Virtual Scanner is an end-to-end hybrid Magnetic Resonance Imaging (MRI) simulator/console designed to be zero-footprint and modular.


Gehua Tong¹, Sairam Geethanath¹, Keerthi Sravan¹, Ravi Marina¹, Manso Jimeno¹, Enlin Qian¹, John Thomas Vaughan Jr.¹



Stable release v2.0, GNU Affero General Public License v3.0

An end-to-end hybrid Magnetic Resonance Imaging (MRI) simulator/console

Virtual Scanner is an open-source MR sequence platform written in Python. Virtual experiments can be run for sequence development, for the education of MR students and radiologists, or as part of a digital twin of a real MR scanner. Regular functionalities include registering subject information, selecting custom sequence parameters to generate a Pulseq sequence, run Bloch simulation directly on the .seq file, regular and deep-learning based reconstruction, and T1 and T2 mapping with ROI analysis on a zero-footprint, web browser UI. Furthermore, it includes Tx and Rx maps and RF pulse magnetization profile simulation as well as non-cartesian as advanced functionalities. Standard sequences (GRE, SE, IRSE, TSE, EPI) implemented in PyPulseq are provided for demonstrating the virtual experiments.

Virtual Scanner consists of two modes: in Standard Mode, a console-like GUI allows users to perform virtual scans and conduct basic analysis; in Advanced Mode, modular simulation/analysis of the entire signal chain may be performed.

designed Virtual Scanner with three main characteristics in mind:

  • Modular: Virtual Scanner consists of modules corresponding to steps in the MRI signal chain. Since modern MRI systems contain multiple levels of hardware and software, it is important for researchers to select the appropriate steps for simulation when developing acquisition paradigms, analysis methods, or hardware components.
  • Zero-footprint: Virtual Scanner was implemented as a web application using the FLASK framework (Pallets, n.d.) with back-end code in Python. The local server can be set up by running a script or using the command line.
  • Open-source: existing tools in the MRI community are incorporated for effective creation and sharing of resources. PulSeq, a multi-vendor MRI pulse sequence format, can be directly fed into the simulator.



1Columbia Magnetic Resonance Research Center, Columbia University in the City of New York, USA