PandaFaye
commented
3 months ago might due to a low memory usage
Open LikithaBommasani opened 1 year ago
PandaFaye
commented
3 months ago might due to a low memory usage
Hello, I didn't understand why I'm getting this error. Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command raise NodeExecutionError(msg) nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node gather_inputs.
Traceback: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 397, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/eddy.py", line 76, in _run_interface get_best_b0_topup_inputs_from( File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/epi_fmap.py", line 211, in get_best_b0_topup_inputs_from spec = read_nifti_sidecar(unique_bids_file) File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/epi_fmap.py", line 42, in read_nifti_sidecar raise Exception("No corresponding json file found") Exception: No corresponding json file found
QSIPrep failed: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command raise NodeExecutionError(msg) nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node gather_inputs.
Traceback: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 397, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/eddy.py", line 76, in _run_interface get_best_b0_topup_inputs_from( File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/epi_fmap.py", line 211, in get_best_b0_topup_inputs_from spec = read_nifti_sidecar(unique_bids_file) File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/epi_fmap.py", line 42, in read_nifti_sidecar raise Exception("No corresponding json file found") Exception: No corresponding json file found
Traceback (most recent call last): File "/usr/local/miniconda/bin/qsiprep", line 8, in
sys.exit(main())
File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/cli/run.py", line 677, in main
qsiprep_wf.run(**plugin_settings)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/base.py", line 178, in run
self._clean_queue(jobid, graph, result=result)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/base.py", line 256, in _clean_queue
raise RuntimeError("".join(result["traceback"]))
RuntimeError: Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node gather_inputs.
Traceback: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 397, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/eddy.py", line 76, in _run_interface get_best_b0_topup_inputs_from( File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/epi_fmap.py", line 211, in get_best_b0_topup_inputs_from spec = read_nifti_sidecar(unique_bids_file) File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/epi_fmap.py", line 42, in read_nifti_sidecar raise Exception("No corresponding json file found") Exception: No corresponding json file found
230802-22:14:24,192 nipype.workflow INFO: [Node] Finished "raw_src", elapsed time 4.909848s. 230802-22:14:24,416 nipype.workflow INFO: [Node] Finished "raw_src", elapsed time 5.28037s. 230802-22:15:06,996 nipype.workflow INFO: [Node] Finished "synthseg", elapsed time 146.970091s. 230802-22:17:11,247 nipype.workflow INFO: [Node] Finished "acpc_reg", elapsed time 219.126629s.