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JHU/KKI_QSM_Toolbox_v3.0
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JHU/KKI_QSM_Toolbox is a MATLAB software with GUI for doing Quantitative Susceptibility Mapping (QSM) processing from MR phase data acquired with gradient echo sequence (GRE).

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Installation
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1.This is a MATLAB based toolbox, need MATLAB installation
2.This toolbox also uses processing routine from FSL, e.g. bet, thus need to have FSL installed.

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Usage 
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1. To start, open MATLAB and go to the folder where this toolbox is located.
2. run QSM.m

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Supported input/output format 
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Supported input file format
a. PAR/REC (Philips v4.2 and above)
b. DICOM (Philips/GE/Siemens/Canon)
c. EnhancedDICOM (Philips) 
d. .mat (MATLAB, customized, check "readerwrapper.m" under /QSM_Utilily/fileIO/)

Output file format
a. internal/final results are saved in MATLAB native format (.mat)
b. some results are also saved with a copy of NIFTI format (.nii.gz)

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Documentation
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For detailed use of the Toolbox, read the manual

A brief description of the toolbox output is given below:
*_PhaseUnwrapped_echo2-5[Path/Lap/NLFPath].mat: 
Unwrapped phase using [path/laplacian/nonlinear fitting+path] method, echo 2-5 (user-defined) was selected for QSM processing

*GREMag#.nii.gz 		: GRE Magnitude Image of selected echo for brain masking
*GREMag#_brain.nii.gz		: GRE Magnitude Image of brain only, using FSL BET 
*GREMag#_brain_mask.nii.gz	: brain mask from FSL BET
*_brain_mask_echo#_r#_t##.mat	: final brain mask used for QSM

*[SMV/PDF/LBVSMV/iRSHARP]_[avg/LSlope/NLSlope]_echo2-5.mat: 
Frequency map (in Hz) or local field map generated using [VSHARP/PDF/LBV+VSHARP/iRSHARP] method, taking [echo averaging/linear fitting/nonlinear fitting], with echo2-5(user-defined). Have corresponding .nii.gz file too.

*R2star.mat/R2star.nii.gz	: R2 star map

*chi_[iLSQR/TKD/iTKD/MEDI/SFCR/SFCR+0]: 
QSM map calculated using different methods. Have corresponding .nii.gz file.

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Disclaimer
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This Matlab package is available publicly, in the hope that it will be useful, 
but without any warranty and without even the implied warranty of merchantability or fitness for a particular purpose. 
It is designed to help researchers in the field of Magnetic Resonance Imaging who may have interests in doing QSM. 
It is not intended for use in a clinical setting.

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Contributions
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Major GUI and pipeline Authors: 
 Jiri van Bergen and Xu Li
 Affiliation: Radiology @ JHU & Kirby Center @ Kennedy Krieger Institute (KKI)
 Contact via xuli@mri.jhu.edu
 
 Other contributors include:
 Joseph Gillen, Craig Jones, Jonathan Farrell, Issel Lim and Jiadi Xu (Kirby Center @ KKI)
 Lijun Bao, Jinsheng Fang (Xiamen University)
 
 Some Codes are from or modifed from other publicly availabe codes including
 1. MEDI Toolbox:		http://weill.cornell.edu/mri/pages/qsm.html
 2. Berkin Bilgic Software: 	http://martinos.org/~berkin/software.html

