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recon-all -s exited with ERRORS ERROR: Flag -lh-only unrecognized #398

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labdelmo opened this issue Apr 8, 2024 · 2 comments
Open

recon-all -s exited with ERRORS ERROR: Flag -lh-only unrecognized #398

labdelmo opened this issue Apr 8, 2024 · 2 comments
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bug Something isn't working

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@labdelmo
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labdelmo commented Apr 8, 2024

Hello, when running ASLPREP, I get this error message. Please help me debug it. I have ASLPREP version: v0.6.0 and Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a and I'm running ASLPREP using DOCKER.

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/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 _autorecon_surfs0.

Cmdline:
	recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -lh-only -openmp 8 -subjid sub-01 -sd /out/aslprep/sourcedata/freesurfer 
Stdout:
	ERROR: Flag -lh-only unrecognized.
	-autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -lh-only -openmp 8 -subjid sub-01 -sd /out/aslprep/sourcedata/freesurfer
	Linux 8559b23dfa2d 5.15.146.1-microsoft-standard-WSL2 #1 SMP Thu Jan 11 04:09:03 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

	recon-all -s  exited with ERRORS at Mon Apr  8 00:49:25 UTC 2024
Stderr:
Traceback:
	RuntimeError: subprocess exited with code 1.
@labdelmo labdelmo added the bug Something isn't working label Apr 8, 2024
@tsalo
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tsalo commented Apr 8, 2024

I think I need to increase the installed FreeSurfer version. I'll look into fixing it today.

@labdelmo
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labdelmo commented Apr 8, 2024

That would help me a lot, thank you so much!

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