Perelman School of Medicine at the University of Pennsylvania

Center for Magnetic Resonance & Optical Imaging


Custom software written for various MRI quantification, computer simulation, as well as information related to MR hardware design and implementation.The programs below are developed in-house for pulse sequence design and image processing. All programs should be considered works in progress. Please email the respective authors with comments and errors.

T1rho/T2 processing GUI

This MatLab GUI will assist in processing T1rho- or T2-weighted images to create T1rho or T2 parametric maps.  Software is compiled using MatLab 2007b and was tested on 2011b.  Includes 2D in-plane co-registration Affine algorithms to correct for rigid-body distortions between data sets.

Visit the T1rho and T2 processing page

Matpulse – Shinnar-LeRoux RF Pulse Synthesis

MATPULSE is a graphical user interface written in the Matlab programming language designed to generate amplitude modulated RF pulses for a desired spectral response. The program implements the Shinnar-LeRoux (SLR) algorithm for pulse sysnthesis.

Visit the Matpulse page.

BreastPro – Rapid Bilateral Breast Imaging

MRI pulse sequences and analysis software for simultaneous 3D bilateral back-projection imaging of dynamic contrast-enhancement in the breasts.

Visit the BreastPro page.

Cylinder – Electrode Recording Cylinder Visualization

CYLINDER is a GUI driven program that uses MRI to quantitatively determine recording electrode trajectories and their intersection with desired brain anatomy. This program can be used to guide electrode placement specific to the anatomy of an individual subject.

Visit the Cylinder page.

O2 Analysis – Analysis Software for 3He MRI

This software calculates regional VA/Q ratios from the regional measurements of PAO2 by a variation on methods used to calculate PAO2 from a known VA/Q ratio.

Visit the Analysis-pro page.

ImScribe – Automated brain MRI FOV determination for Siemens MRI

ImScribe is a Matlab program designed to automate the specification of the acquisition Field-of-View with Siemens MRI scanners. The program is particularly suited for neuro-imaging, including fMRI.

Shed – Automated parcellation of functional activation maps

Shed is a Matlab program designed to partition statistical activation maps into separate regions based on local peaks and cluster extents. Using a GUI interface, the program implements the watershedalgorithm to divide contiguous sub-regions of a statistical map without the need for manual intervention or user-bias.

SVS_B1cal – Calibrate the Transmit Reference Voltage on Siemens MRI scanners

SVS_B1cal is a Matlab program which determines the correct Transmit Reference voltage for an ROI specified by an SVS voxel. The program reads the spectroscopy signal from several SVS acquisitions acquired with varied transmit reference voltages. The program is designed to allow for quick transmit B1 calibration of a desired ROI.

RestLess – Real time monitoring of subject motion during fMRI scanning

RestLess is a Matlab program which monitors subject motion in real time during fMRI scanning on Siemens MRI scanners. The systems processes dicom images written in real time by the Siemens automated Dicom Export utility. It can display either absolute or relative subject motion and is capable of keeping up with TR times as fast as 1000ms.

QAscripts – assorted scripts for QA of functional neuroimaging data

QAscripts is a .zip archive of BASH scripts designed to perform automated image quality checks on BOLD, DTI, and perfusion images. The scripts assume a linux environment with installation of both AFNI and FSL.

2D Mutual Information Image Co-registration (MATLAB)

Author:  Matthew Sochor

Co-registers two images through rotation and translation in 2 dimensions. See the link for more documentation. Code is written in c++ and compiled in MATLAB and available for download here.