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FMRIPrep version 20.1.0
Not sure if that is in fMRIPrep or SDCFlows that the workflow name is set, but I get the following error if B0FieldIdentifier contains a - , and this will likely occur for other characters (I have no knowledge on dot files syntax though).
File "/opt/conda/lib/python3.8/site-packages/fmriprep/cli/run.py", line 77, in main
fmriprep_wf.write_graph(graph2use="colored", format="svg", simple_form=True)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/workflows.py", line 465, in write_graph
outfname = format_dot(dotfilename, format=format)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/utils.py", line 1404, in format_dot
formatted_dot, _ = _run_dot(dotfilename, format_ext=format)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/utils.py", line 1420, in _run_dot
res = CommandLine(cmd, terminal_output="allatonce", resource_monitor=False).run()
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 822, in _run_interface
self.raise_exception(runtime)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 749, in raise_exception
raise RuntimeError(
RuntimeError: Command:
dot -Tsvg -o"...../workdir/fmriprep_wf/graph.svg" ".../workdir/fmriprep_wf/graph.dot"
Standard output:
Standard error:
Error: ..../workdir/fmriprep_wf/graph.dot: syntax error in line 29 near '-'
dot file contains something like fmriprep_wf_single_subject_01_wf_fmap_preproc_wf_in_b0id-test on the offending line.
The text was updated successfully, but these errors were encountered:
bpinsard
changed the title
B0FieldIdentifier: some characters should be replaced to set workflow to avoid crashes in graph creation
B0FieldIdentifier: some characters should be replaced to set workflow name to avoid crashes in graph creation
Nov 4, 2022
We use the B0FieldIdentifier as an entity at the output (estimated fieldmaps). But the B0FieldIdentifier can definitely have hyphens, so we probably want to revise the workflow names and the datasinks.
tsalo
linked a pull request
Apr 2, 2024
that will
close
this issue
FMRIPrep version 20.1.0
Not sure if that is in fMRIPrep or SDCFlows that the workflow name is set, but I get the following error if B0FieldIdentifier contains a
-
, and this will likely occur for other characters (I have no knowledge on dot files syntax though).dot file contains something like
fmriprep_wf_single_subject_01_wf_fmap_preproc_wf_in_b0id-test
on the offending line.The text was updated successfully, but these errors were encountered: