Fmriprep report missing brains?

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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

sub-05_acq-conventional_T1w_seg_brainmask
sub-05_acq-conventional_T1w_seg_brainmask.png1108×470 198 KB

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.

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@psadil I would recommend trying to open the reports with Chrome/Chromium. As far as I remember, those are the only browsers that can render the reports properly.

HTH,
Matteo

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@mvdoc … ah, yeah, that does it. thanks.

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The new FMRIPREP 1.0.14 should work on Firefox and Safari too :slight_smile:

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