Attempting to conduct fmriprep with fmriprep v 23.1.4 and getting this strange error. I removed the work directory and reran this participant but still got the same issue. Any ideas?
230914-21:59:16,55 nipype.workflow INFO:
fMRIPrep workflow graph with 27920 nodes built successfully.
230914-22:02:02,546 nipype.workflow IMPORTANT:
fMRIPrep started!
230914-22:04:05,609 nipype.workflow WARNING:
Some nodes exceed the total amount of memory available (280.00GB).
230914-22:07:21,261 nipype.workflow INFO:
[Node] Setting-up “fmriprep_23_1_wf.single_subject_SID000743_wf.func_preproc_ses_19_task_pinellocalizer_acq_mb8_run_08_wf.bold_fsLR_resampling_wf.select_surfaces” in “/dartfs-hpc/scratch/f003z4j/fmriprep-work/work-SID000743/fmriprep_23_1_wf/single_subject_SID000743_wf/func_preproc_ses_19_task_pinellocalizer_acq_mb8_run_08_wf/bold_fsLR_resampling_wf/_hemi_L/select_surfaces”.
230914-22:07:21,272 nipype.workflow INFO:
[Node] Setting-up “fmriprep_23_1_wf.single_subject_SID000743_wf.func_preproc_ses_19_task_pinellocalizer_acq_mb8_run_08_wf.bold_fsLR_resampling_wf.select_surfaces” in “/dartfs-hpc/scratch/f003z4j/fmriprep-work/work-SID000743/fmriprep_23_1_wf/single_subject_SID000743_wf/func_preproc_ses_19_task_pinellocalizer_acq_mb8_run_08_wf/bold_fsLR_resampling_wf/_hemi_R/select_surfaces”.
230914-22:07:21,299 nipype.workflow INFO:
[Node] Executing “select_surfaces” <nipype.interfaces.utility.wrappers.Function>
230914-22:07:21,303 nipype.workflow INFO:
[Node] Finished “select_surfaces”, elapsed time 0.000312s.
230914-22:07:21,303 nipype.workflow WARNING:
Storing result file without outputs
230914-22:07:21,308 nipype.workflow WARNING:
[Node] Error on “fmriprep_23_1_wf.single_subject_SID000743_wf.func_preproc_ses_19_task_pinellocalizer_acq_mb8_run_08_wf.bold_fsLR_resampling_wf.select_surfaces” (/dartfs-hpc/scratch/f003z4j/fmriprep-work/work-SID000743/fmriprep_23_1_wf/single_subject_SID000743_wf/func_preproc_ses_19_task_pinellocalizer_acq_mb8_run_08_wf/bold_fsLR_resampling_wf/_hemi_L/select_surfaces)
230914-22:07:21,309 nipype.workflow INFO:
[Node] Executing “select_surfaces” <nipype.interfaces.utility.wrappers.Function>
230914-22:07:21,313 nipype.workflow INFO:
[Node] Finished “select_surfaces”, elapsed time 0.00032s.
230914-22:07:21,313 nipype.workflow INFO:
[Node] Setting-up “fmriprep_23_1_wf.single_subject_SID000743_wf.func_preproc_ses_19_task_movemap_acq_mb8_run_07_wf.bold_fsLR_resampling_wf.select_surfaces” in “/dartfs-hpc/scratch/f003z4j/fmriprep-work/work-SID000743/fmriprep_23_1_wf/single_subject_SID000743_wf/func_preproc_ses_19_task_movemap_acq_mb8_run_07_wf/bold_fsLR_resampling_wf/_hemi_L/select_surfaces”.
230914-22:07:21,313 nipype.workflow WARNING:
Storing result file without outputs
230914-22:07:21,318 nipype.workflow WARNING:
[Node] Error on “fmriprep_23_1_wf.single_subject_SID000743_wf.func_preproc_ses_19_task_pinellocalizer_acq_mb8_run_08_wf.bold_fsLR_resampling_wf.select_surfaces” (/dartfs-hpc/scratch/f003z4j/fmriprep-work/work-SID000743/fmriprep_23_1_wf/single_subject_SID000743_wf/func_preproc_ses_19_task_pinellocalizer_acq_mb8_run_08_wf/bold_fsLR_resampling_wf/_hemi_R/select_surfaces)
230914-22:07:21,323 nipype.workflow INFO:
[Node] Setting-up “fmriprep_23_1_wf.single_subject_SID000743_wf.func_preproc_ses_19_task_movemap_acq_mb8_run_07_wf.bold_fsLR_resampling_wf.select_surfaces” in “/dartfs-hpc/scratch/f003z4j/fmriprep-work/work-SID000743/fmriprep_23_1_wf/single_subject_SID000743_wf/func_preproc_ses_19_task_movemap_acq_mb8_run_07_wf/bold_fsLR_resampling_wf/_hemi_R/select_surfaces”.
230914-22:07:21,352 nipype.workflow INFO:
[Node] Executing “select_surfaces” <nipype.interfaces.utility.wrappers.Function>
230914-22:07:21,353 nipype.workflow INFO:
[Node] Finished “select_surfaces”, elapsed time 0.000304s.
230914-22:07:21,353 nipype.workflow WARNING:
Storing result file without outputs
230914-22:07:21,358 nipype.workflow WARNING:
[Node] Error on “fmriprep_23_1_wf.single_subject_SID000743_wf.func_preproc_ses_19_task_movemap_acq_mb8_run_07_wf.bold_fsLR_resampling_wf.select_surfaces” (/dartfs-hpc/scratch/f003z4j/fmriprep-work/work-SID000743/fmriprep_23_1_wf/single_subject_SID000743_wf/func_preproc_ses_19_task_movemap_acq_mb8_run_07_wf/bold_fsLR_resampling_wf/_hemi_L/select_surfaces)
230914-22:07:21,360 nipype.workflow INFO:
[Node] Executing “select_surfaces” <nipype.interfaces.utility.wrappers.Function>
230914-22:07:21,361 nipype.workflow INFO:
[Node] Finished “select_surfaces”, elapsed time 0.000304s.
230914-22:07:21,361 nipype.workflow WARNING:
Storing result file without outputs
230914-22:07:21,366 nipype.workflow WARNING:
[Node] Error on “fmriprep_23_1_wf.single_subject_SID000743_wf.func_preproc_ses_19_task_movemap_acq_mb8_run_07_wf.bold_fsLR_resampling_wf.select_surfaces” (/dartfs-hpc/scratch/f003z4j/fmriprep-work/work-SID000743/fmriprep_23_1_wf/single_subject_SID000743_wf/func_preproc_ses_19_task_movemap_acq_mb8_run_07_wf/bold_fsLR_resampling_wf/_hemi_R/select_surfaces)
230914-22:07:21,431 nipype.workflow INFO:
[Node] Setting-up “fmriprep_23_1_wf.single_subject_SID000743_wf.func_preproc_ses_19_task_movemap_acq_mb8_run_06_wf.bold_fsLR_resampling_wf.select_surfaces” in “/dartfs-hpc/scratch/f003z4j/fmriprep-work/work-SID000743/fmriprep_23_1_wf/single_subject_SID000743_wf/func_preproc_ses_19_task_movemap_acq_mb8_run_06_wf/bold_fsLR_resampling_wf/_hemi_L/select_surfaces”.
230914-22:07:21,435 nipype.workflow INFO:
[Node] Setting-up “fmriprep_23_1_wf.single_subject_SID000743_wf.func_preproc_ses_19_task_movemap_acq_mb8_run_06_wf.bold_fsLR_resampling_wf.select_surfaces” in “/dartfs-hpc/scratch/f003z4j/fmriprep-work/work-SID000743/fmriprep_23_1_wf/single_subject_SID000743_wf/func_preproc_ses_19_task_movemap_acq_mb8_run_06_wf/bold_fsLR_resampling_wf/_hemi_R/select_surfaces”.
230914-22:07:21,467 nipype.workflow INFO:
[Node] Executing “select_surfaces” <nipype.interfaces.utility.wrappers.Function>
230914-22:07:21,468 nipype.workflow INFO:
[Node] Finished “select_surfaces”, elapsed time 0.000298s.
230914-22:07:21,469 nipype.workflow WARNING:
Storing result file without outputs
230914-22:07:21,472 nipype.workflow INFO:
[Node] Executing “select_surfaces” <nipype.interfaces.utility.wrappers.Function>
230914-22:07:21,473 nipype.workflow INFO:
[Node] Finished “select_surfaces”, elapsed time 0.000297s.
230914-22:07:21,473 nipype.workflow WARNING:
Storing result file without outputs
230914-22:07:21,475 nipype.workflow WARNING:
[Node] Error on “fmriprep_23_1_wf.single_subject_SID000743_wf.func_preproc_ses_19_task_movemap_acq_mb8_run_06_wf.bold_fsLR_resampling_wf.select_surfaces” (/dartfs-hpc/scratch/f003z4j/fmriprep-work/work-SID000743/fmriprep_23_1_wf/single_subject_SID000743_wf/func_preproc_ses_19_task_movemap_acq_mb8_run_06_wf/bold_fsLR_resampling_wf/_hemi_L/select_surfaces)
230914-22:07:21,477 nipype.workflow WARNING:
[Node] Error on “fmriprep_23_1_wf.single_subject_SID000743_wf.func_preproc_ses_19_task_movemap_acq_mb8_run_06_wf.bold_fsLR_resampling_wf.select_surfaces” (/dartfs-hpc/scratch/f003z4j/fmriprep-work/work-SID000743/fmriprep_23_1_wf/single_subject_SID000743_wf/func_preproc_ses_19_task_movemap_acq_mb8_run_06_wf/bold_fsLR_resampling_wf/_hemi_R/select_surfaces)
230914-22:07:21,542 nipype.workflow ERROR:
Node select_surfaces.a0 failed to run on host n03.hpcc.dartmouth.edu.
230914-22:07:21,546 nipype.workflow ERROR:
Saving crash info to /dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/derivatives/fmriprep/sub-SID000743/log/20230914-212735_5666d499-44f9-4e2b-af0f-43e0aea6d87f/crash-20230914-220721-f003z4j-select_surfaces.a0-8c0cadd2-2508-41a2-9d2b-6e5232a91d06.txt
Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py”, line 67, in run_node
result[“result”] = node.run(updatehash=updatehash)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 527, in run
result = self._run_interface(execute=True)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 645, in _run_interface
return self._run_command(execute)
File “/opt/conda/envs/fmriprep/lib/python3.10/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 select_surfaces.
Traceback:
Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py”, line 397, in run
runtime = self._run_interface(runtime)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/utility/wrappers.py”, line 142, in _run_interface
out = function_handle(**args)
TypeError: _select_surfaces() missing 3 required positional arguments: ‘surfaces’, ‘morphometrics’, and ‘spherical_registrations’
230914-22:07:21,552 nipype.workflow CRITICAL:
fMRIPrep failed: Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py”, line 67, in run_node
result[“result”] = node.run(updatehash=updatehash)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 527, in run
result = self._run_interface(execute=True)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 645, in _run_interface
return self._run_command(execute)
File “/opt/conda/envs/fmriprep/lib/python3.10/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 select_surfaces.
Traceback:
Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py”, line 397, in run
runtime = self._run_interface(runtime)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/utility/wrappers.py”, line 142, in _run_interface
out = function_handle(**args)
TypeError: _select_surfaces() missing 3 required positional arguments: ‘surfaces’, ‘morphometrics’, and ‘spherical_registrations’
Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/cli/run.py”, line 162, in main
fmriprep_wf.run(**config.nipype.get_plugin())
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/workflows.py”, line 638, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/base.py”, line 178, in run
self._clean_queue(jobid, graph, result=result)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/base.py”, line 256, in _clean_queue
raise RuntimeError(“”.join(result[“traceback”]))
RuntimeError: Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py”, line 67, in run_node
result[“result”] = node.run(updatehash=updatehash)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 527, in run
result = self._run_interface(execute=True)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 645, in _run_interface
return self._run_command(execute)
File “/opt/conda/envs/fmriprep/lib/python3.10/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 select_surfaces.
Traceback:
Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py”, line 397, in run
runtime = self._run_interface(runtime)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/utility/wrappers.py”, line 142, in _run_interface
out = function_handle(**args)
TypeError: _select_surfaces() missing 3 required positional arguments: ‘surfaces’, ‘morphometrics’, and ‘spherical_registrations’
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/bin/fmriprep”, line 8, in
sys.exit(main())
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/cli/run.py”, line 227, in main
failed_reports = generate_reports(
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/reports/core.py”, line 96, in generate_reports
report_errors = [
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/reports/core.py”, line 97, in
run_reports(
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/reports/core.py”, line 79, in run_reports
return Report(
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/reports/core.py”, line 307, in init
self._load_config(Path(config or pkgrf(“niworkflows”, “reports/default.yml”)))
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/reports/core.py”, line 48, in _load_config
self.index(settings[“sections”])
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/reports/core.py”, line 394, in index
self.errors = [read_crashfile(str(f)) for f in error_dir.glob(“crash*.")]
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/reports/core.py”, line 394, in
self.errors = [read_crashfile(str(f)) for f in error_dir.glob("crash.*”)]
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/utils/misc.py”, line 184, in read_crashfile
return _read_txt(path)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/utils/misc.py”, line 241, in _read_txt
cur_key, cur_val = tuple(line.split(" = ", 1))
ValueError: not enough values to unpack (expected 2, got 1)