BrkRaw DTI Extension

This hook adds Diffusion Tensor Imaging (DTI) support to BrkRaw, providing both conversion and quality-control tools for diffusion datasets.

Features

1. DTI Conversion

• Automatically exports .bval and .bvec files (FSL format) alongside the converted NIfTI image.
• Correctly reorients diffusion gradient vectors (bvecs) from the logical acquisition frame to the image frame (RAS+) using the affine.

2. DTI Viewer & Quality Control

• Adds a dedicated DTI tab to the BrkRaw Viewer.
• DTI Calculation: Performs real-time tensor fitting using Ordinary Least Squares (OLS).
• Visualization:
  • Fractional Anisotropy (FA)
  • Mean Diffusivity (MD)
  • Directionally Encoded Color FA (DEC-FA)
• DEC-FA QC: Enables immediate visual verification of gradient orientation:
  • Red: Left-Right (L-R)
  • Green: Anterior-Posterior (A-P)
  • Blue: Superior-Inferior (S-I)

Usage

Conversion

The hook is automatically applied to scans with diffusion directions (PVM_DwNDiffDir > 0).

brkraw convert /path/to/study -s 10

Viewer

Open the BrkRaw Viewer and select a DTI scan. A DTI tab will appear under the Extensions panel.

Tip: Right-click the extensions tab to detach it into a separate window for easier inspection.

1. Click Calculate DTI.
2. Wait for the tensor fitting to complete.
3. Use the dropdown menu to switch between FA, MD, DEC-FA, and b0 views.

Installation

pip install .
brkraw hook install dti