TOPPE is a simple, modular framework for rapid prototyping of pulse sequences on General Electric MRI scanners.
Working with TOPPE involves three basic steps:
- Design the RF and gradient waveforms you want to play out on the scanner, using any suitable method.
- Create TOPPE sequence files (gray boxes). This is done by first writing each unique sequence block, or module, to a ‘.mod’ file using the ‘mat2mod.m’ MATLAB script. You then create a file named ‘scanloop.txt’ that specifies the order in which to play out the modules, waveform amplitudes, and other dynamic sequence information. Finally, create a small file named ‘modules.txt’ that lists the various modules.
- Copy the files you created to /usr/g/bin/ on the scanner, and run the TOPPE binary executable (green box) which loads the files and executes the sequence. The TOPPE executable only needs to be compiled and installed once per scanner software upgrade.
The following example shows the TOPPE files for a sequence containing four different modules:
DOWNLOAD TOPPE SOURCE CODE
TOPPE MATLAB code is open source and is available at:
Alternatively, from a console you can copy the entire MATLAB repository to a local folder as follows:
git clone https://github.com/toppemri/matlab
The TOPPE binary executable (psd) is written in ‘EPIC’ and is available for download from the following private repository:
Or from a console:
git clone https://github.com/toppemri/psd
Please contact firstname.lastname@example.org for access to this repository (requires a GE research agreement).
Compiling the TOPPE interpreter
To compile the TOPPE binary psd (e.g., ‘toppev2’), navigate to the ‘/psd/’ subfolder in the EPIC source distribution and compile in the usual way:
prep_psd_dir; psdqmake hw;
Copy the resulting executable files, i.e., toppev2 and toppev2.psd.o, to /usr/g/bin/ on the scanner.
Running an example TOPPE sequence
The MATLAB code repository contains several complete pulse sequence examples, such as 3D spoiled gradient-echo (SPGR) and stack-of-spirals echo-shifted dynamic imaging (PRESTO fMRI). For example, to execute the 3D SPGR example, do the following:
- Navigate to https://github.com/toppeMRI/matlab/tree/master/examples/v2, select the ‘3dspgr’ folder, and download the file ‘scan,3dspgr.tgz’.
- Copy scan,3dspgr.tgz to /usr/g/bin/ on the scanner and untar:
tar xzf scan,3dspgr.tgz
- Prescribe the TOPPE interpreter, i.e., toppev2:
- Select Axial 2D pulse sequence; Family: ’Gradient Echo’; pulse: ’GRE’; PSD Name: ’toppev2’;
- Prescribe a single axial slice.
- Other settings do not matter but must be specified. Suggested values are: Slice thickness 3, slice spacing 0, number of slices 1.
- Download the sequence, run auto-prescan, and scan.
The TOPPE User Guide
Additional details and instructions are provided in this MRM paper and in the TOPPE user guide. Latex source code for this guide is open-source, available in the following repository:
To get a copy of the repository, do:
git clone https://github.com/toppemri/UserGuide
USING TOPPE AS A GE INTERPRETER FOR Pulseq (under development)
Pulseq (https://pulseq.github.io) is a platform-independent file format for specifying arbitrary MR sequences. In preliminary work we have used TOPPE as a GE interpreter of Pulseq files, which involves converting a Pulseq file to TOPPE files using the ‘seq2ge.m’ MATLAB script included in the TOPPE distribution. We also provide a script ‘ge2seq.m’ for converting TOPPE to Pulseq format. For more details about Pulseq, see the following paper:
TOPPE was developed at the fMRI laboratory at University of Michigan.
For questions, contact Jon-Fredrik Nielsen at email@example.com or firstname.lastname@example.org.