Missing report output

[markushs]

Hi!

I'm new to fmriprep and have been playing around with a stripped down version of a dataset: one participant, one functional multiband BOLD series + sbref, T1w+T2w anatomicals, two spin echo epi scans with opposite phase encoding for inhomogeneity corrections; all BIDS-validated.

I'm on OSX with Docker 18.06.1 and from the terminal output everything seems to run smoothly (some warnings, but no errors or crashes). However the final html-report is never populated with more than the Summary+Anatomical (i.e. the Functional section is missing). Moreover, the func reportlets don't get produced, nor does the func folder and its content in the output directory.

I mentioned some warnings, they typically look like this (the "No contour levels were found" message being repeated over and over):

 [Node] Setting-up "fmriprep_wf.single_subject_ACON1PILOT5P4_wf.func_preproc_ses_fmapse_task_loc_acq_ACon104_run_01_wf.bold_confounds_wf.rois_plot" in "/scratch/fmriprep_wf/single_subject_ACON1PILOT5P4_wf/func_preproc_ses_fmapse_task_loc_acq_ACon104_run_01_wf/bold_confounds_wf/rois_plot".
181022-14:53:15,888 nipype.workflow INFO:
	 [Node] Running "rois_plot" ("niworkflows.interfaces.masks.ROIsPlot")
/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range.
  warnings.warn("No contour levels were found"

 [Node] Running "bold_rpt" ("niworkflows.interfaces.registration.SimpleBeforeAfterRPT")
181022-14:52:20,227 nipype.workflow INFO:
	 [Node] Finished "fmriprep_wf.single_subject_ACON1PILOT5P4_wf.func_preproc_ses_fmapse_task_loc_acq_ACon104_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass".
/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range.
  warnings.warn("No contour levels were found"

[Node] Finished "fmriprep_wf.single_subject_ACON1PILOT5P4_wf.func_preproc_ses_fmapse_task_loc_acq_ACon104_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks".
/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range.
  warnings.warn("No contour levels were found"

Here's an example of a command line I've been running (I've tried several with the same result):

docker run -it --rm \
-v /Users/markushs/Documents/testing_fmriprep/data_bids:/data:delegated \
-v /Users/markushs/Documents/testing_fmriprep/out:/out:delegated \
-v /Users/markushs/Documents/testing_fmriprep/work:/scratch:delegated \
-v /Users/markushs/Documents/testing_fmriprep/license.txt:/opt/freesurfer/license.txt \
poldracklab/fmriprep:latest /data /out participant \
-w /scratch \
--output-space T1w \
--ignore slicetiming \
--fs-no-reconall \
--nthreads 3 \
--stop-on-first-crash

(specifying mounts as delegated after seeing #1012, however same problem without :delegated)

Any ideas why the reports are missing? May be related to #1313, however I don't get any errors.

Thanks!
Markus