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tashrifbillah authored Apr 30, 2019
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216 changes: 195 additions & 21 deletions LICENSE
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MIT License

Copyright (c) 2018 Psychiatry Neuroimaging Lab @ BWH/HMS

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
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SOFTWARE.
The SlicerDiffusionQC license below is a BSD style license, with extensions
to cover contributions and other issues specific to SlicerDiffusionQC. It is
inpsired by [3D Slicer License](https://github.com/Slicer/Slicer/blob/master/License.txt).


SlicerDiffusionQC Contribution and Software License Agreement ("Agreement")
Version 1.0 (December 20, 2005)

This Agreement covers contributions to and downloads from the
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Your contribution of software and/or data to SlicerDiffusionQC (including prior
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PART A. CONTRIBUTION AGREEMENT - License to Brigham with Right to
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This Agreement shall be governed by and construed in accordance with
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36 changes: 27 additions & 9 deletions README.md
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![](Misc/pnl-bwh-hms.png)

[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.2576412.svg)](https://doi.org/10.5281/zenodo.2576412) [![Python](https://img.shields.io/badge/Python-2.7%20%7C%203.6-green.svg)]() [![Platform](https://img.shields.io/badge/Platform-linux--64%20%7C%20osx--64-orange.svg)]()

Developed by Tashrif Billah and Isaiah Norton, Brigham and Women's Hospital (Harvard Medical School).


Table of Contents
=================

* [SlicerDiffusionQC](#slicerdiffusionqc)
* [Citation](#citation)
* [Installation](#installation)
* [Usage](#usage)
* [Tests](#tests)
* [Automatic processing:](#automatic-processing)
* [Slicer GUI manual processing:](#slicer-gui-manual-processing)
* [File description](#file-description)
* [Submit issues](#submit-issues)

Table of Contents created by [gh-md-toc](https://github.com/ekalinin/github-markdown-toc)


# SlicerDiffusionQC

[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.2576412.svg)](https://doi.org/10.5281/zenodo.2576412) [![Python](https://img.shields.io/badge/Python-2.7%20%7C%203.6-green.svg)]() [![Platform](https://img.shields.io/badge/Platform-linux--64%20%7C%20osx--64-orange.svg)]() [![License](https://img.shields.io/badge/License-MIT-yellow.svg)]()

This is a complete slicer module for quality checking of diffusion weighted MRI. It
identifies bad gradients by comparing distance of each gradient to a median line. The median line is obtained from
Expand All @@ -14,7 +34,6 @@ of Yogesh Rathi, Asst. Professor, Harvard Medical School.
The MATLAB SignalDropQCTool is available at [here](https://github.com/pnlbwh/SignalDropQCTool).
On the other hand, the SlicerDiffusionQC is a faster, cleaner, and more user oriented version of that software.

Developed by Tashrif Billah and Isaiah Norton, Brigham and Women's Hospital (Harvard Medical School).

![Screenshot of DiffusionQC gradient-check module](Misc/DiffusionQC-screenshot.png)

Expand All @@ -24,8 +43,7 @@ Developed by Tashrif Billah and Isaiah Norton, Brigham and Women's Hospital (Har

If you use our software in your research, please cite as below:

Tashrif Billah, Isaiah Norton, Yogesh Rathi, Sylvain Bouix, and Carquex Come, Slicer Diffusion QC Tool, https://github.com/pnlbwh/SlicerDiffusionQC, 2018, DOI: 10.5281/zenodo.2576412

Billah, Tashrif; Norton, Isaiah; Rathi, Yogesh; Bouix, Sylvain, Come, Carquex; Slicer Diffusion QC Tool, https://github.com/pnlbwh/SlicerDiffusionQC, 2018, DOI: 10.5281/zenodo.2576412

# Installation

Expand Down Expand Up @@ -66,12 +84,12 @@ Switches:
```


# Testing installation
# Tests


i) Download the [sample](https://github.com/pnlbwh/SlicerDiffusionQC/blob/master/Test/Baseline/SiemensTrio-Syngo2004A-1.nrrd) dwi image.
Type `GradQC` in `Slicer>Modules` search icon, and select it from the drop down menu. Load the sample dwi, check `Create the mask` and hit `Process`.
If the process completes without any error, installation is successfull. You can observe the output files in sample dwi image directory.
If the process completes without any error, installation is successful. You can observe the output files in sample dwi image directory.


ii) From the command line, you can test as follows:
Expand Down Expand Up @@ -108,7 +126,7 @@ git lfs install
```


# For automatic processing:
# Automatic processing:

The following are example command line calls:

Expand All @@ -134,7 +152,7 @@ iv) When you want to specify an output diretory:
The above command line calls save temporary `.npy` files and final results- `inputPrefix_modified.nrrd` and `inputPrefix_QC.csv`.


# For Slicer GUI manual processing:
# Slicer GUI manual processing:

1. Type `GradQC` in `Slicer>Modules` search icon, and select it from the drop down menu.

Expand Down Expand Up @@ -214,7 +232,7 @@ Clone the repository `git clone https://github.com/pnlbwh/SlicerDiffusionQC.git`
The [SlicerExecutionModel wrapper](diffusionQC/diffusionQC.xml) describes the input/output of this script for use by Slicer. The Slicer scripted GUI module code is within the SlicerDiffusionQC subdirectory.


# Submit issues:
# Submit issues

Feel free to submit an issue on this github repository. We shall get back to you as early as we can.

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