Keywords: Software Tools, Data Acquisition, Open-source

Motivation: Pulse-sequence development has been challenging due to high software complexity and limited documentation. Moreover, proprietary licenses make sharing developments difficult.

Goal(s): To provide an open-source solution based on modern software engineering principles that simplifies the design, implementation, and dissemination of sequences.

Approach: Our vendor-agnostic “mtrk” framework is based on a compact, human-readable descriptive language (SDL) in JSON format. SDL files can be generated with any programming language and can be played on MRI scanners or tested with simulators.

Results: Python libraries for SDL generation and tools for interactive sequence design and visualization are presented. mtrk sequences were equivalent to vendor sequences in experiments.

Impact: mtrk will lower the burden for students and researchers to develop and disseminate sequences. It will aid reproducible research, as developments can be publicly shared. Moreover, it will allow exploring innovative concepts such as remote calculation and cloud-driven “sequence-as-a-service” models.

Keywords: Software Tools, Brain

Motivation: Achieving full advantage of radial acquisition and reconstruction by conducting the complete analysis in the polar coordinate system. 

Goal(s): Implement a comprehensive end-to-end fMRI analysis software package with a graphical user interface.

Approach: Radially acquired fMRI was reconstructed natively in the polar coordinate system using the Polar Fourier Transform, followed by utilizing preprocessing steps (motion correction and brain extraction) implemented in the polar coordinate system to perform statistical analysis.

Results: The software package performs reconstruction, preprocessing, and statistical analyses of radially acquired fMRI data in the polar coordinate system and is validated using fMRI of 31 healthy subjects. 

Impact: This software package facilitates the native polar analysis of radially acquired fMRI that increases the specificity and/or improves the spatial resolution, particularly in task-based brain mapping studies with the region of interest considerably smaller than the field of view

Keywords: Software Tools, Software Tools, Open-source, MaRCoS

Motivation: MaRCoS integrates hardware, firmware, and software for MRI scanner control, focusing on system reliability but overlooking user experience.

Goal(s): Develop MaRGA (MaRCoS Graphical Application), a user-friendly Graphical User Interface (GUI) for low-field MRI community, ensuring intuitive MaRCoS control and clinical environment compatibility.

Approach: Designed MaRGA with simplified panels and updated API, enabling features like DICOM image export, clinical protocol management, and streamlined image reconstructions.

Results: Tested MaRGA on 0.2 T and 72 mT scanners in lab and hospital settings, enhancing workflow efficiency and user satisfaction through customizable controls and improved overall experience.

Impact: The introduction of MaRGA, a user-friendly Graphical User Interface (GUI) for low-field MRI scanner control, enhances user experience and workflow efficiency with MaRCoS. MaRGA significantly improves the operation of low-field MRI scanners in both laboratory and clinical settings.

Keywords: Software Tools, Software Tools, modular, sequence design, online reconstruction

Motivation: Developing robust MRF acquisitions and reconstructions requires meticulous manual tracking of parameters and dependencies, as well as integration of diverse tools. Increasing ease of development and use, regardless of research or clinical purposes, would help with broader adoption and understanding of MRF.

Goal(s): Improve tooling to increase MRF research flexibility while maximizing traceability of acquisitions and reconstructions.

Approach: Develop a unified Python framework, mrftools, supporting MRF-specific modular sequence abstraction, integration of reconstruction dependencies, and online reconstruction.

Results: Built-in support for many common techniques and high extensibility for research use is demonstrated for both sequence and reconstruction development.

Impact: By providing a unified framework for sequence development and reconstruction, mrftools streamlines workflow, ensuring traceability and repeatability of MRF for research or clinical usage. Key contributions lie in MRF-specific modular sequence design, the integration of reconstruction dependencies, and online reconstruction.

Keywords: Software Tools, Software Tools, NUFFT, Non-Cartesian

Motivation: Non-Cartesian imaging remains complicated to use for MRI due to the high computational cost of the Non-Uniform Fourier Transform for image reconstruction. 

Goal(s): To provide a uniform interface for reconstructing magnetic resonance images from non-Cartesian k-space data and a collection of non-Cartesian sampling trajectories 

Approach: We propose an open-source Python package (https://github.com/mind-inria/mri-nufft/) providing a standard interface to existing NUFFT libraries, with extended models for multi-coil imaging and static-field (B0) inhomogeneities correction.

Results: MRI-NUFFT can generate sampling trajectories, compliant with hardware constraints, as well as simple forward/adjoint operations and density compensation for use in advanced image reconstruction scenarios.

Impact: With MRI-NUFFT, non-Cartesian MRI  trajectories and reconstruction algorithms become accessible, efficient, and affordable to everyone for research and education purposes.

Keywords: Software Tools, Software Tools, Data Acquisition; Neuroscience

Motivation: Many cutting-edge MR neuroimaging paradigms require real-time decision making and precise FOV positioning.  We present two software tools to support such paradigms.

Goal(s): Develop two modules. 
1) vSend: opens a socket and sends imaging data to another computer in a vendor-agnostic format, enabling real-time analysis.
2) AAhijack: reads a matrix from a socket and overwrites the Siemens AutoAlign matrix, enabling online slice prescription.

Approach: Modules are implemented as Siemens image reconstruction modules (ICE functors) in C++ and two slice prescription systems utilizing the modules are demonstrated.

Results: The slice prescription systems have comparable performance and various advantages and disadvantages.

Impact: The software tools presented have enabled a variety of cutting-edge MR neuroimaging paradigms including real-time fMRI, motion tracker calibration, real-time shimming, fetal head-pose detection and automated FOV prescription, reacquisition planning and single-slice BOLD imaging FOV prescription. 

Keywords: Software Tools, Diffusion/other diffusion imaging techniques

Motivation: Prostate MRI primarily relies on diffusion-weighted imaging (DWI) but is notoriously challenged by low SNR, impacting the diagnostic process. 

Goal(s): To implement  the state-of-the-art tensor denoising method for prostate DWI

Approach: We applied the tMPPCA algorithm that makes use of the redundancy in multi-dimensional data to separate the most significant components (the diffusion-signal) and the remaining the thermal/scanner noise. We quantified the denoising efficacy with comprehensive qualitative and quantitative analysis.

Results: The tMP-PCA method, previously proved to be efficient on ex-vivo scans are extremely effective to enhance in-vivo prostate MRI images when a similar multi-dimensional protocol is followed.

Impact: The tMPPCA  can effectively reduce noise without the trade-off of blurring—an achievement that has critical implications in cancer detection. This study is the first in-vivo implementation of tMPPCA for enhancing prostate DWI, employed under 10 minutes of scan time.

Keywords: Software Tools, Simulations

Motivation: To reproduce geometric distortions around air bubbles imaged with a 7 Tesla MRI system using Bloch simulation.

Goal(s): To find a strategy to calculate geometric distortion caused by susceptibility effects in Bloch simulation.

Approach: Inhomogeneous magnetic fields were calculated using summing up magnetic fields generated by magnetic dipoles in the air bubbles in a spherical phantom.

Results: Geometric distortions were reproduced by the Bloch simulations using the inhomogeneous magnetic fields calculated by summation of the magnetic fields generated by the magnetic dipoles in the air bubbles. Bubbles deformed by the strong static magnetic field were observed.

Impact: Geometric distortion around arbitrary shaped air bubbles was reproduced by the Bloch simulation. An air bubble at 7T was found to be deformed by the strong static magnetic field and the large diamagnetic susceptibility of water.

Keywords: Software Tools, Velocity & Flow, Unwrapping

Motivation: Low-V_enc PC-MRI acquisitions present the advantage of higher velocity-to-noise ratio (VNR). To the best of the author’s knowledge, no Python-based public repository exists with 4D flow MRI unwrapping algorithms and realistic examples.  

Goal(s): To share a collection of simple unwrapping tools for 4D Flow MRI and test their performance.

Approach: To use three established unwrapping techniques to create a Python package to unwrap 4D flow MRI data.

Results: We demonstrate the performance of these algorithms on aortic data including multiple V_enc values and undersampling factors.  

Impact: The Python repository with a collection of simple unwrapping tools facilitates access to unwrapping techniques. These scripts can readily be used to unwrap any PC-MRI dataset.

Keywords: Software Tools, Pulse Sequence Design, Pulseq, vendor-agnostic sequences

Motivation: To enable vendor-neutral MR pulse sequence programming for rapid prototyping and reproducible research.

Goal(s): Implement an accurate interpreter of Pulseq files for GE scanners.

Approach: We convert the Pulseq file, which is a streaming-based description, to a ‘segment’-based representation where each segment consists of sub-sequences (groups) of Pulseq blocks that are always executed together and in a particular order. This segment is then executed repeatedly with different  waveform amplitudes.

Results: The proposed Pulseq interpreter for GE scanners allows the execution of arbitrary Pulseq sequences. The same interpreter source code (written in EPIC) can be compiled for all recent GE MRI scanner software versions.

Impact: The proposed interpreter allows researchers to design sequences in Pulseq and execute them on GE scanners. This allows rapid prototyping of novel sequences, and identical implementations across sites. Pulseq and the proposed ‘segment’-based description are equivalent vendor-independent sequence descriptions.

Keywords: Software Tools, Simulations, Bloch equations

Motivation: Computational cost of the Bloch simulation was high.

Goal(s): This research aims to reduce the computational cost.

Approach: A new computation method using grouped isochromats is proposed. The proposed method shared computation of the isochromats whose parameters were same for each part of gradients. The processing time of two sequences were evaluated using a phantom (consisting of approximately 4 million isochromats) with and without the proposed method.

Results: The proposed method accelerated the simulation up to 7.7 times.

Impact: The proposed method accelerated up to 7.7 times for simulating the Bloch equations. The proposed method shared computation of the isochromats whose parameters were same for each part of gradients.

Keywords: Software Tools, Data Processing, principal component analysis

Motivation: We address the critical problem of the low signal-to-noise ratio (SNR) of in vivo MR spectroscopic imaging (MRSI) at 1.5 tesla using principal component analysis (PCA).

Goal(s): We seek to improve the translatability of MRSI acquired in 1.5T clinical scanners by improving data visualization using PCA reconstruction (PCAR).

Approach: We initially corrected for spectral phase and frequency variations in multivolume ³¹P and ¹H MRSI data noninvasively acquired at 1.5 T from human subjects and subsequently used PCAR. 

Results: We validate the improvement of the MRSI data after PCAR by demonstrating signals that were not distinguishable in the original datasets.

Impact: Principal component analysis reconstruction (PCAR) improves the accuracy to assess spectral signals from multivolume ³¹P and ¹H MR spectroscopic imaging data acquired on highly accessible 1.5T clinical scanners, increasing their potential to become noninvasive metabolic biomarkers of human diseases.

Keywords: Software Tools, Software Tools

Motivation: Open-source imaging significantly advances MR accessibility. The construction of an open-source scanner required the development of an open-source console

Goal(s): This work aims to develop acquisition tools to calibrate the system hardware, acquire signals in the form of 1D, 2D, and 3D images, and provide a visualization  of the acquisition trajectories.

Approach: Using the PyPulseq and the MaRCoS libraries, we implemented the adjustment (RF, gradients, shim), and acquisition sequences (1D, 2D, 3D) as well as a plotting tool for Cartesian trajectories. 

Results: The acquisition tools were run  on the scanner, successfully defining calibration values, obtaining signals, and plotting trajectories.

Impact: As part of the MRI4ALL Hackathon, this work integrates and advances a toolset for acquisition support, compatible with vendor-agnostic libraries like PyPylseq and MaRCoS.  This demonstration contributes to the expedited construction of a standalone low-field MRI scanner in a laboratory.

Keywords: Software Tools, Phantoms, digital reference object

Motivation: Concern over gadolinium contrast injections for research purposes limits in vivo testing of new imaging methods. An in-silica optimization strategy is needed when developing advanced reconstructions in the setting of free-breathing abdominal DCE MRI.

Goal(s): Demonstrate a framework for testing performance of different reconstructions.

Approach: A publicly available DRO was used to generate simulated free-breathing abdominal DCE k-space data. Data was then reconstructed using different reconstruction settings for MOCCO and SENSE.

Results: This approach allowed head-to-head comparisons of different reconstruction methods as well as comparison with the ground truth data used to generate the DRO.

Impact: The proposed testing approach allows researchers to test numerous combinations of acquisitions and reconstructions while having ground truth as a benchmark.   

Keywords: Software Tools, Software Tools

Motivation: Automate collecting of MRI raw data from the Philips MR scanners.

Goal(s): To create a tool that will allow users to extract selected scan data in raw format and save specific scan information for later use.

Approach: Using a Philips PRIDE interface to gathers raw data and schedule a job to execute during afterhours on the Scanner Console.

Results: The simple tool allows to collect complete raw data in under 3 mins at the end of the scan and associate the data with respective DICOM information for later association or annotation.

Impact: Collection and storage of the complete acquisition raw data with associated DICOM information for potential use in the future using a flexible tool with a small footprint.

Keywords: Software Tools, Simulations, Motion modelling

Motivation: KomaMRI is a newly released Pulseq-compatible MRI simulator. Albeit the simulator includes dynamic imaging, motion type is limited to analytical expressions.

Goal(s): To provide KomaMRI with additional dynamic properties irrespective of the motion type.

Approach: To expand the phantom class to account for sampled arbitrary trajectories and to interpolate spin positions at time instants needed for the simulation. The simulation kernel is valid almost “as is” and only the demagnetization of the spins leaving the volume needs to be accounted for.

Results: 2D Cardiac cine with bright-blood effect, tagging and flow both with in-house and XCAT phantoms are dealt with now in KomaMRI.

Impact: KomaMRI is expected to be used for designing and testing novel pulse sequences. The added capabilities provided by the extension we propose increase its potential associated by enabling the simulator to deal with any sort of motion for sequence design.