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
SPM12 : https://www.fil.ion.ucl.ac.uk/spm/software/spm12/
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');.
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
The objective is to remove the "salt and pepper" background noise from the UNI image.
Use a INV2 as pseudo mask. No user tuning required.
Based on : https://github.com/srikash/3dMPRAGEise.git
Use a INV1 + INV2 + regularisation factor. The regularisation factor has to be tuned by the user.
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
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 immediately :
When you are settled with your regularization level, use "normal" job SPM > Tools > MP2RAGE > Remove background :
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
| 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" |