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
• Marques, J. P., Kober, T., Krueger, G., van der Zwaag, W., Van de Moortele, P.-F., & Gruetter, R. (2010). MP2RAGE, a self bias-field corrected sequence for improved segmentation and T1-mapping at high field. NeuroImage, 49(2), 1271–1281. https://doi.org/10.1016/j.neuroimage.2009.10.002

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 <<, 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 :

Normal

When you are setteled with your regularization level, use "normal" job SPM > Tools > MP2RAGE > Remove background :

Estimate T1

This job will estimate T1map and R1map using sequence parameters and the UNI image.
Based on :

• Marques, J. P., Kober, T., Krueger, G., van der Zwaag, W., Van de Moortele, P.-F., & Gruetter, R. (2010). MP2RAGE, a self bias-field corrected sequence for improved segmentation and T1-mapping at high field. NeuroImage, 49(2), 1271–1281. https://doi.org/10.1016/j.neuroimage.2009.10.002

Comments on the parameters

Parameter name	Description	dcm2niix json sidecar field	on Siemens scanners
UNI image	input T1 weighted	x	this image has the suffix \_UNI_image
Magnetic field strength B0 (T)	in Tesla (T)	MagneticFieldStrength	x
MR2RAGE TR (s)	Repetition time (TR) of the MP2RAGE	RepetitionTime	TR
EchoSpacing (s)	in seconds (s), TR of the GRE readout	does not exist	tab Sequence > Part 1 > Echos pacing
Inversin Times (s)	in seconds (s), such as [TI1 TI2]	InversionTime	TI
Flip Angles (°)	in degree (°), such as [FA1 FA2]	FlipAngle	Flip angle
Number of slices per slab	Number of slices per slab	does not exist	Slices per slab
PartialFourierInSlice	The value range is 0 to 1	PartialFourier	SlicePartialFourier, not PhasePartialFourier expressed as a fraction such as 8/8, 7/8, ...
Fat saturation pulse	x	does not exist	tab Contrast > Fat Sat the option can be "nonce, "water excitation normal", "water excitation fast"