Example usage - Functional MRI

The support for the visualQC of fMRI scans is offered for datasets stored in the BIDS format. Usage is as simple as passing on the path to the root folder of the BIDS dataset via the --bids_dir or -b flag:

visualqc_func_mri --bids_dir /new_great_project/ds042

which searches that dataset to identify various subjects and sessions that have the necessary imaging data ready for inspection. VisualQC shows one session at a time for a given subject.

The identifying details for that session are shown in the top right corner as usual. The interface allows you to review the data in great detail, either as a carpet plot entirely (all time points/frames at once), or one time-point/frame at a time (by right clicking on a specific time point). You can further zoom into any slice within that time point shown on the screen – please refer to the Review interface page to learn some shortcuts and tricks to familiarize yourself with the interface.

Please read the documentation in Command line usage - Functional MRI on the remaining options/flags for this module as they are more or less self-explanatory.

Notable flags are

• --no_preproc to avoid applying any preprocessing before showing the data
• --name_pattern or -n to specify a regex pattern to limit which sessions/subjects to include for your review.

Note the outlier detection part is not yet fully tested/validated for this module.

As with other modules of VisualQC, you can choose which views, how many slices and rows to display using the Layout command line arguments i.e. --views, --num_slices and --num_rows.