NBLtools

Diffusion MRI preprocessing pipeline developed by the Neuroimaging & Biophysics Lab (NBL).

Overview

NBLtools automates the key preprocessing steps for diffusion MRI data:

• Denoising (TORTOISE)
• Gibbs ringing correction
• SynB0-DISCO synthetic reverse phase-encode generation (when no reverse blip data is available)
• Topup susceptibility-induced distortion correction
• Optibet robust brain masking
• Eddy current and motion correction (CPU and GPU/CUDA)
• Quality control reporting

For detailed installation instructions, data organization, and usage documentation, visit the NBLtools website.

Quick Start

Native installation

# With reverse phase-encode data:
run_all_tu ./subject01 -f -p -b 1 -i -t -m -e -c 0 -q

# With SynB0-DISCO (no reverse phase-encode data):
run_all_tu ./subject01 -f -y -p -t -m -e -c 0 -q

Run run_all_tu without arguments to see all available options.

Docker

Pull the pre-built image:

docker pull ghcr.io/nbl-research/nbltools:latest

Create a launch script (e.g. run_nbltools.sh):

#!/bin/bash
docker run -it \
  -v /path/to/your/data:/data \
  -v /var/run/docker.sock:/var/run/docker.sock \
  -v /path/to/freesurfer:/freesurfer \
  -e HOST_DATA=/path/to/your/data \
  -e HOST_FREESURFER=/path/to/freesurfer \
  -e FREESURFER=/freesurfer \
  ghcr.io/nbl-research/nbltools bash

Replace the paths with your actual data directory and FreeSurfer license location. The Docker socket and FreeSurfer mounts are only needed for SynB0-DISCO (-y flag).

Building the Docker image

To build from source:

git clone https://github.com/nbl-research/nbltools.git
cd nbltools
docker build -t nbltools .

Support

• Documentation
• Issue tracker
• Email: info.nblresearch@gmail.com