Setup

Create virtual environment (optional)

Download and install Miniconda and create a new conda environment:

conda create -y -n scanometrics python=3.12
conda activate scanometrics

Requirements

Latest versions of DL+DiReCT require the installation of nighres as well as Freesurfer version 7.4.1.

Installation

You can install ScanOMetrics by cloning the code from our GitHub repo and using pip. First cd to the folder you want to download ScanOMetrics to, and run the following (a scanometrics folder in your current directory will be created):

(scanometrics)$ git clone https://github.com/SCAN-NRAD/ScanOMetrics.git
(scanometrics)$ cd ScanOMetrics
(scanometrics)$ pip install .

Data formatting

ScanOMetrics heavily relies on the dataset structure to follow the format recommended by the BIDS initiative on Brain Imaging Data Structure. Make sure your data is properly organized before running ScanOMetrics.

MRI processing tools

ScanOMetrics relies on either Freesurfer or DL+DiReCT to process MRI scans available in BIDS directories. Installation instructions are found on each tool’s websites.

Graphical User Interface

ScanOMetrics main functionalities can be accessed through the dedicated GUI.

Command line usage

Advanced features are available through our Command line implementation.