SOFTWARE PACKAGES

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1. QUANTITATIVE T2 AND PROTON DENSITY (PD) MAPPING 
   We are sharing a software package for post-processing multi-echo spin-echo (MESE) MRI datasets into quantitative T2 relaxation and proton density (PD) maps. Genuine quantification of T2 relaxation times in vivo is highly challenging because of long scan times required for full spin-echo acquisitions. In MESE protocols the simulated and indirect echoes, non-rectangular slice profiles, and inhomogeneous B1+ field profiles contaminate the echo train and bias the T2 values. The EMC-based quantitative T2 mapping package relies on computer simulations of Bloch equations to enable generation of accurate T2 maps at clinically feasible scan times. The package is based on a T2 mapping technique called the echo modulation curve (EMC) algorithm, which relies on accurate Bloch simulations that mimic the exact signal evolution in MESE pulse sequences. The algorithm employs a range of parameters, including RF pulse shapes, gradient pulses, and the exact timing diagram of the protocol as run on the scanner.
    

2. MULTICOMPONENT T2 (MCT2) MYELIN-WATER-FRACTION (MWF) MAPPING
   The mcT2 MWF mapping software turns standard multi-echo spin-echo (MESE) MRI scans into quantitative maps of myelin content in brain white matter. Contrast in MESE MRI images is associated with white matter integrity and with multiple pathologies, including inflammation, demyelination, gliosis, and unregulated iron accumulation. MESE images, however, do not natively provide insights specific to myelin. 
   The mcT2 MWF mapping software uses an advanced algorithm to analyze MESE MRI signal into “pools” that correspond to cellular compartments, such as the water trapped between layers of myelin. The analysis allows researchers to estimate the relative amount of myelin in each voxel via myelin-water fraction. By providing whole‑brain, quantitative maps of myelin from clinically accessible MRI data, this resource helps bridge the gap between basic myelin biology and in vivo human and animal studies.
    

3. MP-PCA DENOISING​
   We provide a software package for denoising multi-echo spin-echo (MESE) MRI data with an approach known as Marchenko-Pastur principal component analysis (MP-PCA).
   By applying the MP-PCA denoising algorithm to complex or magnitude images (such as DICOM format images), the software cleans up noisy MESE MRI data prior to quantitative mapping of T2 or myelin-water fraction. The denoising leads to more stable parametric maps and more reliable detection of subtle tissue changes, especially in regimes characterized by low signal-to-noise ratio (SNR).

The packages are implemented in MATLAB with compiled C/C++ back‑end code and are intended for research use only.

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