Could fmriprep provide a summary 2D image for data quality review?

1

Hello,
Is it possible to make a summary text or HTML file for data quality review like AFNI (@ss_review_driver)? For example, a report including subject IDs and their information of head motion ( num TRs above mot limit), TSNR, etc.

2

Have you checked out MRIQC? I believe the group reports will provide the information you’re looking for (and more!).

Examples here: https://poldracklab.github.io/mriqc/ MRIQC also generates a CSV file with summary statistics per participant/session in addition to the visual reports. If you’ve got a BIDS-compliant dataset it’s quite easy to use, similar to running fmriprep.

These are the image quality metrics that MRIQC reports: https://mriqc.readthedocs.io/en/stable/iqms/t1w.html
https://mriqc.readthedocs.io/en/stable/iqms/bold.html

1 Like
3

Thanks a lot. Very useful suggestion. It seems that I should use MRIQC to control data quailty first, and then feed good data to fmriprep.

4

That is the preferred workflow. First make sure your raw data look good, second run fMRIPrep only on those participants whose data passed QC.