MRIQC warnings: hat mask too small, detected zero-filled frame

[rikki.l...@gmail.com]

Hi all,

I’m currently working with 400+ T1w images that I downloaded from an open-access database. Given that I didn’t collect the images myself and therefore can’t be sure of their quality, I decided to try MRIQC for the first time.

MRIQC (version: 0.15.2rc1) ran on the HPC cluster without issue, but when I checked the individual anatomical reports, I noticed two warning messages under “Workflow details”:

• Detected hat mask was too small
• Detected a zero-filled frame, has the image been rotated?

I couldn’t visually identify any obvious errors in the images I reviewed, so I re-ran MRIQC with the “–verbose-reports” argument. Below is an image of the “hat” mask. It looks quite different to the one shown in the example provided in the MRIQC documentation and others I’ve checked on OpenNeuro:

I also noticed some unexpected output in the brain mask and brain tissue segmentation:

Based on the above, I want to know the following:

• What is likely to be causing the warnings?
• Do the warnings indicate the presence of issues that might have affected the IQMs derived by MRIQC?
• If so, how do I address these issues?

Any help would be very much appreciated! I’ve spent far too long searching Google for solutions…

Cheers,
Rikki

[Xue Zhang]

Hi Rikki,

I am facing the same warning with my data, did you figure out what caused this warning? Appreciate your reply very much!!

Best,

Xue

[Rikki Lissaman]

Hi Xue,

I'm afraid I didn't work out what was causing the warning. In the end, I opted for a different QC method that was aligned to my analysis.

If you're looking for answers, you could try to revive my thread on NeuroStars: https://neurostars.org/t/mriqc-warnings-hat-mask-too-small-detected-zero-filled-frame/6809. Maybe someone will see it and reply this time!

Sorry I can't be more helpful.

Best wishes,

Rikki