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:
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…