Problem with MRIQC verbose-reports plots

1

Hello everyone,

I am running mriqc with singularity on a server cluster and everything works fine, except that I ran into some issues with the additional plots appended to the participant-level reports when providing the --verbose-reports argument. Specifically, the animations visualising co-registration to MNI space are blank (i.e. it shows everything except for the brain slices themselves) for both T1w and bold images. Furthermore, the brain mask and brain tissue segmentation plots display implausible (random) red outlines for the first three slices for T1w reports while the rest of the slices look as expected (This problem only occurs for one of the datasets I tested however).

When running the T1w reports I receive the following output log. The first line I always get when running mriqc, but the second one is specific to the --verbose-reports argument:

/usr/local/miniconda/lib/python3.6/site-packages/grabbit/core.py:410: UserWarning: No valid root directory found for domain ‘derivatives’. Falling back on the Layout’s root directory. If this isn’t the intended behavior, make sure the config file for this domain includes a ‘root’ key.
“‘root’ key.” % config[‘name’])

/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”

When running the bold reports I don’t receive this warning but a different one:

mriqc.report:WARNING Building bold report: no exclude index was found

I hope someone knows a solution to this problem and I appreciate your help.
Kind regards,

Alex

2

Have you tried opening the reports in chrome? What version of MRIQC are you using?

3

Thanks for the quick response! The problem with the co-registration plot animation was indeed just a browser issue. I use Firefox by default but in Chrome I could view it just fine.

The “issue” with red lines in the other plot I think I could answer myself. The first slices for this particular dataset display the level of the spinal cord, which coincide with the lower boundary of the brain mask. I think what is happening is that the plot is trying to display a surface in the axial plane which results in these weird visualisations (I’m using mriqc v0.11.0 by the way). I assume there is no way to influence the position of the first slice to be visualised in the plot (otherwise please let me know). Here is a picture for reference:

mriqc_brain_mask

Thanks again for the advise!