Skip to content

AFNI's SkullStrip needs a $DISPLAY again after version 16.2.07 #2206

@oesteban

Description

@oesteban

Summary

It seems that AFNI's 3dSkullStrip is again linking libraries that need a functional X server.

Actual behavior

2017-09-25 20:17:53,524 workflow:INFO Running: 3dSkullStrip -input /scratch/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..circle-tests..sub-50137..anat..sub-50137_T1w.nii.gz/skullstrip/sub-50137_T1w_conformed_corrected.nii.gz -prefix sub-50137_T1w_conformed_corrected_skullstrip.nii.gz 2017-09-25 20:17:53,613 workflow:ERROR ['Node skullstrip.a0 failed to run on host 96ff9afc656c.'] 2017-09-25 20:17:53,614 workflow:INFO Saving crash info to /scratch/out/logs/crash-20170925-201753-root-skullstrip.a0-c8da4299-b3c4-4afd-bda5-14d2a723f97d.txt 2017-09-25 20:17:53,614 workflow:INFO Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 52, in run_node result['result'] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 372, in run self._run_interface() File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 482, in _run_interface self._result = self._run_command(execute) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 613, in _run_command result = self._interface.run() File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1084, in run runtime = self._run_wrapper(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1758, in _run_wrapper runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/afni/base.py", line 188, in _run_interface return super(AFNICommand, self)._run_interface(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/afni/base.py", line 126, in _run_interface return super(AFNICommandBase, self)._run_interface(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1792, in _run_interface self.raise_exception(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1716, in raise_exception **runtime.dictcopy())) RuntimeError: Command: 3dSkullStrip -input /scratch/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..circle-tests..sub-50137..anat..sub-50137_T1w.nii.gz/skullstrip/sub-50137_T1w_conformed_corrected.nii.gz -prefix sub-50137_T1w_conformed_corrected_skullstrip.nii.gz Standard output: Standard error: freeglut (3dSkullStrip): failed to open display ':1' Return code: 1 Interface SkullStrip failed to run. 

Expected behavior

The interface should run, opening an Xvfb if no X is available.

Other

  • How to replicate the behavior
  • Script/Workflow details
  • Platform details:
  • Execution environment

All of that on MRIQC's tests: https://circleci.com/gh/poldracklab/mriqc/1935

Metadata

Metadata

Assignees

No one assigned

    Labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions