B0 fieldmap realistic simulation

Generation of B0 fieldmap based on anatomical MRIs of 60 adult subjects. The fieldmaps are generated from the segmented tissues and assignment of susceptibility values.

Pipeline

3D Render of segmentations

Sagittal mosaic of simulated B0 maps

Dataset

Link to OpenNeuro BIDS dataset to be provided soon.

Installation

Python depedencies

In a new virtual environment (recommended), install this repository:

git clone https://github.com/shimming-toolbox/b0-fieldmap-realistic-simulation.git
cd b0-fieldmap-realistic-simulation
pip install -e requirements.txt

Install the susceptibility-to-fieldmap project,

git clone https://github.com/shimming-toolbox/susceptibility-to-fieldmap-fft
cd susceptibility-to-fieldmap-fft
git checkout d9f785b082fb145d547ff03ae53f23f1564ccc38
pip install -e .

Slicer3D

Install via their website, https://www.slicer.org

Open the application, then navigate to the Python terminal (see Python "snake" logo in the top toolbar) and run:

import slicer
slicer.util.pip_install('click')

Usage

Main pipeline

Note: for all *.sh script files, you'll need to provide execution permissions,

chmod +xxx $SCRIPT

where $SCRIPT is the *.sh filename for that script.

For convenience, we recommend you set the variable BIDS_DIR in your shell to the datasets BIDS directory,

BIDS_DIR = /path/to/bids/dir

This way, you can copy-paste the commands below directly.

Create shell scripts customized for your BIDS directory

Step 1: Smooth & merge From within this directory, first generate the script for smoothing using 3D Slicer & merging of the labels:

./b0realsim/step_1_generate_smoothing.sh -b $BIDS_DIR

Output: run_1_smooth.sh

Step 2: Labels to chi Then, generate the script that will, for each subject, map the labels to their chi values.

./b0realsim/step_2_generate_chi.sh -b $BIDS_DIR]

Output: run_2_compute_chimaps.sh

Step 3: Chi to B0 field map Lastly, generate the script that will, for each subject, simulate the B0 field map using the chi map generated in the previous step.

./b0realsim/step_3_generate_b0.sh -b $BIDS_DIR

Output: run_3_compute_b0maps.sh

Run pipeline scripts

Now, provide execute permission (chmod +xxx $SCRIPT) each pipeline scripts you just generated and then run them in order

./run_1_smooth.sh - runtime: ~2 hours

./run_2_compute_chimaps.sh - runtime: ~1 minute

./run_3_compute_b0maps.sh - runtime: ~30 minutes

Outputs

Smoothed & merged labels $BIDS_DIR/derivatives/labels/$SUBJECT/anat/

Chi maps $BIDS_DIR/derivatives/$SUBJECT/anat/

B0 maps $BIDS_DIR/derivatives/$SUBJECT/fmap/

Plot saggital mosaic of B0 maps

python b0realsim/visualization/plot_mosaic.py -b $BIDS_DIR - runtime ~3 minutes

Output: subject-mosaic.png

Fetch additional information

To compute the age/weight/height statistics for the subjects,

python b0realsim/stats/subjects.py -b $BIDS_DIR