Command line implementation

This page summarizes advanced features of ScanOMetrics, accessible through command line.

Processing MRI data

To process new MRI scans, check the tutorial on MRI processing for more details.

Single subject evaluation

If you have processed MRI scans from a subject, you can compare them to a normative dataset by following the tutorial on Subject evaluation.

Group evaluation

ScanOMetrics is mainly intended for single subject evaluation. However, we also provide a way to perform group comparisons, by following this tutorial.

Fit a normative model

We provide a selection of normative models for subject and group evaluation. However, if you want to create your own normative model for ScanOMetrics, you can do so by following the tutorial on Fitting normative data.

Adding a processing module

We provide default processing modules, as wrappers around Freesurfer and DL+DiReCT. If you’d like to implement your own processing pipeline, you can follow some basic ideas here.