.. OSPREY_BIDS documentation master file, created by
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Welcome to OSPREY_BIDS's documentation!
=======================================

.. image:: https://zenodo.org/badge/197683508.svg
  :target: https://doi.org/10.5281/zenodo.14226196

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 <https://github.com/schorschinho/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 <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005209>`_ 
   functionality. OSPREY_BIDS takes as input a `BIDS dataset <https://bids-specification.readthedocs.io/en/stable/>`_,
   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.







.. toctree::
   :maxdepth: 2
   :caption: Contents:

   installation
   usage
   expected_inputs
   processing_pipeline_details
   mrs_processing_details