AxSI 0.0.5

AxSI for MRI data

Usage Guide

Overview

This documentation provides details on how to use the AxSI parser for analyzing MRI data using various input parameters.

Run from Command Line

To execute the program via the command line, use the following syntax:

AxSI_main.py \
  --subj-folder /path/to/subject_folder \
  --data /path/to/data.nii.gz \
  --bval /path/to/bval.bval \
  --bvec /path/to/bvec.bvec \
  --mask /path/to/mask.nii.gz \
  --small-delta 20 \
  --big-delta 50 \
  --gmax 8.0 \
  --gamma-val 4258 \
  --num-processes 4 \
  --num-threads 8 \
  --linear-lsq-method gurobi \
  --nonlinear-lsq-method scipy \
  --debug-mode

Required Arguments

• --subj-folder: Path to the subject folder
• --data: Path to the data file
• --bval: Path to the bval file
• --bvec: Path to the bvec file
• --mask: Path to the mask file

Optional Arguments

• --small-delta (default: 15): Gradient duration in milliseconds.
• --big-delta (default: 45): Time to scan (time interval) in milliseconds.
• --gmax (default: 7.9): Gradient maximum amplitude in G/cm.
• --gamma-val (default: 4257): Gyromagnetic ratio.
• --num-processes (default: 1): Number of processes to run in parallel.
• --num-threads (default: 1): Number of threads to run in parallel.
• --linear-lsq-method (default: R-quadprog): Method for linear least squares. **Choices **: R-quadprog, gurobi, scipy, cvxpy
• --nonlinear-lsq-method (default: R-minpack): Method for nonlinear least squares. **Choices **: R-minpack, scipy, lsq-axsi
• --debug-mode: Enable debug mode. If not provided, debug mode is disabled by default.

Examples

Basic Example

AxSI_main.py \
  --subj-folder ./subject1 \
  --data ./data.nii.gz \
  --bval ./bval.bval \
  --bvec ./bvec.bvec \
  --mask ./mask.nii.gz

Advanced Example with Custom Parameters

AxSI_main.py \
  --subj-folder ./subject1 \
  --data ./data.nii.gz \
  --bval ./bval.bval \
  --bvec ./bvec.bvec \
  --mask ./mask.nii.gz \
  --small-delta 25 \
  --big-delta 55 \
  --gmax 9.0 \
  --gamma-val 4260 \
  --num-processes 8 \
  --num-threads 16 \
  --linear-lsq-method scipy \
  --nonlinear-lsq-method lsq-axsi \
  --debug-mode

NIfTI Viewer

Overview

This is a Dash-based web application that allows users to interactively visualize slices of 3D or 4D NIfTI files ( commonly used in neuroimaging). Users can select slices along different axes, apply various color maps, and visualize data dynamically using sliders for timepoints (in 4D data) and slice indices.

Features

Input File Handling

• The NIfTI file path is provided as a command-line argument using argparse.
• The script loads and processes the provided file using the nibabel library.

Visualization

• Supports visualization along three axes: axial, sagittal, and coronal.
• Provides several color maps (e.g., gray, viridis, plasma) for the visualization.
• Interactive user interface for exploring slices.

4D Data Support

• If the input NIfTI file contains 4D data (e.g., time-series or multi-volume data), a slider lets users navigate through different timepoints.

User Controls

• Dropdown menus to select the viewing axis and color map.
• Sliders for selecting specific slices and timepoints.

Output

• The visualization is rendered as an interactive plot using Plotly.

Getting Started

Run the script from the command line, providing the NIfTI file path as an argument:

nifti_viewer.py --nifti_file /path/to/your/file.nii.gz

Example

nifti_viewer.py --nifti_file example_data/pasi.nii.gz

The app runs at http://127.0.0.1:8050 by default, displaying the interactive visualization.

Python version

This project is currently using Python 3.12

Installation

It is recommended to use virtualenv to create a clean python environment.

To install lsqAxSI, use pip:

pip install AxSI

Execution

The main script shipped with this project is AxSI.py, see its options by running:

AxSI_main.py -h