darya-chyzhyk commented 8 years ago

When "deleteorient = True" there is an error:

........................................................................... /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

........................................................................... /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 > 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):

........................................................................... /usr/lib/python2.7/dist-packages/IPython/terminal/ipapp.py in start(self=) 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

........................................................................... /usr/lib/python2.7/dist-packages/IPython/terminal/interactiveshell.py in mainloop(self=, 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

........................................................................... /usr/lib/python2.7/dist-packages/IPython/terminal/interactiveshell.py in interact(self=, 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

........................................................................... /usr/lib/python2.7/dist-packages/IPython/core/interactiveshell.py in run_cell(self=, 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 = 2661
2662 # Execute any registered post-execution functions. 2663 # unless we are silent 2664 post_exec = [] if silent else self._post_execute.iteritems()

........................................................................... /usr/lib/python2.7/dist-packages/IPython/core/interactiveshell.py in run_ast_nodes(self=, nodelist=[<_ast.Expr object>], cell_name='', interactivity='last', compiler=) 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):

........................................................................... /usr/lib/python2.7/dist-packages/IPython/core/interactiveshell.py in run_code(self=, 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"getipython().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"getipython().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:

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

........................................................................... /usr/lib/python2.7/dist-packages/IPython/core/interactiveshell.py in magic(self=, arg_s=u'run preprocess.py') 2160 compound statements. 2161 """ 2162 # TODO: should we issue a loud deprecation warning here? 2163 magicname, , 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 #-------------------------------------------------------------------------

........................................................................... /usr/lib/python2.7/dist-packages/IPython/core/interactiveshell.py in run_line_magic(self=, 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 > 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.

........................................................................... /volatile/darya/Documents/experiments/preprocessing_adnidod/ in run(self=, 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 #-----------------------------------------------------------------------------

........................................................................... /usr/lib/python2.7/dist-packages/IPython/core/magic.py in (f=, _a=(, 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 = (, u'preprocess.py', None, ) k = {} 192 193 if callable(arg): 194 # "Naked" decorator call (just @foo, no args) 195 func = arg

........................................................................... /usr/lib/python2.7/dist-packages/IPython/core/magics/execution.py in run(self=, 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'] = namesave 641 else:

........................................................................... /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:

........................................................................... /usr/lib/python2.7/dist-packages/IPython/core/interactiveshell.py in safe_execfile(self=, 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:

........................................................................... /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=, 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 outputdir, = 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 commented 8 years ago

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

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

mrahim commented 8 years ago

1.3.0

AlexandreAbraham commented 8 years ago

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

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

dohmatob commented 8 years ago

+1. Somebody wants to take on this ?

On Tue, Aug 9, 2016 at 11:14 AM, Alexandre Abraham <notifications@github.com

wrote:

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

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

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/neurospin/pypreprocess/issues/246#issuecomment-238497968, or mute the thread https://github.com/notifications/unsubscribe-auth/AAms1IVPh0ngw84k_gd1GOa0iH_E0Wnbks5qeETagaJpZM4Jf3HJ .

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

dohmatob commented 8 years ago

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 gmdopp@gmail.com wrote:

+1. Somebody wants to take on this ?

On Tue, Aug 9, 2016 at 11:14 AM, Alexandre Abraham < notifications@github.com> wrote:

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

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

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/neurospin/pypreprocess/issues/246#issuecomment-238497968, or mute the thread https://github.com/notifications/unsubscribe-auth/AAms1IVPh0ngw84k_gd1GOa0iH_E0Wnbks5qeETagaJpZM4Jf3HJ .

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 commented 8 years ago

ResearchCode

AlexandreAbraham commented 8 years ago

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

dohmatob commented 8 years ago

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 <notifications@github.com

wrote:

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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/neurospin/pypreprocess/issues/246#issuecomment-238502203, or mute the thread https://github.com/notifications/unsubscribe-auth/AAms1NkRozaK374EpMtI3m3K1FKvG1spks5qeEkRgaJpZM4Jf3HJ .

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

AlexandreAbraham commented 7 years ago

The neverending issue!

darya-chyzhyk commented 7 years ago

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=) 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=, 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 = self._run_command = execute = True 505 os.chdir(old_cwd) 506 507 def _saveresults(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 = self._interface.run = <bound method Realign.run of > 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=, *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 > 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=, 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 > 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=, 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 > 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=, *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 > 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=, 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 > 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=, 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 > 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=, 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.

neurospin / pypreprocess

deleteorientation bug #246

ResearchCode