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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
628 stars 290 forks source link

Some workflows fail building in RTD #806

Closed oesteban closed 5 years ago

oesteban commented 6 years ago 
Running Sphinx v1.6.5
making output directory...
loading translations [en]... done
loading pickled environment... not yet created
loading intersphinx inventory from https://docs.python.org/objects.inv...
intersphinx inventory has moved: https://docs.python.org/objects.inv -> https://docs.python.org/2/objects.inv
building [mo]: targets for 0 po files that are out of date
building [json]: targets for 15 source files that are out of date
updating environment: 15 added, 0 changed, 0 removed
reading sources... [  6%] anat/base
reading sources... [ 13%] api/index
Creating bold processing workflow for "/completely/made/up/path/sub-01_task-nback_bold.nii.gz".
No valid layout: building empty workflow.
Slice-timing correction will be included.
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/anat_preproc_wf/index-3.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/anat_preproc_wf/index-3.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/anat_preproc_wf/index-3.dot.pdf (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/skullstrip_ants_wf/index-4.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/skullstrip_ants_wf/index-4.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/skullstrip_ants_wf/index-4.dot.pdf (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/surface_recon_wf/index-5.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/surface_recon_wf/index-5.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/surface_recon_wf/index-5.dot.pdf (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/autorecon_resume_wf/index-6.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/autorecon_resume_wf/index-6.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/autorecon_resume_wf/index-6.dot.pdf (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/gifti_surface_wf/index-7.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/gifti_surface_wf/index-7.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/gifti_surface_wf/index-7.dot.pdf (graph2use=orig, simple_form=True).
Creating bold processing workflow for "/completely/made/up/path/sub-01_task-nback_bold.nii.gz".
No valid layout: building empty workflow.
Slice-timing correction will be included.
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bold_reference_wf/index-9.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bold_reference_wf/index-9.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bold_reference_wf/index-9.dot.pdf (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/enhance_and_skullstrip_bold_wf/index-10.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/enhance_and_skullstrip_bold_wf/index-10.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/enhance_and_skullstrip_bold_wf/index-10.dot.pdf (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/skullstrip_bold_wf/index-11.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/skullstrip_bold_wf/index-11.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/skullstrip_bold_wf/index-11.dot.pdf (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bold_hmc_wf/index-12.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bold_hmc_wf/index-12.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bold_hmc_wf/index-12.dot.pdf (graph2use=orig, simple_form=True).
Slice-timing correction will be included.
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bold_stc_wf/index-13.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bold_stc_wf/index-13.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bold_stc_wf/index-13.dot.pdf (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bbreg_wf/index-15.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bbreg_wf/index-15.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bbreg_wf/index-15.dot.pdf (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bold_surf_wf/index-17.png (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bold_surf_wf/index-17.svg (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bold_surf_wf/index-17.pdf (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bold_mni_trans_wf/index-18.png (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bold_mni_trans_wf/index-18.svg (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bold_mni_trans_wf/index-18.pdf (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bold_confs_wf/index-19.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bold_confs_wf/index-19.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/bold_confs_wf/index-19.dot.pdf (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/ica_aroma_wf/index-20.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/ica_aroma_wf/index-20.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/api/ica_aroma_wf/index-20.dot.pdf (graph2use=orig, simple_form=True).
reading sources... [ 20%] api/interfaces
reading sources... [ 26%] changes
reading sources... [ 33%] citing
reading sources... [ 40%] contributors
reading sources... [ 46%] index
reading sources... [ 53%] installation
reading sources... [ 60%] license
reading sources... [ 66%] links
reading sources... [ 73%] sdc/base
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/fmap_unwarp_report_wf/base-1.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/fmap_unwarp_report_wf/base-1.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/fmap_unwarp_report_wf/base-1.dot.pdf (graph2use=orig, simple_form=True).
reading sources... [ 80%] sdc/estimation
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/fmap_wf/estimation-1.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/fmap_wf/estimation-1.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/fmap_wf/estimation-1.dot.pdf (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/phdiff_wf/estimation-2.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/phdiff_wf/estimation-2.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/phdiff_wf/estimation-2.dot.pdf (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/nonlinear_sdc_wf/estimation-3.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/nonlinear_sdc_wf/estimation-3.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/nonlinear_sdc_wf/estimation-3.dot.pdf (graph2use=orig, simple_form=True).
reading sources... [ 86%] sdc/unwarping
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/pepolar_unwarp_wf/unwarping-1.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/pepolar_unwarp_wf/unwarping-1.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/pepolar_unwarp_wf/unwarping-1.dot.pdf (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/prepare_epi_wf/unwarping-2.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/prepare_epi_wf/unwarping-2.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/prepare_epi_wf/unwarping-2.dot.pdf (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/sdc_unwarp_wf/unwarping-3.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/sdc_unwarp_wf/unwarping-3.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/sdc/sdc_unwarp_wf/unwarping-3.dot.pdf (graph2use=orig, simple_form=True).
reading sources... [ 93%] usage
reading sources... [100%] workflows
Creating bold processing workflow for "/completely/made/up/path/sub-01_task-nback_bold.nii.gz".
No valid layout: building empty workflow.
Slice-timing correction will be included.
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/anat_preproc_wf/workflows-2.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/anat_preproc_wf/workflows-2.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/anat_preproc_wf/workflows-2.dot.pdf (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/surface_recon_wf/workflows-3.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/surface_recon_wf/workflows-3.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/surface_recon_wf/workflows-3.dot.pdf (graph2use=orig, simple_form=True).
Creating bold processing workflow for "/completely/made/up/path/sub-01_task-nback_bold.nii.gz".
No valid layout: building empty workflow.
Slice-timing correction will be included.
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/bold_reference_wf/workflows-5.dot.png (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/bold_reference_wf/workflows-5.dot.svg (graph2use=orig, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/bold_reference_wf/workflows-5.dot.pdf (graph2use=orig, simple_form=True).
Slice-timing correction will be included.
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/bold_stc_wf/workflows-6.png (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/bold_stc_wf/workflows-6.svg (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/bold_stc_wf/workflows-6.pdf (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/bold_hmc_wf/workflows-7.png (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/bold_hmc_wf/workflows-7.svg (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/bold_hmc_wf/workflows-7.pdf (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/bold_mni_trans_wf/workflows-9.png (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/bold_mni_trans_wf/workflows-9.svg (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/bold_mni_trans_wf/workflows-9.pdf (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/bold_surf_wf/workflows-10.png (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/bold_surf_wf/workflows-10.svg (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/bold_surf_wf/workflows-10.pdf (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/discover_wf/workflows-11.png (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/discover_wf/workflows-11.svg (graph2use=colored, simple_form=True).
Generated workflow graph: /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/_build/wf_directive/discover_wf/workflows-11.pdf (graph2use=colored, simple_form=True).

/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/niworkflows/nipype/workflows/dmri/mrtrix/group_connectivity.py:16: UserWarning: cmp not installed
  warnings.warn('cmp not installed')
/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/niworkflows/nipype/interfaces/fsl/preprocess.py:1597: UserWarning: This has not been fully tested. Please report any failures.
  warn('This has not been fully tested. Please report any failures.')
/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/niworkflows/nipype/interfaces/fsl/preprocess.py:1597: UserWarning: This has not been fully tested. Please report any failures.
  warn('This has not been fully tested. Please report any failures.')
/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/fmriprep/workflows/base.py:docstring of fmriprep.workflows.base.init_fmriprep_wf:7: WARNING: Exception occurred in plotting index-1
 from /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/api/index.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/nipype/sphinxext/plot_workflow.py", line 464, in run_code
    exec(code, ns)
  File "<string>", line 29, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/fmriprep/workflows/base.py", line 158, in init_fmriprep_wf
    spaces=output_spaces),
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/niworkflows/nipype/interfaces/base.py", line 1252, in __init__
    from_file=from_file, resource_monitor=resource_monitor, **inputs)
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/niworkflows/nipype/interfaces/base.py", line 782, in __init__
    self.inputs = self.input_spec(**inputs)
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/niworkflows/nipype/interfaces/base.py", line 359, in __init__
    super(BaseTraitedSpec, self).__init__(**kwargs)
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/niworkflows/nipype/interfaces/traits_extension.py", line 189, in validate
    self.error(object, name, value)
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/traits/trait_handlers.py", line 173, in error
    value )
traits.trait_errors.TraitError: The 'freesurfer_home' trait of a BIDSFreeSurferDirInputSpec instance must be an existing directory name, but a value of None <class 'NoneType'> was specified.
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/fmriprep/workflows/base.py:docstring of fmriprep.workflows.base.init_single_subject_wf:10: WARNING: Exception occurred in plotting index-2
 from /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/api/index.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/nipype/sphinxext/plot_workflow.py", line 464, in run_code
    exec(code, ns)
  File "<string>", line 29, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/fmriprep/workflows/base.py", line 430, in init_single_subject_wf
    ignore_aroma_err=ignore_aroma_err)
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/fmriprep/workflows/bold/base.py", line 318, in init_func_preproc_wf
    use_fieldwarp=(fmaps is not None or use_syn))
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/fmriprep/workflows/bold/registration.py", line 184, in init_bold_reg_wf
    (mask_t1w_tfm, outputnode, [('output_image', 'bold_mask_t1')])
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 233, in connect
    infostr))
Exception: Some connections were not found
Module gen_ref has no input called fov_mask
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
docstring of fmriprep.workflows.bold.base.init_func_preproc_wf:3: WARNING: Exception occurred in plotting index-8
 from /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/api/index.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/nipype/sphinxext/plot_workflow.py", line 464, in run_code
    exec(code, ns)
  File "<string>", line 22, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/fmriprep/workflows/bold/base.py", line 318, in init_func_preproc_wf
    use_fieldwarp=(fmaps is not None or use_syn))
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/fmriprep/workflows/bold/registration.py", line 184, in init_bold_reg_wf
    (mask_t1w_tfm, outputnode, [('output_image', 'bold_mask_t1')])
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 233, in connect
    infostr))
Exception: Some connections were not found
Module gen_ref has no input called fov_mask
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
docstring of fmriprep.workflows.bold.registration.init_bold_reg_wf:10: WARNING: Exception occurred in plotting index-14
 from /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/api/index.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/nipype/sphinxext/plot_workflow.py", line 464, in run_code
    exec(code, ns)
  File "<string>", line 6, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/fmriprep/workflows/bold/registration.py", line 184, in init_bold_reg_wf
    (mask_t1w_tfm, outputnode, [('output_image', 'bold_mask_t1')])
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 233, in connect
    infostr))
Exception: Some connections were not found
Module gen_ref has no input called fov_mask
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
docstring of fmriprep.workflows.bold.registration.init_fsl_bbr_wf:16: WARNING: Exception occurred in plotting index-16
 from /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/api/index.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/nipype/sphinxext/plot_workflow.py", line 464, in run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/fmriprep/workflows/bold/registration.py", line 505, in init_fsl_bbr_wf
    schedule=op.join(os.getenv('FSLDIR'), 'etc/flirtsch/bbr.sch')),
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/posixpath.py", line 89, in join
    genericpath._check_arg_types('join', a, *p)
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/genericpath.py", line 143, in _check_arg_types
    (funcname, s.__class__.__name__)) from None
TypeError: join() argument must be str or bytes, not 'NoneType'
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/workflows.rst:15: WARNING: Exception occurred in plotting workflows-1
 from /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/workflows.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/nipype/sphinxext/plot_workflow.py", line 464, in run_code
    exec(code, ns)
  File "<string>", line 29, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/fmriprep/workflows/base.py", line 430, in init_single_subject_wf
    ignore_aroma_err=ignore_aroma_err)
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/fmriprep/workflows/bold/base.py", line 318, in init_func_preproc_wf
    use_fieldwarp=(fmaps is not None or use_syn))
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/fmriprep/workflows/bold/registration.py", line 184, in init_bold_reg_wf
    (mask_t1w_tfm, outputnode, [('output_image', 'bold_mask_t1')])
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 233, in connect
    infostr))
Exception: Some connections were not found
Module gen_ref has no input called fov_mask
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/workflows.rst:185: WARNING: Exception occurred in plotting workflows-4
 from /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/workflows.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/nipype/sphinxext/plot_workflow.py", line 464, in run_code
    exec(code, ns)
  File "<string>", line 22, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/fmriprep/workflows/bold/base.py", line 318, in init_func_preproc_wf
    use_fieldwarp=(fmaps is not None or use_syn))
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/fmriprep/workflows/bold/registration.py", line 184, in init_bold_reg_wf
    (mask_t1w_tfm, outputnode, [('output_image', 'bold_mask_t1')])
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 233, in connect
    infostr))
Exception: Some connections were not found
Module gen_ref has no input called fov_mask
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
WARNING: FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/workflows.rst:300: WARNING: Exception occurred in plotting workflows-8
 from /home/docs/checkouts/readthedocs.org/user_builds/fmriprep/checkouts/latest/docs/workflows.rst:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/nipype/sphinxext/plot_workflow.py", line 464, in run_code
    exec(code, ns)
  File "<string>", line 6, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/fmriprep/workflows/bold/registration.py", line 184, in init_bold_reg_wf
    (mask_t1w_tfm, outputnode, [('output_image', 'bold_mask_t1')])
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 233, in connect
    infostr))
Exception: Some connections were not found
Module gen_ref has no input called fov_mask
looking for now-outdated files... none found
pickling environment... done
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writing output... [100%] workflows

generating indices... genindex py-modindex
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writing additional pages... search
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copying static files... WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist
done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 96 warnings.
Closing display (if virtual)
oesteban commented 6 years ago

This has been narrowed down to:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/nipype/sphinxext/plot_workflow.py", line 485, in run_code
    exec(code, ns)
  File "<string>", line 2, in <module>
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/site-packages/fmriprep/workflows/bold/registration.py", line 553, in init_fsl_bbr_wf
    schedule=op.join(os.getenv('FSLDIR'), 'etc/flirtsch/bbr.sch')),
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/posixpath.py", line 89, in join
    genericpath._check_arg_types('join', a, *p)
  File "/home/docs/checkouts/readthedocs.org/user_builds/fmriprep/envs/latest/lib/python3.5/genericpath.py", line 143, in _check_arg_types
    (funcname, s.__class__.__name__)) from None
TypeError: join() argument must be str or bytes, not 'NoneType'

in fmriprep/workflows/bold/registration.py", line 553

stale[bot] commented 5 years ago

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.

effigies commented 5 years ago

This might have been resolved in #1459.

oesteban commented 5 years ago

Agree, I think this is not an issue anymore.