sararanjbar / mrqy

MRQy is a quality assurance and checking tool for quantitative assessment of magnetic resonance imaging (MRI) data.

Front-end View

Backend View

Table of Contents

• Description
• Prerequisites
• Running
• Basic Information
  • Measurements
  • User Interface
• Feedback and usage

Description

This tool takes MRI datasets in the file formats (.dcm, .nii, .nii.gz or .mha) as the input.
Two Python scripts (QC.py and QCF.py) are used to generate several tags and noise/information measurements for quality assessment. These scripts save the calculated measures in a .tsv file as well as generate .png thumbnails for all images in a subject volume. These are then fed to .js scripts to create the user interface (index.html) output. A schematic illustrating the framework of the tool is as follows.

Prerequisites

The current version of the tool has been tested on the Python vresion 3.7.4. The required Python packages are listed in the following figure.

Running

To test that the code is working fine please try

D:\Downloads\MRQy-master>python QC.py --help

The output should be

usage: QC.py [-h] output_folder_name [inputdir [inputdir ...]]

positional arguments:
  output_folder_name  the subfolder name on the
                      '...\UserInterface\Data\output_folder_name' directory.
  inputdir            input foldername consists of *.mha (*.nii or *.dcm)
                      files. For example: 'E:\Data\Rectal\input_data_folder'

optional arguments:
  -h, --help          show this help message and exit
  

Standard usage is to run QC.py output_folder_name “input directory” i.e.

python QC.py output_folder_name "E:\Data\Rectal\RectalCancer_Multisite\input_data_folder"

There is no need to make a subfolder in the Data directory, just specify its name in the command like above code line.
Every action will be printed in the output console.
The thumbnail images in the format of .png will be saved on "...\UserInterface\Data\output_folder_name" with its original filename as its subfolder's name. Afterward, double click "index.html" (on e.g. "D:\Downloads\MRQy-master\UserInterface") to open front end user interface, select the respective results.tsv file from the e.g. "D:\Downloads\MRQy-master\UserInterface\Data\output_folder_name" directory.

Basic Information

Measurements

The measures of the MRQy tool are listed in the following table.

User Interface

The following figures show the user interface of the tool (index.html).

Feedback and usage

Please report and issues, bugfixes, ideas for enhancements via the "Issues" tab

You can cite this in any associated publication as:
Sadri, AR, Janowczyk, A, Zou, R, Verma, R, Antunes, J, Madabhushi, A, Tiwari, P, Viswanath, SE, "MRQy: An Open-Source Tool for Quality Control of MR Imaging Data", https://arxiv.org/abs/2004.04871v2, 2020

If you do use the tool in your own work, please drop us a line to let us know.