pulseq-cest
Welcome to the pulseq-cest repository, a project to faciliate reproducibility in CEST MRI research using the open Pulseq standard. The repository consists of two parts:
-
pulseq-cest-library: Here, published and approved CEST preparation periods are made available. This allows exact comparison of CEST preparation periods with newly developed or adapted blocks for reproducible CEST research. All .seq-files can be loaded in MATLAB for plotting and detailed inspection. This library is maintained in a separate repository but is included in the pulseq-cest installation.
-
pulseq-cest-sim: In this folder you can find the Bloch-McConnell simulation that can be used to simulate and compare different .seq-files for different settings.
More information about both parts can be found in the corresponding repository or subfolder.
If you prefer python over MATLAB, have a look at the python version of the project here.
Installation
There are 3 ways to install pulseq-cest, listed here in the recommended order:
1. If you have git installed
- Clone the repository
- Open MATLAB
- Run install_pulseqcest.m
- External packages will be cloned
2. If you do not have git installed
- Download pulseq-cest as .zip
- Unpack it
- Open MATLAB
- Run install_pulseqcest.m
- External packages will be downloaded as .zip and unpacked
3. If you want to do everything manually, or 1. and 2. don't work for you
- Download pulseq-cest as .zip
- Unpack it
- Download pulseq-cest-library as .zip
- Unpack it in the parent directory of pulseq-cest
- Download yamlmatlab as .zip
- Unpack it in pulseq-cest/pulseq-cest-sim
- Download Pulseq as .zip (make sure its 1.3 or commit ed8cf4231dc7a5caaf828211486287afcdbac230)
- Unpack it in pulseq-cest/pulseq-cest-sim
- Add the pulseq-cest folder and the subfolders to your MATLAB search path
Getting started
To get an overview about the project and how the .seq-files and simulations work, go to the examples folder. There you will find an example .seq-file for which you can display the different sequence events and run the simulation.
For plotting, just run the following code in the console:
>> seq = SequenceSBB;
>> seq.read('examples/APTw_3T_example.seq');
>> seq.plotSaturationPhase();You can have a look at the RF amplitude and phase, as well as the gradient events.
If you want to run the Bloch-McConnell simulation for that Z-spectrum experiment with a standard setting for 3 T, just run:
>> simulateExample();For more infos check the subfolder Readmes.