Update README.md

README.md

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 # SlicerMp2rageBackgroundSuppression
-This is an extension for 3D Slicer that is used to filter background noise (aka denoising) for MP2RAGE Image acquisitions.
 
-Required Inputs:
+This is an extension for 3D Slicer that provides tools for working with MRI
+images using the MP2RAGE contrast. Currently it supplies a single tool for suppressing divide-by-zero background noise (aka denoising).
+
+The MP2RAGE MRI contrast<sup>[1](#1)</sup> is acquired by simultaneously collecting two MPRAGE images at different inversion times and combining them to form a new, derived contrast. MP2RAGE generates excellent T1-weighted images and is useful for generating other derived contrasts (e.g. T1 maps, synthetic white matter-nulled T1s, and synthetic FGATIR<sup>[2](#2)</sup>). However, it contains “salt-and-pepper” noise, rather than zero values, in areas of low or no signal. This noise can cause algorithms developed for traditional T1 images processing to fail. A “denoising” (more accurately, background suppression) method for eliminating such noise has been published<sup>[3](#3)</sup>, but it relies on additional phase data which is typically not available. This extension implements a method for retrospectively applying a similar noise suppression approach which relies only on available scanner output images.
+
+## Installation Instructions
+1. In Slicer, open the Extensions Manager 
+(View &rarr Extensions Manager).
+
+2. Search for `MP2RAGE` and click `INSTALL`
+
+3. Restart Slicer.
+
+
+### Alternate Installation Method: Manual Installation Via Github
+For development and testing, the extension may also be installed from the
+project's GitHub repository.
+
+1.	Open a terminal, change directory to the path that you will input into Step 3, and type into the command line:
+
+    `git clone [email protected]:harellab/SlicerMp2rageBackgroundSuppression.git`
+
+2.	Open Slicer and go to Edit &rarr; Application Settings &rarr; Modules
+3.	Copy the mp2rageBackgroundSuppression directory path into the Additional module paths and click ok
+
+    Note: the module path will be the directory where the github was cloned 
+    with ~/mp2rageBackgroundSuppression/BackgroundNoiseSuppression
+![Alt text](doc/AdditionalModulePaths.png)
+
+4. Restart Slicer and go back to 
+Edit &rarr; Application Settings &rarr; Modules. Make sure the BackgroundNoiseSupression module checkbox is checked, click and drag the module to the Favorite Modules list.
+![Alt text](doc/FavoriteModules.png)
+
+## Usage
+
+### Required Inputs:
 1. MP2RAGE uniform images (UNI) 
 2. The first inversion recovery sequence (INV1) from MP2RAGE
 3. The second inversion recovery sequence (INV2) from MP2RAGE
 
-Extension Workflow:
+### Extension Workflow:
 1. Load the MP2RAGE data sets (UNI, INV1, INV2) into 3D Slicer as volumes.
 ![Alt text](Screenshot1.png)
 
@@ -15,15 +49,22 @@ Extension Workflow:
 ![Alt text](Screenshot2.png)
 
 
-Disclaimer
+## Disclaimer
 
 Mp2rageBackgroundSuppression, same as 3D Slicer, is a research software. It is NOT an FDA-approved medical device. It is not intended for clinical use. The user assumes full responsibility to comply with the appropriate regulations.
 
-Support
+## Support
 
 Please feel free to contact The Harel Lab github organization for questions, feedback, suggestions or bugs. https://github.com/harellab/SlicerMp2rageBackgroundSuppression/issues
 
-Acknowledgments
+## Acknowledgments
 
 Development of mp2rageBackgroundSuppression was supported in part by the following NIH grants:
-Udall NIH P50 NS123109
+Udall NIH P50 NS123109
+
+## References
+<a id="1">1.</a> Marques JP, Kober T, Krueger G, Van Der Zwaag W, Van De Moortele PF, Gruetter R. MP2RAGE, a self bias-field corrected sequence for improved segmentation and T1-mapping at high field. *NeuroImage*. 2010;49(2):1271-1281. doi:10.1016/j.neuroimage.2009.10.002
+
+<a id="2">2.</a> Middlebrooks EH, Tao S, Zhou X, et al. Synthetic Inversion Image Generation using MP2RAGE T1 Mapping for Surgical Targeting in Deep Brain Stimulation and Lesioning. *Ster Funct Neurosurg*. 2023;101(5):326-331. doi:10.1159/000533259
+
+<a id="3">3.</a> O’Brien KR, Kober T, Hagmann P, et al. Robust T1-Weighted Structural Brain Imaging and Morphometry at 7T Using MP2RAGE. Margulies D, ed. *PLoS ONE*. 2014;9(6):e99676. doi:10.1371/journal.pone.0099676