DOCKER: Bundle FreeSurfer 7

[effigies]

Replaces #2552.

[effigies]

@mgxd Plan: I'll run ds000210 locally with this, including FreeSurfer, tonight.

[codecov-commenter]

Codecov Report

Merging #2779 (b24bbfa) into master (3ce5ec9) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #2779   +/-   ##
=======================================
  Coverage   45.51%   45.51%           
=======================================
  Files          44       44           
  Lines        3421     3421           
=======================================
  Hits         1557     1557           
  Misses       1864     1864           

---

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[effigies]

	 [Node] Setting-up "fmriprep_21_0_wf.single_subject_02_wf.anat_preproc_wf.surface_recon_wf.autorecon1" in "/scratch/fmriprep_21_0_wf/single_subject_02_wf/anat_preproc_wf/surface_recon_wf/autorecon1".
220518-01:28:56,445 nipype.workflow INFO:
	 [Node] Running "autorecon1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon1 -i /scratch/fmriprep_21_0_wf/single_subject_02_wf/anat_preproc_wf/anat_validate/sub-02_T1w_ras_valid.nii.gz -noskullstrip -openmp 7 -subjid sub-02 -sd /out/sourcedata/freesurfer
220518-01:28:56,605 nipype.workflow WARNING:
	 Storing result file without outputs
220518-01:28:56,605 nipype.workflow WARNING:
	 [Node] Error on "fmriprep_21_0_wf.single_subject_02_wf.anat_preproc_wf.surface_recon_wf.autorecon1" (/scratch/fmriprep_21_0_wf/single_subject_02_wf/anat_preproc_wf/surface_recon_wf/autorecon1)
220518-01:28:57,518 nipype.workflow ERROR:
	 Node autorecon1 failed to run on host fc4cbfb6266e.
220518-01:28:57,526 nipype.workflow ERROR:
	 Saving crash info to /out/sub-02/log/20220518-012712_de361c70-6374-4fd9-9ee2-fe31fcc9d19a/crash-20220518-012857-root-autorecon1-821b47d3-25f4-47ac-9392-3d5e2c86f23f.txt
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
    result = self._interface.run(cwd=outdir)
  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:
recon-all -autorecon1 -i /scratch/fmriprep_21_0_wf/single_subject_02_wf/anat_preproc_wf/anat_validate/sub-02_T1w_ras_valid.nii.gz -noskullstrip -openmp 7 -subjid sub-02 -sd /out/sourcedata/freesurfer
Standard output:
ERROR: could not configure recon-all parameters
Standard error:
Failed to import the site module
Error processing line 1 of /opt/freesurfer/python/lib/python3.6/site-packages/google_auth-1.33.1-py3.9-nspkg.pth:

Traceback (most recent call last):
  File "/opt/freesurfer/python/lib/python3.6/site.py", line 168, in addpackage
    exec(line)
  File "<string>", line 1, in <module>
  File "<frozen importlib._bootstrap>", line 568, in module_from_spec
AttributeError: 'NoneType' object has no attribute 'loader'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/freesurfer/python/lib/python3.6/site.py", line 553, in <module>
    main()
  File "/opt/freesurfer/python/lib/python3.6/site.py", line 540, in main
    known_paths = addsitepackages(known_paths)
  File "/opt/freesurfer/python/lib/python3.6/site.py", line 328, in addsitepackages
    addsitedir(sitedir, known_paths)
  File "/opt/freesurfer/python/lib/python3.6/site.py", line 207, in addsitedir
    addpackage(sitedir, name, known_paths)
  File "/opt/freesurfer/python/lib/python3.6/site.py", line 178, in addpackage
    import traceback
ModuleNotFoundError: No module named 'traceback'
Return code: 1

Will debug.

[effigies]

Oh. Obviously it's because we're excluding a ton of Python.

[effigies]

@mgxd This works, along with some patches to sMRIPrep. Since it took a few attempts and it picked up partial runs, I will rerun from scratch today, to verify.