Hello - I am running a level3 analysis with nipype. My script was working a few months ago, but now I get the following error (pasted below). I am using Python 3.10.6 and nipype 1.8.3. Any help debugging would be greatly appreciated!
RuntimeError Traceback (most recent call last)
RuntimeError: Traceback (most recent call last):
File "/apps/python/3.10/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/apps/python/3.10/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run
result = self._run_interface(execute=True)
File "/apps/python/3.10/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 1361, in _run_interface
result = self._collate_results(
File "/apps/python/3.10/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 1274, in _collate_results
raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Subnodes of node: flameo failed:
Subnode 0 failed
Error: Traceback (most recent call last):
File "/apps/python/3.10/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 401, in run
outputs = self.aggregate_outputs(runtime)
File "/apps/python/3.10/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 430, in aggregate_outputs
predicted_outputs = self._list_outputs() # Predictions from _list_outputs
File "/apps/python/3.10/lib/python3.10/site-packages/nipype/interfaces/fsl/model.py", line 1149, in _list_outputs
assert len(pes) >= 1, "No pe volumes generated by FSL Estimate"
AssertionError: No pe volumes generated by FSL Estimate
Traceback (most recent call last):
File "/apps/python/3.10/lib/python3.10/site-packages/nipype/pipeline/engine/utils.py", line 94, in nodelist_runner
result = node.run(updatehash=updatehash)
File "/apps/python/3.10/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run
result = self._run_interface(execute=True)
File "/apps/python/3.10/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 642, in _run_interface
return self._run_command(execute)
File "/apps/python/3.10/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command
raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node _flameo0.
Traceback (most recent call last):
File "/apps/python/3.10/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 401, in run
outputs = self.aggregate_outputs(runtime)
File "/apps/python/3.10/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 430, in aggregate_outputs
predicted_outputs = self._list_outputs() # Predictions from _list_outputs
File "/apps/python/3.10/lib/python3.10/site-packages/nipype/interfaces/fsl/model.py", line 1149, in _list_outputs
assert len(pes) >= 1, "No pe volumes generated by FSL Estimate"
AssertionError: No pe volumes generated by FSL Estimate
The above exception was the direct cause of the following exception:
RuntimeError Traceback (most recent call last)
Cell In[3], line 36
29 level3.config = {
30 "execution": {
31 "crashdump_dir": crashdumps_dir
32 }
33 }
35 level3.write_graph("workflow_graph.dot")
---> 36 level3.run(plugin='MultiProc', plugin_args={'n_procs':n_procs})
File /apps/python/3.10/lib/python3.10/site-packages/nipype/pipeline/engine/workflows.py:638, in Workflow.run(self, plugin, plugin_args, updatehash)
636 if str2bool(self.config["execution"]["create_report"]):
637 self._write_report_info(self.base_dir, self.name, execgraph)
--> 638 runner.run(execgraph, updatehash=updatehash, config=self.config)
639 datestr = datetime.utcnow().strftime("%Y%m%dT%H%M%S")
640 if str2bool(self.config["execution"]["write_provenance"]):
File /apps/python/3.10/lib/python3.10/site-packages/nipype/pipeline/plugins/base.py:212, in DistributedPluginBase.run(self, graph, config, updatehash)
206 if len(errors) > 1:
207 error, cause = (
208 RuntimeError(f"{len(errors)} raised. Re-raising first."),
209 error,
210 )
--> 212 raise error from cause
RuntimeError: 3 raised. Re-raising first.