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README.md

mrQ

mrQ is a software package designed to calculate MR parameters (T1 and PD) using spoiled gradient echo scans (SPGR, FLASH). Using T1 and PD maps, mrQ performs the evaluation of macromolecular tissue volume (MTV) and the apparent volume of the interacting water protons (VIP) as well as the water-surface interaction rate (SIR). This is version 2.1 of the mrQ software package.

To learn more about how to use mrQ please see the wiki: https://github.com/mezera/mrQ/wiki

For more information, please contact:

Aviv Mezer: aviv.mezer(AT)elsc.huji.ac.il

Shai Berman: shai.berman(AT)mail.huji.ac.il

Jonathan Bain: jonathan.bain(AT)mail.huji.ac.il

For updates, discussions, troubleshooting and more, visit our interactive forum at:

https://groups.google.com/forum/#!forum/mrq-forum

References

The software and the tissue parameters are described in the following article:

Mezer A, Yeatman JD, Stikov N, Kay KN, Cho NJ, Dougherty RF, Perry LM, Parvizi J, Hua LH, Butts-Pauly K and Wandell BA. Quantifying the local tissue volume and composition in individual brains with magnetic resonance imaging. Nature Medicine 19, 1667-1672 (2013). http://www.nature.com/nm/journal/v19/n12/full/nm.3390.html?WT.ec_id=NM-201312

and in the following conference presentation:

Mezer A, Rokem A, Berman S. Hastie T and Wandell BA "Evaluating quantitative proton-density-mapping methods" Human Brain Mapping 2016

Mezer A, Rokem A, Hastie T and Wandell B. "Proton density mapping: Removing receive-inhomogeneity using multi-coil information and T1 regularization". ISMRM 23rd Annual Meeting & Exhibition. Toronto, Ontario, Canada. 2 June 2015. http://ismrm.org/15/program_files/TueTP03.htm

For the patent, see:

Mezer, Aviv A., Robert F. Dougherty, and Brian A. Wandell. Methods for Detecting Abnormalities and Degenerative Processes in Soft Tissue Using Magnetic Resonance Imaging (MRI). The Board Of Trustees Of The Leland Stanford Junior University, assignee. Patent US9002428 B2. 7 Apr. 2015.

For an application of mrQ, see:

Yeatman JD, Wandell BA and Mezer A. Lifespan maturation and degeneration of human brain white matter. Nature Communications 5 (2014). http://www.nature.com/ncomms/2014/140917/ncomms5932/abs/ncomms5932.html

Versions

Version 1

Version 1 (v.1) is the code that was used by Mezer et al. in their Nature Medicine article (2013). The code is available at: https://github.com/mezera/mrQ/tree/v1.0

Version 2

Version 2 (v.2) was released in autumn 2015 and was developed by the Mezer lab of the Hebrew University of Jerusalem, Israel, in collaboration with the VISTA lab of Stanford University, USA.

Version 2.1

Version 2 (v.2.1) was released in summer 2016 and was developed by the Mezer lab of the Hebrew University of Jerusalem, Israel, in collaboration with the VISTA lab of Stanford University, USA.

The code in this repository was developed

Aviv Mezer & Brian Wandell form the Mezer Lab Wandell Lab & Vistaosft Team, Copyright 2013

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