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@hstojic
Description
Summary
I get an error defining SPM model level 1, with multiple runs and concatenate_runs set to True. I made sure that I have the same regressors in each run. The culprit seems to be the nipype code that adds run specific dummy variables (code) - regressor_names are not updated with these added variables and then error is raised at this line as of course it cannot find the regressor name.
Here is the error part from stdout:
[Node] Error on "stimuli_LSA_test_pipeline.model" (/media/hstojic/dataneuro/fnclearning_fmri/dProcessed/nipype_work/stimuli_LSA_test_pipeline/_subject_s057/model) [Node] Error on "stimuli_LSA_test_pipeline.model" (/media/hstojic/dataneuro/fnclearning_fmri/dProcessed/nipype_work/stimuli_LSA_test_pipeline/_subject_s057/model) --------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) <ipython-input-9-a5adcf3b88b5> in <module>() 2 pipeline.run( 3 'MultiProc', ----> 4 plugin_args = {'n_procs': pars_gen['resources']['n_cores']} 5 ) /home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.pyc in run(self, plugin, plugin_args, updatehash) 593 if str2bool(self.config['execution']['create_report']): 594 self._write_report_info(self.base_dir, self.name, execgraph) --> 595 runner.run(execgraph, updatehash=updatehash, config=self.config) 596 datestr = datetime.utcnow().strftime('%Y%m%dT%H%M%S') 597 if str2bool(self.config['execution']['write_provenance']): /home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/pipeline/plugins/base.pyc in run(self, graph, config, updatehash) 160 if result['traceback']: 161 notrun.append( --> 162 self._clean_queue(jobid, graph, result=result)) 163 else: 164 self._task_finished_cb(jobid) /home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/pipeline/plugins/base.pyc in _clean_queue(self, jobid, graph, result) 222 223 if str2bool(self._config['execution']['stop_on_first_crash']): --> 224 raise RuntimeError("".join(result['traceback'])) 225 crashfile = self._report_crash(self.procs[jobid], result=result) 226 if jobid in self.mapnodesubids: RuntimeError: Traceback (most recent call last): File "/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node result['result'] = node.run(updatehash=updatehash) File "/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run result = self._run_interface(execute=True) File "/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface return self._run_command(execute) File "/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command result = self._interface.run(cwd=outdir) File "/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 521, in run runtime = self._run_interface(runtime) File "/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/algorithms/modelgen.py", line 453, in _run_interface self._generate_design() File "/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/algorithms/modelgen.py", line 628, in _generate_design outliers=outliers) File "/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype/algorithms/modelgen.py", line 372, in _generate_standard_design info.regressor_names[j] IndexError: list index out of range
If my interpretation is correct I can send a pull request, its an easy fix with a single line I think:
infoout.regressor_names.extend(['run' + str(i + 1)])
at this line. I already tested it and that seems to work.
Platform details:
{'commit_hash': '8690d55d9',
'commit_source': 'installation',
'networkx_version': '2.1',
'nibabel_version': '2.3.0',
'nipype_version': '1.1.2',
'numpy_version': '1.15.4',
'pkg_path': '/home/hstojic/.pyenv/nipy/local/lib/python2.7/site-packages/nipype',
'scipy_version': '1.1.0',
'sys_executable': '/home/hstojic/.pyenv/nipy/bin/python',
'sys_platform': 'linux2',
'sys_version': '2.7.12 (default, Nov 20 2017, 18:23:56) \n[GCC 5.4.0 20160609]',
'traits_version': '4.6.0'}
Execution environment
- My python environment outside container