SEQ_BRUKER_a_MP2RAGE_CS_360

Documentation	Paper	Build Status

Rawdata for tests are available here : https://zenodo.org/records/14046657

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SEQ_BRUKER_a_MP2RAGE_CS_360.jl is a Julia package that implements a reconstruction for an accelerated MP2RAGE sequence for Bruker scanner (PV360-3.5 and PV360-3.6). The reconstruction is performed using MRIReco.jl

More information and examples are available in the article and in the

How to give credit

If you use this package please acknowledge us by citing : https://doi.org/10.1002/mrm.27438

Additionally, if you use the sequence available in the MR sequence folder, please contact us to sign the sequence transfer agreement : [email protected]

Bruker sequence and protocol

The sequence, implemented for Bruker Paravision PV-360: 3.5 & 3.6, and the corresponding protocol for fully-sampled is available in the folder MR sequence.

Compressed-sensing implementation is available through the standard Bruker tab Resolution/Encoding. If you want to perform a compressed-sensing experiment with an acceleration of 2 like the one used here : acceleration factor = 50% and use a calibration size of 5%

##$PVM_EncCSUndersampling=50
##$PVM_EncCSCenterRatio=5

Source code is available in this private directory : https://github.com/aTrotier/a_MP2RAGE_CS_360

Julia

A good ressource to learn how to use Julia can be found here : https://modernjuliaworkflows.org/ especially this part

Installation To use the code, we recommend downloading Julia version 1.10 with juliaup.

Windows

1. Install juliaup

winget install julia -s msstore

2. Add Julia 1.10.4

juliaup add 1.10.4

3. Make 1.10.4 default

juliaup default 1.10.4

Mac

1. Install juliaup

curl -fsSL https://install.julialang.org | sh

You may need to run source ~/.bashrc or source ~/.bash_profile or source ~/.zshrc if juliaup is not found after installation.

Alternatively, if brew is available on the system you can install juliaup with

brew install juliaup

2. Add Julia 1.10.4

juliaup add 1.10.4

3. Make 1.10.4 default

juliaup default 1.10.4

Linux

1. Install juliaup

curl -fsSL https://install.julialang.org | sh

You may need to run source ~/.bashrc or source ~/.bash_profile or source ~/.zshrc if juliaup is not found after installation.

Alternatively, use the AUR if you are on Arch Linux or zypper if you are on openSUSE Tumbleweed.

2. Add Julia 1.10.4

juliaup add 1.10.4

3. Make 1.10.4 default

juliaup default 1.10.4

Package Installation

You can install the package in any project with the following command :

• launch julia with the command julia
• enter the Julia package manager by typing ] in the REPL. (the REPL should turn in blue)
• if you want to activate an environment, type : activate . (otherwise the package will be installed in the global environment)
• In order to add our unregistered package, type add https://github.com/CRMSB/SEQ_BRUKER_a_MP2RAGE_CS_360
• if you want to use the package in your script just add the following line : using SEQ_BRUKER_a_MP2RAGE_CS_360

How to use the package

Follow the example in the documentation

Steps :

• Define the path to the bruker dataset

path_bruker = joinpath(datadir, "MP2RAGE_FULLY")

• Perform the reconstruction

d = reconstruction_MP2RAGE(path_bruker; mean_NR=true)

• write the results in the qBIDS format

subject_name = "sub_01"
dir_path = "" # directory path where the files will be create
write_bids_MP2RAGE(d,subject_name,dir_path)