https://github.com/cyclotronresearchcentre/mp2rage

SPM implementation of https://github.com/JosePMarques/MP2RAGE-related-scripts

https://github.com/cyclotronresearchcentre/mp2rage

Repository

SPM implementation of https://github.com/JosePMarques/MP2RAGE-related-scripts

https://github.com/CyclotronResearchCentre/mp2rage/blob/master/

# mp2rage
SPM implementation of https://github.com/JosePMarques/MP2RAGE-related-scripts  
Based on :
* O'Brien KR, Kober T, Hagmann P, Maeder P, Marques J, Lazeyras F, et al. (2014) Robust T1-Weighted Structural Brain Imaging and Morphometry at 7T Using MP2RAGE. PLoS ONE 9(6): e99676. https://doi.org/10.1371/journal.pone.0099676
* O'Brien K, Krueger G, Lazeyras F, Gruetter R, Roche A, A simple method to denoise MP2RAGE; 2013; Salt Lake City, Utah.pp. 269. http://archive.ismrm.org/2013/0269.html

## Requirements
SPM12 : https://www.fil.ion.ucl.ac.uk/spm/software/spm12/


## Installation
Clone the repo : `git clone https://github.com/benoitberanger/mp2rage`,
or use direct download link [>> here <<](https://github.com/benoitberanger/mp2rage/archive/master.zip),
then place freshly downloaded/cloned directory in `spm12/toolbox/`, such as `spm12/toolbox/mp2rage`.
You can also use a symlink, such as `ln -s path/to/mp2rage path/to/spm12/toolbox/mp2rage`

That's all.

If you already started SPM in your MATLAB session, don't forget to refresh SPM paths with `spm_jobman('initcfg');`.


## How it works
This repo is an extension of _spm12_, you can use the Batch Editor (`spm_jobman`) and open the tab SPM > Tools > MP2RAGE > choose-your-job

### Remove background
The objective is to remove the "salt and pepper" background noise from the UNI image.  
Based on :
* O'Brien KR, Kober T, Hagmann P, Maeder P, Marques J, Lazeyras F, et al. (2014) Robust T1-Weighted Structural Brain Imaging and Morphometry at 7T Using MP2RAGE. PLoS ONE 9(6): e99676. https://doi.org/10.1371/journal.pone.0099676
* O'Brien K, Krueger G, Lazeyras F, Gruetter R, Roche A, A simple method to denoise MP2RAGE; 2013; Salt Lake City, Utah.pp. 269. http://archive.ismrm.org/2013/0269.html

#### Interactive
To determine which regularization factor to use, you can use the job SPM > Tools > MP2RAGE > Interactive remove background  
This will display the original UNI image and the denoised version with a popup where you can enter the regularization level and check the result immediatly :  
![irmbg](https://github.com/benoitberanger/mp2rage/blob/master/example/interactive_rmbg.gif)

#### Normal
When you are setteled with your regularization level, use "normal" job SPM > Tools > MP2RAGE > Remove background :  
![rmbg](https://github.com/benoitberanger/mp2rage/blob/master/example/rmbg_gui.png)

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