Feeling confused/silly about this, but I’ve just run fmriprep v1.0.8 via fmriprep-docker on a single subject using the
--anat-only flag (full command at the bottom), but the report seems to be missing figures. Or rather, the figures didn’t include a brain. Here’s an example of what I mean
I haven’t noticed any other error in the files that were generated (all files under derivatives/freesurfer and derivatives/fmriprep/sub-05/anat seem fine), and the full report says that there are no error to report. This was run with a clean working directory. This has happened when I ran other subjects in the dataset as well.
fmriprep-docker -w $PWD/derivatives/work --fs-license-file $PWD/code/license.txt $PWD $PWD/derivatives participant --participant_label 05 --anat-only
It was run on an Ubuntu 16.04.4 virtual machine.