object>>
args = [u'preprocess.py']
kwargs = {}
2087 return result
2088
2089 def run_cell_magic(self, magic_name, line, cell):
2090 """Execute the given cell magic.

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/volatile/darya/Documents/experiments/preprocessing_adnidod/ in run(self=<IPython.core.magics.execution.ExecutionMagics object>, parameter_s=u'preprocess.py', runner=None, file_finder=)
1
----> 2
3
4
5 # -- coding: utf-8 --
6 """Implementation of execution-related magic functions.
7 """
8 #-----------------------------------------------------------------------------
9 # Copyright (c) 2012 The IPython Development Team.
10 #
11 # Distributed under the terms of the Modified BSD License.
12 #
13 # The full license is in the file COPYING.txt, distributed with this software.
14 #-----------------------------------------------------------------------------

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/usr/lib/python2.7/dist-packages/IPython/core/magic.py in (f=, _a=(<IPython.core.magics.execution.ExecutionMagics object>, u'preprocess.py', None, ), *_k={})
186 validate_type(magic_kind)
187
188 # This is a closure to capture the magic_kind. We could also use a class,
189 # but it's overkill for just that one bit of state.
190 def magic_deco(arg):
--> 191 call = lambda f, _a, *_k: f(_a, *_k)
f =
a = (<IPython.core.magics.execution.ExecutionMagics object>, u'preprocess.py', None, )
k = {}
192
193 if callable(arg):
194 # "Naked" decorator call (just @foo, no args)
195 func = arg

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/usr/lib/python2.7/dist-packages/IPython/core/magics/execution.py in run(self=<IPython.core.magics.execution.ExecutionMagics object>, parameter_s=u'preprocess.py', runner=>, file_finder=)
632 except (KeyError):
633 nruns = 1
634 self._run_with_timing(run, nruns)
635 else:
636 # regular execution
--> 637 run()
run =
638
639 if 'i' in opts:
640 self.shell.user_ns['name'] = __name__save
641 else:

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/usr/lib/python2.7/dist-packages/IPython/core/magics/execution.py in run()
618 if runner is None:
619 runner = self.shell.safe_execfile
620
621 def run():
622 runner(filename, prog_ns, prog_ns,
--> 623 exit_ignore=exit_ignore)
624
625 if 't' in opts:
626 # timed execution
627 try:

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/usr/lib/python2.7/dist-packages/IPython/core/interactiveshell.py in safe_execfile(self=<IPython.terminal.interactiveshell.TerminalInteractiveShell object>, fname=u'/volatile/darya/Documents/experiments/preprocessing_adnidod/preprocess.py', _where=({'BASE_DIR': '/volatile/darya/Documents/experiments/preprocessing_adnidod/data_2_subj', 'builtins': {'ArithmeticError': <type 'exceptions.ArithmeticError'>, 'AssertionError': <type 'exceptions.AssertionError'>, 'AttributeError': <type 'exceptions.AttributeError'>, 'BaseException': <type 'exceptions.BaseException'>, 'BufferError': <type 'exceptions.BufferError'>, 'BytesWarning': <type 'exceptions.BytesWarning'>, 'DeprecationWarning': <type 'exceptions.DeprecationWarning'>, 'EOFError': <type 'exceptions.EOFError'>, 'Ellipsis': Ellipsis, 'EnvironmentError': <type 'exceptions.EnvironmentError'>, ...}, 'file': u'preprocess.py', 'name': 'main', 'nonzero': <function >, 'package': None, 'do_subjects_preproc': , 'fetch_spm_auditory': , 'generate_subject_stats_report': , 'jobfile': 'adnidod_config.ini', ...}, {'BASE_DIR': '/volatile/darya/Documents/experiments/preprocessing_adnidod/data_2_subj', 'builtins': {'ArithmeticError': <type 'exceptions.ArithmeticError'>, 'AssertionError': <type 'exceptions.AssertionError'>, 'AttributeError': <type 'exceptions.AttributeError'>, 'BaseException': <type 'exceptions.BaseException'>, 'BufferError': <type 'exceptions.BufferError'>, 'BytesWarning': <type 'exceptions.BytesWarning'>, 'DeprecationWarning': <type 'exceptions.DeprecationWarning'>, 'EOFError': <type 'exceptions.EOFError'>, 'Ellipsis': Ellipsis, 'EnvironmentError': <type 'exceptions.EnvironmentError'>, ...}, 'file': u'preprocess.py', 'name': 'main', 'nonzero': <function >, 'package': None, 'do_subjects_preproc': , 'fetch_spm_auditory': , 'generate_subject_stats_report': , 'jobfile': 'adnidod_config.ini', ...}), *_kw={'exit_ignore': False, 'raise_exceptions': False})
2485 # Python inserts the script's directory into sys.path
2486 dname = os.path.dirname(fname)
2487
2488 with prepended_to_syspath(dname):
2489 try:
-> 2490 py3compat.execfile(fname,*where)
fname = u'/volatile/darya/Documents/experiments/preprocessing_adnidod/preprocess.py'
where = ({'BASE_DIR': '/volatile/darya/Documents/experiments/preprocessing_adnidod/data_2_subj', 'builtins': {'ArithmeticError': <type 'exceptions.ArithmeticError'>, 'AssertionError': <type 'exceptions.AssertionError'>, 'AttributeError': <type 'exceptions.AttributeError'>, 'BaseException': <type 'exceptions.BaseException'>, 'BufferError': <type 'exceptions.BufferError'>, 'BytesWarning': <type 'exceptions.BytesWarning'>, 'DeprecationWarning': <type 'exceptions.DeprecationWarning'>, 'EOFError': <type 'exceptions.EOFError'>, 'Ellipsis': Ellipsis, 'EnvironmentError': <type 'exceptions.EnvironmentError'>, ...}, 'file': u'preprocess.py', 'name': 'main', 'nonzero': <function >, 'package': None, 'do_subjects_preproc': , 'fetch_spm_auditory': , 'generate_subject_stats_report': , 'jobfile': 'adnidod_config.ini', ...}, {'BASE_DIR': '/volatile/darya/Documents/experiments/preprocessing_adnidod/data_2_subj', 'builtins': {'ArithmeticError': <type 'exceptions.ArithmeticError'>, 'AssertionError': <type 'exceptions.AssertionError'>, 'AttributeError': <type 'exceptions.AttributeError'>, 'BaseException': <type 'exceptions.BaseException'>, 'BufferError': <type 'exceptions.BufferError'>, 'BytesWarning': <type 'exceptions.BytesWarning'>, 'DeprecationWarning': <type 'exceptions.DeprecationWarning'>, 'EOFError': <type 'exceptions.EOFError'>, 'Ellipsis': Ellipsis, 'EnvironmentError': <type 'exceptions.EnvironmentError'>, ...}, 'file': u'preprocess.py', 'name': 'main', 'nonzero': <function >, 'package': None, 'do_subjects_preproc': , 'fetch_spm_auditory': , 'generate_subject_stats_report': , 'jobfile': 'adnidod_config.ini', ...})
2491 except SystemExit as status:
2492 # If the call was made with 0 or None exit status (sys.exit(0)
2493 # or sys.exit() ), don't bother showing a traceback, as both of
2494 # these are considered normal by the OS:

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/usr/lib/python2.7/dist-packages/IPython/utils/py3compat.py in execfile(fname=u'/volatile/darya/Documents/experiments/preprocessing_adnidod/preprocess.py', *where=({'BASE_DIR': '/volatile/darya/Documents/experiments/preprocessing_adnidod/data_2_subj', 'builtins': {'ArithmeticError': <type 'exceptions.ArithmeticError'>, 'AssertionError': <type 'exceptions.AssertionError'>, 'AttributeError': <type 'exceptions.AttributeError'>, 'BaseException': <type 'exceptions.BaseException'>, 'BufferError': <type 'exceptions.BufferError'>, 'BytesWarning': <type 'exceptions.BytesWarning'>, 'DeprecationWarning': <type 'exceptions.DeprecationWarning'>, 'EOFError': <type 'exceptions.EOFError'>, 'Ellipsis': Ellipsis, 'EnvironmentError': <type 'exceptions.EnvironmentError'>, ...}, 'file': u'preprocess.py', 'name': 'main', 'nonzero': <function >, 'package': None, 'do_subjects_preproc': , 'fetch_spm_auditory': , 'generate_subject_stats_report': , 'jobfile': 'adnidod_config.ini', ...}, {'BASE_DIR': '/volatile/darya/Documents/experiments/preprocessing_adnidod/data_2_subj', 'builtins': {'ArithmeticError': <type 'exceptions.ArithmeticError'>, 'AssertionError': <type 'exceptions.AssertionError'>, 'AttributeError': <type 'exceptions.AttributeError'>, 'BaseException': <type 'exceptions.BaseException'>, 'BufferError': <type 'exceptions.BufferError'>, 'BytesWarning': <type 'exceptions.BytesWarning'>, 'DeprecationWarning': <type 'exceptions.DeprecationWarning'>, 'EOFError': <type 'exceptions.EOFError'>, 'Ellipsis': Ellipsis, 'EnvironmentError': <type 'exceptions.EnvironmentError'>, ...}, 'file': u'preprocess.py', 'name': 'main', 'nonzero': <function >, 'package': None, 'do_subjects_preproc': , 'fetch_spm_auditory': , 'generate_subject_stats_report': , 'jobfile': 'adnidod_config.ini', ...}))
199 def execfile(fname, *where):
200 if isinstance(fname, unicode):
201 filename = fname.encode(sys.getfilesystemencoding())
202 else:
203 filename = fname
--> 204 builtin.execfile(filename, *where)
filename = '/volatile/darya/Documents/experiments/preprocessing_adnidod/preprocess.py'
where = ({'BASE_DIR': '/volatile/darya/Documents/experiments/preprocessing_adnidod/data_2_subj', 'builtins': {'ArithmeticError': <type 'exceptions.ArithmeticError'>, 'AssertionError': <type 'exceptions.AssertionError'>, 'AttributeError': <type 'exceptions.AttributeError'>, 'BaseException': <type 'exceptions.BaseException'>, 'BufferError': <type 'exceptions.BufferError'>, 'BytesWarning': <type 'exceptions.BytesWarning'>, 'DeprecationWarning': <type 'exceptions.DeprecationWarning'>, 'EOFError': <type 'exceptions.EOFError'>, 'Ellipsis': Ellipsis, 'EnvironmentError': <type 'exceptions.EnvironmentError'>, ...}, 'file': u'preprocess.py', 'name': 'main', 'nonzero': <function >, 'package': None, 'do_subjects_preproc': , 'fetch_spm_auditory': , 'generate_subject_stats_report': , 'jobfile': 'adnidod_config.ini', ...}, {'BASE_DIR': '/volatile/darya/Documents/experiments/preprocessing_adnidod/data_2_subj', 'builtins': {'ArithmeticError': <type 'exceptions.ArithmeticError'>, 'AssertionError': <type 'exceptions.AssertionError'>, 'AttributeError': <type 'exceptions.AttributeError'>, 'BaseException': <type 'exceptions.BaseException'>, 'BufferError': <type 'exceptions.BufferError'>, 'BytesWarning': <type 'exceptions.BytesWarning'>, 'DeprecationWarning': <type 'exceptions.DeprecationWarning'>, 'EOFError': <type 'exceptions.EOFError'>, 'Ellipsis': Ellipsis, 'EnvironmentError': <type 'exceptions.EnvironmentError'>, ...}, 'file': u'preprocess.py', 'name': 'main', 'nonzero': <function >, 'package': None, 'do_subjects_preproc': , 'fetch_spm_auditory': , 'generate_subject_stats_report': , 'jobfile': 'adnidod_config.ini', ...})
205
206
207
208

...........................................................................
/volatile/darya/Documents/experiments/preprocessing_adnidod/preprocess.py in ()
26 # directory that contains the files
27 BASE_DIR = '/volatile/darya/Documents/experiments/preprocessing_adnidod/data_2_subj'
28 jobfile = 'adnidod_config.ini' #("")
29
30 # preprocess the data
---> 31 results = do_subjects_preproc(jobfile, dataset_dir=BASE_DIR)
32
33
34
35

...........................................................................
/volatile/darya/.local/lib/python2.7/site-packages/pypreprocess/nipype_preproc_spm_utils.py in do_subjects_preproc(subject_factory=[{'onset': [None], 'anat': '/volatile/darya/Docum...ipype_results': {}, 'warpable': ['anat', 'func']}, {'onset': [None], 'anat': '/volatile/darya/Docum...ipype_results': {}, 'warpable': ['anat', 'func']}], session_ids=None, *_preproc_params={'TA': 'TR * (1 - 1 / nslices)', 'TR': 3.0, 'anat_write_voxel_sizes': [1.0, 1.0, 1.0], 'caching': True, 'coreg_anat_to_func': False, 'coregister': True, 'coregister_reslice': False, 'coregister_software': 'spm', 'dartel': False, 'dataset_description': '\n

This ADNIDOD resting-state fMRI study includ...x 3 mm\n

Shape : 64 x 64 x 48

\n\n', ...})
1709 if k in preproc_params:
1710 backup_params[k] = preproc_params.pop(k)
1711
1712 # run classic preproc
1713 subjects = Parallel(n_jobs=n_jobs)(delayed(do_subject_preproc)(
-> 1714 subject_data, *_preproc_params) for subject_data in subjects)
subject_data = {'onset': [None], 'anat': '/volatile/darya/Docum...ipype_results': {}, 'warpable': ['anat', 'func']}
preproc_params = {'TA': 'TR * (1 - 1 / nslices)', 'TR': 3.0, 'anat_write_voxel_sizes': [1.0, 1.0, 1.0], 'caching': True, 'coreg_anat_to_func': False, 'coregister': True, 'coregister_reslice': False, 'coregister_software': 'spm', 'dartel': False, 'dataset_description': '\n

This ADNIDOD resting-state fMRI study includ...x 3 mm\n

Shape : 64 x 64 x 48

\n\n', ...}
subjects = [{'onset': [None], 'anat': '/volatile/darya/Docum...ipype_results': {}, 'warpable': ['anat', 'func']}, {'onset': [None], 'anat': '/volatile/darya/Docum...ipype_results': {}, 'warpable': ['anat', 'func']}]
1715
1716 # run DARTEL
1717 preproc_params.update(backup_params)
1718 if newsegment:

...........................................................................
/usr/lib/python2.7/dist-packages/joblib/parallel.py in call(self=Parallel(n_jobs=2), iterable=<generator object >)
655 if pre_dispatch == "all" or n_jobs == 1:
656 # The iterable was consumed all at once by the above for loop.
657 # No need to wait for async callbacks to trigger to
658 # consumption.
659 self._iterating = False
--> 660 self.retrieve()
self.retrieve = <bound method Parallel.retrieve of Parallel(n_jobs=2)>
661 # Make sure that we get a last message telling us we are done
662 elapsed_time = time.time() - self._start_time
663 self._print('Done %3i out of %3i | elapsed: %s finished',
664 (len(self._output),

---------------------------------------------------------------------------
Sub-process traceback:
---------------------------------------------------------------------------
AttributeError                                     Tue Aug  9 10:41:06 2016

PID: 11724 Python 2.7.6: /usr/bin/python
...........................................................................
/volatile/darya/.local/lib/python2.7/site-packages/pypreprocess/nipype_preproc_spm_utils.pyc in do_subject_preproc(subject_data={'onset': [None], 'anat': '/volatile/darya/Docum...ipype_results': {}, 'warpable': ['anat', 'func']}, deleteorient=True, slice_timing=True, slice_order='ascending', interleaved=True, ref_slice=1, TR=3.0, TA='TR * (1 - 1 / nslices)', slice_timing_software='spm', realign=True, realign_reslice=False, register_to_mean=True, realign_software='spm', coregister=True, coregister_reslice=False, coreg_anat_to_func=False, coregister_software='spm', segment=True, normalize=True, dartel=False, fwhm=0.0, anat_fwhm=0.0, func_write_voxel_sizes=[3.0, 3.0, 3.0], anat_write_voxel_sizes=[1.0, 1.0, 1.0], smooth_software='spm', hardlink_output=True, report=True, tsdiffana=True, parent_results_gallery=<pypreprocess.reporting.base_reporter.ResultsGallery object>, last_stage=True, preproc_undergone=None, prepreproc_undergone='', caching=True, **kwargs={'dataset_description': '\n

This ADNIDOD resting-state fMRI study includ...x 3 mm\n

Shape : 64 x 64 x 48

\n\n', 'dataset_dir': '/volatile/darya/Documents/experiments/preprocessing_adnidod/data_2_subj', 'dataset_id': '/volatile/darya/Documents/experiments/preprocessing_adnidod/data_2_subj', 'matlab_exec': None, 'newsegment': False, 'output_modulated_tpms': False, 'spm_dir': None})
1224 else:
1225 assert isinstance(subject_data, SubjectData), (
1226 "subject_datta must be SubjectData instance or dict, "
1227 "got %s" % type(subject_data))
1228
-> 1229 subject_data.sanitize(deleteorient=deleteorient, niigz2nii=True)
1230 subject_data.failed = False
1231
1232 # use EPI template for anat if anat is None
1233 if subject_data.anat is None:

...........................................................................
/volatile/darya/.local/lib/python2.7/site-packages/pypreprocess/subject_data.pyc in sanitize(self={'onset': [None], 'anat': '/volatile/darya/Docum...ipype_results': {}, 'warpable': ['anat', 'func']}, deleteorient=True, niigz2nii=True)
388 # .dcm, .ima -> .nii
389 self._dcm2nii()
390
391 # delete orientation meta-data
392 if deleteorient:
--> 393 self._delete_orientation()
394
395 # .nii.gz -> .nii extraction for SPM & co.
396 if niigz2nii:
397 self._niigz2nii()

...........................................................................
/volatile/darya/.local/lib/python2.7/site-packages/pypreprocess/subject_data.pyc in _delete_orientation(self={'onset': [None], 'anat': '/volatile/darya/Docum...ipype_results': {}, 'warpable': ['anat', 'func']})
167 warnings.warn("'%s' attribute of is None! Skipping" % attr)
168 break
169 else:
170 self.func = [mem.cache(delete_orientation)(
171 self.func[sess], self.session_output_dirs[sess])
--> 172 for sess in range(self.n_sessions)]
173
174 # deleteorient for anat
175 if self.anat is not None:
176 self.anat = mem.cache(delete_orientation)(

...........................................................................
/usr/lib/python2.7/dist-packages/joblib/memory.pyc in call(self=MemorizedFunc(func=<function delete_orientation ...od/data_2_subj_results/0003107/cache_dir/joblib'), *args=('/volatile/darya/Documents/experiments/preprocess...br_raw_20130927141408560_4967_S199091_I387201.nii', '/volatile/darya/Documents/experiments/preprocessing_adnidod/data_2_subj_results/0003107/func'), **kwargs={})
476 return MemorizedResult(self.cachedir, self.func, argument_hash,
477 metadata=metadata, verbose=self._verbose - 1,
478 timestamp=self.timestamp)
479
480 def call(self, *args, **kwargs):
--> 481 return self._cached_call(args, kwargs)[0]
482
483 def reduce(self):
484 """ We don't store the timestamp when pickling, to avoid the hash
485 depending from it.

...........................................................................
/usr/lib/python2.7/dist-packages/joblib/memory.pyc in _cached_call(self=MemorizedFunc(func=<function delete_orientation ...od/data_2_subj_results/0003107/cache_dir/joblib'), args=('/volatile/darya/Documents/experiments/preprocess...br_raw_20130927141408560_4967_S199091_I387201.nii', '/volatile/darya/Documents/experiments/preprocessing_adnidod/data_2_subj_results/0003107/func'), kwargs={})
423 if self._verbose > 10:
424 _, name = get_func_name(self.func)
425 self.warn('Computing func %s, argument hash %s in '
426 'directory %s'
427 % (name, argument_hash, output_dir))
--> 428 out, metadata = self.call(_args, *_kwargs)
429 if self.mmap_mode is not None:
430 # Memmap the output at the first call to be consistent with
431 # later calls
432 out = _load_output(output_dir, _get_func_fullname(self.func),

...........................................................................
/usr/lib/python2.7/dist-packages/joblib/memory.pyc in call(self=MemorizedFunc(func=<function delete_orientation ...od/data_2_subj_results/0003107/cache_dir/joblib'), *args=('/volatile/darya/Documents/experiments/preprocess...br_raw_20130927141408560_4967_S199091_I387201.nii', '/volatile/darya/Documents/experiments/preprocessing_adnidod/data_2_subj_results/0003107/func'), **kwargs={})
668 """
669 start_time = time.time()
670 output_dir, _ = self._get_output_dir(*args, **kwargs)
671 if self._verbose > 0:
672 print(format_call(self.func, args, kwargs))
--> 673 output = self.func(_args, *_kwargs)
674 self._persist_output(output, output_dir)
675 duration = time.time() - start_time
676 metadata = self._persist_input(output_dir, duration, args, kwargs)
677

...........................................................................
/volatile/darya/.local/lib/python2.7/site-packages/pypreprocess/io_utils.pyc in delete_orientation(imgs=['/volatile/darya/Documents/experiments/preprocess...br_raw_20130927141408560_4967_S199091_I387201.nii'], output_dir='/volatile/darya/Documents/experiments/preprocessing_adnidod/data_2_subj_results/0003107/func', output_tag='')
329 output_img = os.path.join(output_dir,
330 output_tag + os.path.basename(img))
331 new_img = nibabel.load(img)
332 new_img.set_sform(np.zeros((4, 4)))
333 new_img.set_qform(np.eye(4))
--> 334 new_img.header['dim_info'] = 0
335 nibabel.save(new_img, output_img)
336 output_imgs.append(output_img)
337
338 if not_list:

AttributeError: 'Nifti1Image' object has no attribute 'header'

---

[AlexandreAbraham]

This is very weird. Can you run this in your terminal?

python -c 'import nibabel; print(nibabel.__version__)'

[mrahim]

1.3.0

[AlexandreAbraham]

In version 1.3, the header is img._header and not img.header.

A safe workaround is to use img.get_header().

[dohmatob]

+1. Somebody wants to take on this ?

On Tue, Aug 9, 2016 at 11:14 AM, Alexandre Abraham <[email protected]

wrote:

In version 1.3, the header is img._header and not img.header.

A safe workaround is to use img.get_header().

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sent from my potato...
http://dohmatob.blogspot.fr/, https://team.inria.fr/parietal/elvis/,
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[dohmatob]

The deletete_orientation function has to be rewritten from scratch. It
looks horrible, and can break in a 1000 different ways.

On Tue, Aug 9, 2016 at 11:15 AM, Elvis Dohmatob [email protected] wrote:

+1. Somebody wants to take on this ?

On Tue, Aug 9, 2016 at 11:14 AM, Alexandre Abraham <
[email protected]> wrote:

In version 1.3, the header is img._header and not img.header.

A safe workaround is to use img.get_header().

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Elvis Dohmatob,
sent from my potato...
http://dohmatob.blogspot.fr/, https://team.inria.fr/parietal/elvis/,
https://github.com/dohmatob

Elvis Dohmatob,
sent from my potato...
http://dohmatob.blogspot.fr/, https://team.inria.fr/parietal/elvis/,
https://github.com/dohmatob

[AlexandreAbraham]

#ResearchCode

[AlexandreAbraham]

@dohmatob the function does not seem that bad to me... Can you be more precise?

[dohmatob]

Mainly design issues.

• We want to work with more general nifti-likes as input
• Obligatory output_dir arg seems a bad idea
• other stuff ?
  Basically, the function should simply delete the orientation meta data and
  return the output image. The whole output file logic should ideally be
  removed.

N.B.: I understand that who ever implemented this function inherited from a
very bad code base from me.

On Tue, Aug 9, 2016 at 11:32 AM, Alexandre Abraham <[email protected]

wrote:

@dohmatob https://github.com/dohmatob the function does not seem that
bad to me... Can you be more precise?

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http://dohmatob.blogspot.fr/, https://team.inria.fr/parietal/elvis/,
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[AlexandreAbraham]

The neverending issue!

[darya-chyzhyk]

The error appear when using delete orientation option

Should orientation meta-date be stripped-off image headers ?
deleteorient = True

 Executing node d703e8c3dea596ceef853fee8927d1f3 in dir: /home/darya/Documents/Inria/data/ADNIDOD_example/results/0006315/cache_dir/nipype_mem/nipype-interfaces-spm-preprocess-Realign/d703e8c3dea596ceef853fee8927d1f3

Traceback (most recent call last):
File "preprocess_example.py", line 49, in
results = do_subjects_preproc(jobfile, dataset_dir=BASE_DIR)
File "/home/darya/.local/lib/python2.7/site-packages/pypreprocess/nipype_preproc_spm_utils.py", line 1713, in do_subjects_preproc
subject_data, **preproc_params) for subject_data in subjects)
File "/home/darya/anaconda2/lib/python2.7/site-packages/sklearn/externals/joblib/parallel.py", line 768, in call
self.retrieve()
File "/home/darya/anaconda2/lib/python2.7/site-packages/sklearn/externals/joblib/parallel.py", line 719, in retrieve
raise exception
sklearn.externals.joblib.my_exceptions.JoblibRuntimeError: JoblibRuntimeError

---

Multiprocessing exception:
...........................................................................
/home/darya/Documents/github/adnidod_preprocess/preprocess_example.py in ()
44 #jobfile = 'adnidod_config.ini' #("")
45 #jobfile = 'audio_config.ini'
46 jobfile = 'adnidod2016_config_example.ini'
47
48 # preprocess the data
---> 49 results = do_subjects_preproc(jobfile, dataset_dir=BASE_DIR)
50
51
52
53

...........................................................................
/home/darya/.local/lib/python2.7/site-packages/pypreprocess/nipype_preproc_spm_utils.py in do_subjects_preproc(subject_factory=[{'drift_model': 'Cosine', 'scratch': '/home/dary...e/results/0003107', 'warpable': ['anat', 'func']}, {'drift_model': 'Cosine', 'scratch': '/home/dary...e/results/0006315', 'warpable': ['anat', 'func']}], session_ids=None, **preproc_params={'TA': 'TR * (1 - 1 / nslices)', 'TR': 3.0, 'anat_write_voxel_sizes': [1.0, 1.0, 1.0], 'caching': True, 'coreg_anat_to_func': False, 'coregister': True, 'coregister_reslice': False, 'coregister_software': 'spm', 'dartel': False, 'dataset_description': '\n

This ADNIDOD resting-state fMRI study includ...x 3 mm\n

Shape : 64 x 64 x 48

\n\n', ...})
1708 if k in preproc_params:
1709 backup_params[k] = preproc_params.pop(k)
1710
1711 # run classic preproc
1712 subjects = Parallel(n_jobs=n_jobs)(delayed(do_subject_preproc)(
-> 1713 subject_data, **preproc_params) for subject_data in subjects)
subject_data = {'drift_model': 'Cosine', 'scratch': '/home/dary...e/results/0006315', 'warpable': ['anat', 'func']}
preproc_params = {'TA': 'TR * (1 - 1 / nslices)', 'TR': 3.0, 'anat_write_voxel_sizes': [1.0, 1.0, 1.0], 'caching': True, 'coreg_anat_to_func': False, 'coregister': True, 'coregister_reslice': False, 'coregister_software': 'spm', 'dartel': False, 'dataset_description': '\n

This ADNIDOD resting-state fMRI study includ...x 3 mm\n

Shape : 64 x 64 x 48

\n\n', ...}
subjects = [{'drift_model': 'Cosine', 'scratch': '/home/dary...e/results/0003107', 'warpable': ['anat', 'func']}, {'drift_model': 'Cosine', 'scratch': '/home/dary...e/results/0006315', 'warpable': ['anat', 'func']}]
1714
1715 # run DARTEL
1716 preproc_params.update(backup_params)
1717 if newsegment:

...........................................................................
/home/darya/anaconda2/lib/python2.7/site-packages/sklearn/externals/joblib/parallel.py in call(self=Parallel(n_jobs=2), iterable=<generator object >)
763 if pre_dispatch == "all" or n_jobs == 1:
764 # The iterable was consumed all at once by the above for loop.
765 # No need to wait for async callbacks to trigger to
766 # consumption.
767 self._iterating = False
--> 768 self.retrieve()
self.retrieve = <bound method Parallel.retrieve of Parallel(n_jobs=2)>
769 # Make sure that we get a last message telling us we are done
770 elapsed_time = time.time() - self._start_time
771 self._print('Done %3i out of %3i | elapsed: %s finished',
772 (len(self._output), len(self._output),

Sub-process traceback:

RuntimeError Tue Jan 17 11:29:32 2017
PID: 17303 Python 2.7.12: /home/darya/anaconda2/bin/python
...........................................................................
/home/darya/anaconda2/lib/python2.7/site-packages/sklearn/externals/joblib/parallel.py in call(self=<sklearn.externals.joblib.parallel.BatchedCalls object>)
126 def init(self, iterator_slice):
127 self.items = list(iterator_slice)
128 self._size = len(self.items)
129
130 def call(self):
--> 131 return [func(*args, **kwargs) for func, args, kwargs in self.items]
func =
args = ({'report_preproc_filename': '/home/darya/Documen...9091_I387201.nii'], 'warpable': ['anat', 'func']},)
kwargs = {'TA': 'TR * (1 - 1 / nslices)', 'TR': 3.0, 'anat_write_voxel_sizes': [1.0, 1.0, 1.0], 'caching': True, 'coreg_anat_to_func': False, 'coregister': True, 'coregister_reslice': False, 'coregister_software': 'spm', 'dartel': False, 'dataset_description': '\n

This ADNIDOD resting-state fMRI study includ...x 3 mm\n

Shape : 64 x 64 x 48

\n\n', ...}
self.items = [(, ({'report_preproc_filename': '/home/darya/Documen...9091_I387201.nii'], 'warpable': ['anat', 'func']},), {'TA': 'TR * (1 - 1 / nslices)', 'TR': 3.0, 'anat_write_voxel_sizes': [1.0, 1.0, 1.0], 'caching': True, 'coreg_anat_to_func': False, 'coregister': True, 'coregister_reslice': False, 'coregister_software': 'spm', 'dartel': False, 'dataset_description': '\n

This ADNIDOD resting-state fMRI study includ...x 3 mm\n

Shape : 64 x 64 x 48

\n\n', ...})]
132
133 def len(self):
134 return self._size
135

...........................................................................
/home/darya/.local/lib/python2.7/site-packages/pypreprocess/nipype_preproc_spm_utils.py in do_subject_preproc(subject_data={'report_preproc_filename': '/home/darya/Documen...9091_I387201.nii'], 'warpable': ['anat', 'func']}, deleteorient=True, slice_timing=True, slice_order='ascending', interleaved=True, ref_slice=1, TR=3.0, TA='TR * (1 - 1 / nslices)', slice_timing_software='spm', realign=True, realign_reslice=False, register_to_mean=True, realign_software='spm', coregister=True, coregister_reslice=False, coreg_anat_to_func=False, coregister_software='spm', segment=True, normalize=True, dartel=False, fwhm=[0.0, 0.0, 0.0], anat_fwhm=[0.0, 0.0, 0.0], func_write_voxel_sizes=[3.0, 3.0, 3.0], anat_write_voxel_sizes=[1.0, 1.0, 1.0], smooth_software='spm', hardlink_output=True, report=True, tsdiffana=True, parent_results_gallery=<pypreprocess.reporting.base_reporter.ResultsGallery object>, last_stage=True, preproc_undergone='

All preprocessing was done using <a href="htt... been applied to the functional images.', prepreproc_undergone='', caching=True, **kwargs={'dataset_description': '\n

This ADNIDOD resting-state fMRI study includ...x 3 mm\n

Shape : 64 x 64 x 48

\n\n', 'dataset_dir': '/home/darya/Documents/Inria/data/ADNIDOD_example/data', 'dataset_id': '/home/darya/Documents/Inria/data/ADNIDOD_example/data', 'matlab_exec': None, 'newsegment': False, 'output_modulated_tpms': False, 'spm_dir': None})
1292 subject_data, caching=caching,
1293 reslice=realign_reslice,
1294 register_to_mean=register_to_mean,
1295 report=report,
1296 hardlink_output=hardlink_output,
-> 1297 software=realign_software
realign_software = 'spm'
1298 )
1299
1300 # handle failed node
1301 if subject_data.failed:

...........................................................................
/home/darya/.local/lib/python2.7/site-packages/pypreprocess/nipype_preproc_spm_utils.py in _do_subject_realign(subject_data={'report_preproc_filename': '/home/darya/Documen...9091_I387201.nii'], 'warpable': ['anat', 'func']}, reslice=False, register_to_mean=True, caching=True, report=True, software='spm', spm_dir=None, matlab_exec=None, spm_mcr=None, hardlink_output=True, **kwargs={})
313 realign = spm.Realign().run
314
315 # run node
316 realign_result = realign(
317 in_files=subject_data.func, register_to_mean=register_to_mean,
--> 318 jobtype=jobtype, **kwargs)
jobtype = 'estwrite'
kwargs = {}
319
320 # failed node
321 if realign_result.outputs is None:
322 subject_data.failed = True

...........................................................................
/home/darya/anaconda2/lib/python2.7/site-packages/nipype/caching/memory.py in call(self=PipeFunc(nipype.interfaces.spm.preprocess.Realig...DOD_example/results/0003107/cache_dir/nipype_mem), **kwargs={'in_files': ['/home/darya/Documents/Inria/data/ADNIDOD_example...br_raw_20130927141408560_4967_S199091_I387201.nii'], 'jobtype': 'estwrite', 'register_to_mean': True})
81 node = Node(interface, name=job_name)
82 node.base_dir = os.path.join(self.base_dir, dir_name)
83
84 cwd = os.getcwd()
85 try:
---> 86 out = node.run()
out = undefined
node.run =
87 finally:
88 # node.run() changes to the node directory - if something goes wrong
89 # before it cds back you would end up in strange places
90 os.chdir(cwd)

...........................................................................
/home/darya/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py in run(self=d67dadf29f94905cbe5dfc3508fe6568, updatehash=False)
389 self.write_report(report_type='preexec', cwd=outdir)
390 savepkl(op.join(outdir, '_node.pklz'), self)
391 savepkl(op.join(outdir, '_inputs.pklz'),
392 self.inputs.get_traitsfree())
393 try:
--> 394 self._run_interface()
self._run_interface =
395 except:
396 os.remove(hashfile_unfinished)
397 raise
398 shutil.move(hashfile_unfinished, hashfile)

...........................................................................
/home/darya/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py in _run_interface(self=d67dadf29f94905cbe5dfc3508fe6568, execute=True, updatehash=False)
499 def _run_interface(self, execute=True, updatehash=False):
500 if updatehash:
501 return
502 old_cwd = os.getcwd()
503 os.chdir(self.output_dir())
--> 504 self._result = self._run_command(execute)
self._result = <nipype.interfaces.base.InterfaceResult object>
self._run_command =
execute = True
505 os.chdir(old_cwd)
506
507 def save_results(self, result, cwd):
508 resultsfile = op.join(cwd, 'result%s.pklz' % self.name)

...........................................................................
/home/darya/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py in _run_command(self=d67dadf29f94905cbe5dfc3508fe6568, execute=True, copyfiles=True)
625 fd = open(cmdfile, 'wt')
626 fd.writelines(cmd + "\n")
627 fd.close()
628 logger.info('Running: %s' % cmd)
629 try:
--> 630 result = self._interface.run()
result = <nipype.interfaces.base.InterfaceResult object>
self._interface.run = <bound method Realign.run of <nipype.interfaces.spm.preprocess.Realign object>>
631 except Exception as msg:
632 self._result.runtime.stderr = msg
633 raise
634

...........................................................................
/home/darya/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py in run(self=<nipype.interfaces.spm.preprocess.Realign object>, **inputs={'ignore_exception': False, 'in_files': ['/home/darya/Documents/Inria/data/ADNIDOD_example...br_raw_20130927141408560_4967_S199091_I387201.nii'], 'jobtype': 'estwrite', 'matlab_cmd': '/usr/local/bin/spm12 run script', 'mfile': True, 'out_prefix': 'r', 'register_to_mean': True, 'use_mcr': True, 'use_v8struct': True, 'write_which': [2, 1]})
1038 endTime=None,
1039 platform=platform.platform(),
1040 hostname=getfqdn(),
1041 version=self.version)
1042 try:
-> 1043 runtime = self._run_wrapper(runtime)
runtime = Bunch(cwd='/home/darya/Documents/Inria/data/ADNI...e Realign failed to run. ',), version=u'12.6914')
self._run_wrapper = <bound method Realign._run_wrapper of <nipype.interfaces.spm.preprocess.Realign object>>
1044 outputs = self.aggregate_outputs(runtime)
1045 runtime.endTime = dt.isoformat(dt.utcnow())
1046 timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime)
1047 runtime.duration = (timediff.days * 86400 + timediff.seconds +

...........................................................................
/home/darya/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py in _run_wrapper(self=<nipype.interfaces.spm.preprocess.Realign object>, runtime=Bunch(cwd='/home/darya/Documents/Inria/data/ADNI...e Realign failed to run. ',), version=u'12.6914'))
995 vdisp_num = vdisp.vdisplay_num
996
997 iflogger.info('Redirecting X to :%d' % vdisp_num)
998 runtime.environ['DISPLAY'] = ':%d' % vdisp_num
999
-> 1000 runtime = self._run_interface(runtime)
runtime = Bunch(cwd='/home/darya/Documents/Inria/data/ADNI...e Realign failed to run. ',), version=u'12.6914')
self._run_interface = <bound method Realign._run_interface of <nipype.interfaces.spm.preprocess.Realign object>>
1001
1002 if self._redirect_x:
1003 vdisp.stop()
1004

...........................................................................
/home/darya/anaconda2/lib/python2.7/site-packages/nipype/interfaces/spm/base.py in _run_interface(self=<nipype.interfaces.spm.preprocess.Realign object>, runtime=Bunch(cwd='/home/darya/Documents/Inria/data/ADNI...e Realign failed to run. ',), version=u'12.6914'))
306
307 def _run_interface(self, runtime):
308 """Executes the SPM function using MATLAB."""
309 self.mlab.inputs.script = self._make_matlab_command(
310 deepcopy(self._parse_inputs()))
--> 311 results = self.mlab.run()
results = undefined
self.mlab.run = <bound method MatlabCommand.run of <nipype.interfaces.matlab.MatlabCommand object>>
312 runtime.returncode = results.runtime.returncode
313 if self.mlab.inputs.uses_mcr:
314 if 'Skipped' in results.runtime.stdout:
315 self.raise_exception(runtime)

...........................................................................
/home/darya/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py in run(self=<nipype.interfaces.matlab.MatlabCommand object>, **inputs={'environ': {}, 'ignore_exception': False, 'mfile': True, 'postscript': ['\n,catch ME,', r"fprintf(2,'MATLAB code threw an exception:\n');", r"fprintf(2,'%s\n',ME.message);", r"if length(ME.stack) ~= 0, fprintf(2,'File:%s\nNa...ME.stack.file,ME.stack.name,ME.stack.line);, end;", 'end;'], 'prescript': [r"fprintf(1,'Executing %s at %s:\n',mfilename(),datestr(now));", 'ver,', 'try,'], 'script': "\n %% Generated by nipype.interfaces.spm\n ... close('all', 'force');\n end;\n ", 'script_file': 'pyscript_realign.m', 'terminal_output': 'allatonce', 'uses_mcr': True})
1038 endTime=None,
1039 platform=platform.platform(),
1040 hostname=getfqdn(),
1041 version=self.version)
1042 try:
-> 1043 runtime = self._run_wrapper(runtime)
runtime = Bunch(cmdline='/usr/local/bin/spm12 run script /...e MatlabCommand failed to run. ',), version=None)
self._run_wrapper = <bound method MatlabCommand._run_wrapper of <nipype.interfaces.matlab.MatlabCommand object>>
1044 outputs = self.aggregate_outputs(runtime)
1045 runtime.endTime = dt.isoformat(dt.utcnow())
1046 timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime)
1047 runtime.duration = (timediff.days * 86400 + timediff.seconds +

...........................................................................
/home/darya/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py in _run_wrapper(self=<nipype.interfaces.matlab.MatlabCommand object>, runtime=Bunch(cmdline='/usr/local/bin/spm12 run script /...e MatlabCommand failed to run. ',), version=None))
1655 )
1656 o, e = proc.communicate()
1657 return o
1658
1659 def _run_wrapper(self, runtime):
-> 1660 runtime = self._run_interface(runtime)
runtime = Bunch(cmdline='/usr/local/bin/spm12 run script /...e MatlabCommand failed to run. ',), version=None)
self._run_interface = <bound method MatlabCommand._run_interface of <nipype.interfaces.matlab.MatlabCommand object>>
1661 return runtime
1662
1663 def _run_interface(self, runtime, correct_return_codes=[0]):
1664 """Execute command via subprocess

...........................................................................
/home/darya/anaconda2/lib/python2.7/site-packages/nipype/interfaces/matlab.py in _run_interface(self=<nipype.interfaces.matlab.MatlabCommand object>, runtime=Bunch(cmdline='/usr/local/bin/spm12 run script /...e MatlabCommand failed to run. ',), version=None))
144 os.system('stty sane')
145 except:
146 # We might be on a system where stty doesn't exist
147 pass
148 if 'MATLAB code threw an exception' in runtime.stderr:
--> 149 self.raise_exception(runtime)
self.raise_exception = <bound method MatlabCommand.raise_exception of <nipype.interfaces.matlab.MatlabCommand object>>
runtime = Bunch(cmdline='/usr/local/bin/spm12 run script /...e MatlabCommand failed to run. ',), version=None)
150 return runtime
151
152 def _format_arg(self, name, trait_spec, value):
153 if name in ['script']:

...........................................................................
/home/darya/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py in raise_exception(self=<nipype.interfaces.matlab.MatlabCommand object>, runtime=Bunch(cmdline='/usr/local/bin/spm12 run script /...e MatlabCommand failed to run. ',), version=None))
1613 def raise_exception(self, runtime):
1614 message = "Command:\n" + runtime.cmdline + "\n"
1615 message += "Standard output:\n" + runtime.stdout + "\n"
1616 message += "Standard error:\n" + runtime.stderr + "\n"
1617 message += "Return code: " + str(runtime.returncode)
-> 1618 raise RuntimeError(message)
message = u'Command:\n/usr/local/bin/spm12 run script /hom...TLABbatch system\n\nLine:\n0\n\n\nReturn code: 0'
1619
1620 @classmethod
1621 def help(cls, returnhelp=False):
1622 allhelp = super(CommandLine, cls).help(returnhelp=True)

RuntimeError: Command:
/usr/local/bin/spm12 run script /home/darya/Documents/Inria/data/ADNIDOD_example/results/0003107/cache_dir/nipype_mem/nipype-interfaces-spm-preprocess-Realign/d67dadf29f94905cbe5dfc3508fe6568/pyscript_realign.m
Standard output:
Warning: Unable to open display ':1'. You will not be able to display graphics on the screen.
SPM12 (6914): /usr/local/src/spm12/spm12_mcr/spm12

---

/ )( _ ( / )
_ \ )/ ) ( Statistical Parametric Mapping
(/(_) (_//_) SPM12 - http://www.fil.ion.ucl.ac.uk/spm/

Warning: Unknown extension: 'script'

In spm_jobman>load_jobs at 334
In spm_jobman at 143
In spm_standalone at 33
Warning: No batch job found in 'script'
In spm_jobman>load_jobs at 343
In spm_jobman at 143
In spm_standalone at 33
Execution failed: scriptExecuting spm_jobman at 17-Jan-2017 11:29:25:

MATLAB Version 7.10.0.499 (R2010a)
MATLAB License Number: unknown
Operating System: Linux 3.13.0-32-generic #57-Ubuntu SMP Tue Jul 15 03:51:08 UTC 2014 x86_64
Java VM Version: Java 1.6.0_12-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode

MATLAB Version 7.10 (R2010a)
MATLAB Compiler Version 4.13 (R2010a)
Signal Processing Toolbox Version 6.13 (R2010a)
SPM version: SPM12 Release: 6914
SPM path: /usr/local/src/spm12/spm12_mcr/spm12/spm.m

Running job #1

Running 'Realign: Estimate & Reslice'

SPM12: spm_realign (v6070) 11:29:28 - 17/01/2017

Failed 'Realign: Estimate & Reslice'
Error using ==> colon
Maximum variable size allowed by the program is exceeded.
In file "/usr/local/src/spm12/spm12_mcr/spm12/spm_realign.m" (???), function "smooth_vol" at line 421.
In file "/usr/local/src/spm12/spm12_mcr/spm12/spm_realign.m" (???), function "realign_series" at line 234.
In file "/usr/local/src/spm12/spm12_mcr/spm12/spm_realign.m" (???), function "spm_realign" at line 136.
In file "/usr/local/src/spm12/spm12_mcr/spm12/config/spm_run_realign.m" (???), function "spm_run_realign" at line 31.

The following modules did not run:
Failed: Realign: Estimate & Reslice

Running job #2

Running 'Realign: Estimate & Reslice'

SPM12: spm_realign (v6070) 11:29:31 - 17/01/2017

Failed 'Realign: Estimate & Reslice'
Error using ==> colon
Maximum variable size allowed by the program is exceeded.
In file "/usr/local/src/spm12/spm12_mcr/spm12/spm_realign.m" (???), function "smooth_vol" at line 421.
In file "/usr/local/src/spm12/spm12_mcr/spm12/spm_realign.m" (???), function "realign_series" at line 234.
In file "/usr/local/src/spm12/spm12_mcr/spm12/spm_realign.m" (???), function "spm_realign" at line 136.
In file "/usr/local/src/spm12/spm12_mcr/spm12/config/spm_run_realign.m" (???), function "spm_run_realign" at line 31.

The following modules did not run:
Failed: Realign: Estimate & Reslice

Execution failed: /home/darya/Documents/Inria/data/ADNIDOD_example/results/0003107/cache_dir/nipype_mem/nipype-interfaces-spm-preprocess-Realign/d67dadf29f94905cbe5dfc3508fe6568/pyscript_realign.mBye for now...

Standard error:
MATLAB code threw an exception:
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the exact #job as displayed in this error message)

Running job #1

File:

Name:
MATLABbatch system

Line:
0

Return code: 0
Interface MatlabCommand failed to run.
Interface Realign failed to run.