Create a FreeSurfer-license canary that can be run by fMRIPrep

[chrisgorgo]

https://openneuro.org/datasets/ds001230/versions/00001?app=FMRIPREP&version=51&job=5a847e689259cd00018b9810

Possible introduced in 1.0.7

--n_cpus 4 --participant_label 3129 --use-aroma --fs-license-file /input/data/b39610adfe02fdce2ad9d30797c567b3/LICENSE --output-space template T1w fsaverage

[Node] Error on "fmriprep_wf.single_subject_3129_wf.anat_preproc_wf.surface_recon_wf.autorecon1" (/root/src/fmriprep/work/fmriprep_wf/single_subject_3129_wf/anat_preproc_wf/surface_recon_wf/autorecon1)
Traceback (most recent call last):
  File "/usr/local/miniconda/bin/fmriprep", line 11, in <module>
    load_entry_point('fmriprep==1.0.7', 'console_scripts', 'fmriprep')()
  File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 267, in main
    fmriprep_wf.run(**plugin_settings)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 602, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 168, in run
    self._clean_queue(jobid, graph, result=result))
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 227, in _clean_queue
    raise RuntimeError("".join(result['traceback']))
RuntimeError: Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 68, 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 487, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 571, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 650, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 516, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 1023, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 960, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
recon-all -autorecon1 -i /snapshot/data/sub-3129/anat/sub-3129_acq-MPRAGE_run-1_T1w.nii.gz -noskullstrip -openmp 3 -subjid sub-3129 -sd /output/data/freesurfer
Standard output:
ERROR: You are trying to re-run an existing subject with (possibly)
 new input data (-i). If this is truly new input data, you should delete
 the subject folder and re-run, or specify a different subject name.
 If you are just continuing an analysis of an existing subject, then 
 omit all -i flags.
Standard error:

Return code: 1

[chrisgorgo]

Looking at recon-all.log I found:

mri_convert.bin /snapshot/data/sub-3129/anat/sub-3129_acq-MPRAGE_run-1_T1w.nii.gz /output/data/freesurfer/sub-3129/mri/orig/001.mgz 
--------------------------------------------------------------------------
ERROR: Invalid FreeSurfer license key found in license file /input/data/b39610adfe02fdce2ad9d30797c567b3/LICENSE
  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu/registration.html to 
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.
--------------------------------------------------------------------------

so there is something wrong with error reporting (but the real reason was bad license).

[effigies]

Interesting. Perhaps we can create a kind of FreeSurfer canary (say mri_convert <some_image>.nii.gz canary.nii.gz) to make sure the license is valid?

[chrisgorgo]

I think it would be worth while to add something like this in the very beginning of the workflow.

[chrisgorgo]

The weird thing is that previously the error was much more clear.

[effigies]

I agree, that is weird.

I also think that maybe it makes sense to do during setup, when we check for the existence of the license file in the first place. So just run a bare MRIConvert interface, rather than try to find a place to insert it into the workflow.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[oesteban]

Perhaps the implementation of the canary should go here in sMRIPrep, but then imported from fMRIPrep to actually run it.