diff --git a/Mp2rage Background Noise Suppression Module Installation.docx b/Mp2rage Background Noise Suppression Module Installation.docx deleted file mode 100644 index 2904d1c..0000000 Binary files a/Mp2rage Background Noise Suppression Module Installation.docx and /dev/null differ diff --git a/README.md b/README.md index c66c437..4e762a1 100644 --- a/README.md +++ b/README.md @@ -1,12 +1,46 @@ # 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[1](#1) 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[2](#2)). 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[3](#3), 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 git@github.com:harellab/SlicerMp2rageBackgroundSuppression.git` + +2. Open Slicer and go to Edit → Application Settings → 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 → Application Settings → 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 \ No newline at end of file +Udall NIH P50 NS123109 + +## References +1. 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 + +2. 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 + +3. 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 \ No newline at end of file diff --git a/doc/AdditionalModulePaths.png b/doc/AdditionalModulePaths.png new file mode 100644 index 0000000..16ec117 Binary files /dev/null and b/doc/AdditionalModulePaths.png differ diff --git a/doc/FavoriteModules.png b/doc/FavoriteModules.png new file mode 100644 index 0000000..a5f8aa8 Binary files /dev/null and b/doc/FavoriteModules.png differ