Center for NMR Research Software

Programs developed by the Center for NMR Research are free for downloading by all interested research parties. If the programs are used for publication purpose, acknowledgement in the manuscript about the programs and CNMRR is appreciated.

Learn More About CNMRR Software

The Birdcage Builder can be used to calculate the capacitances of a Birdcage Coil of a given geometry.

This software is available as a web app (no registration required) or as downloadable desktop software (registration required below).

The version available for download from this website was developed years ago and does not support 64-bit and newer operating systems.

You can try using the online version; also, Penn State alumni at NYU recently developed a newer version of Birdcage Builder that can run on Android systems, plus, with a third-party software, on PC or Mac.

MRIUtil is an application for viewing MRI image data and performing post-processing operations on raw MRI image data as well as reconstructed MRI image data. Operations include T2 and T2* mapping, thickness measurement, etc. It supports reading Analyze, NIFTI, Bruker 2dseq, Philips PAR/REC, GE, Siemens and some basic raw image formats.

Two additional libraries, the vtkCNMRRLibrary and the itkCNMRRLibrary, are available to extend MRIUtil.

The software qMRI is a quantitative MRI image-processing tool. Its features include viewing MRI images, display image intensity profiles, calculating image intensity distributions in ROIs, reorganizing and reconstructing MRI raw data (e.g., GESEPI reconstruction), generating parameter maps (T1, T2, R2, T2*, R2*, R2′), segmentation, generating knee profile, and other basic image processing features. This software also includes special features for olfactory fMRI paradigm.

This software is capable of reading image data from most imaging platforms (Siemens, Philips, Bruker, DICOM, and ANALYZE format). This program is written in Interactive Data Language (IDL).

Partial codes were adopted from Cincinnati Children’s Hospital Image Processing Software (CCHIPS).

Olfactory Network Stimulation Editing Tool (ONSET) is a software for calculating the actual stimulation onset and duration vectors that are used for olfactory fMRI processing.

Since actual odor stimulation onset and duration occur only when the subject’s inhalation overlap with the odor stimulation (the “on” periods) in the paradigm, the original stimulation paradigm is inaccurate for fMRI data processing.

To use ONSET, the respiration trace data, odor delivery timing, and image acquisition timing must be recorded. The software automatically detects the actual onset of odor stimulation based on the timing of the paradigm and the respiration trace.

The actual stimulation onset vector is defined as the start time of each effective inhalation during the odor delivery time. The effective inhalation is the inhalation during odor delivery. The respiration volume is the area under each inhalation and exhalation phase pair.

RF_Tools is a group of MATLAB applications developed for determining electrical properties of tissues and saline for RF field simulations.

The current version can interpolate the conductivity and permittivity of (i) biological tissues and (ii) saline from experimentally measured data [1, 2], as well as use published 4-Cole-Cole fits to the experimentally-measured tissue properties [1]. In many instances the measured data and the fits are not in good agreement, and thus we have included both to aid the user in making informed decisions. You can obtain conductivity and permittivity of 45 different biological tissues ranging in the field strengths from 10Hz to 20GHz.

RF_Tools was developed using MATLAB 2007b and Windows XP. Compatibility was checked on the MATLAB 2006b platform. Older versions of MATLAB were not tested, but may function except for the “print to printer” and “print to PDF” functions.

References

[1] Gabriel C. Compilation of the dielectric properties of body tissues at RF and microwave frequencies. Air Force material command, Books Air Force Base, Texas: AL/OE-TR-1996-0037; 1996.

[2] Herman P Schwan. Electrical properties of tissue and cell suspensions. Advances in Biological and Medical Physics. 1957;5:147-209.

PSUdoMRI is an MRI simulator developed to accurately predict how realistic distributions of the electromagnetic fields used in MRI (DC, switched gradients, and radiofrequency) affect the MR images for arbitrary MRI pulse sequences.

PSUdoMRI is capable of considering multiple RF coils in transmission and in reception, considering correlated noise between RF channels, and calculating the SAR distribution throughout the sample for arbitrary pulse sequences or field distributions.

Simple Matlab GUIs allow for creation of some sample sequences and some simple reconstructions, and some sample field and tissue distribtuions are provided, but the simulation engine is capable of considering any sequence, field or sample geometry that is arranged in the proper format, as described in the manual.

Software Download

Center for NMR Research Software Downloads

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