Welcome to OSPREY_BIDS’s documentation!

DOCUMENTATION IS STILL A WORK IN PROGRESS. ANY DETAILS FOUND ON THESE PAGES SHOULD BE CONSIDERED TEMPORARY/INCOMPLETE UNTIL THIS DISCLAIMER IS REMOVED.

This tool is used in the Healthy Brain and Child Development (HBCD) study for processing magnetic resonance spectroscopy (MRS) data. The tool acts as a BIDS extension to the OSPREY pipeline.

The utility of this application is largely three-fold:

1. To make the core functionality of OSPREY available via Docker/Singularity containers so that users do not need to install any dependencies or have a Matlab license before processing.

2. Extending OPSREY to have BIDS App functionality. OSPREY_BIDS takes as input a BIDS dataset, automates processing by assuming the input follows BIDS guidelines, and structures processing outputs using general BIDS derivatives principles.

3. Registration. OSPREY_BIDS allows for registering high anatomical T1w/T2w images to a localizer image collected immediately before/after the MRS acquisition. This step ensures that even if there is movement between the high-res anatomical and MRS localizer that (a) segmentation-based tissue correction can still occur and (b) the MRS voxel positioning can be displayed on a high-res underlay.

Contents:

• Installation
• Usage
  • Command-Line Arguments
• Expected Inputs
  • Required
  • Optional Inputs
• Processing Pipeline Details
• Configuration of MRS Processing
  • Default processing options
  • Additional processing options
  • Output files