semiQ is a software package designed to calculate the five new semi-quantitative quantifiers described in the following article: "Approximating R1 and R2: A Quantitative Approach to Clinical Weighted MRI". It contains example data from both phantoms and humans. For more information, please contact:
Aviv Mezer: aviv.mezer(AT)elsc.huji.ac.il
Shachar Moskovich: shachar.moskovich(AT)mail.huji.ac.il
- phantoms_run_args.mat contains all arguments needed to produce the new quantifiers, as well as the synthetic quantifiers, using the phantom_run function.
- phantom_run expands the input table T that contains the different values of different lipids.
- division_imgs is a function used to produce 3 division images, T1w/T2w, T1w/PDw and ln(T1w/PDw), using 3 weighted images (T1w, T2w, and PDw), as well as a brain mask.
- correlation_example is a script that calculates the correlations between different quantifiers and quantitative maps, for a single subject. It calls another function, cutoff_mask, which is used to remove extreme values from the quantifiers and the maps.
- relaxivity_example is a script that calculates the relaxivity between quantitative maps, as well as the semi-quantitative relaxivities, using a modified version of MDM_toolbox (https://github.com/shirfilo/MDM_toolbox/tree/master, Shir Filo). It uses the function calc_slopes, which calls the function calc_slopes_fit_manual_bins, which bins the values of the input images using slope_bin function.
- Example_data contains the data of a single subject: T1w, T2w, PDw, R1, R2, PD, seg, mask and the TEs in which the T2w and PDw images were parcelled with.
- MATLAB 2022b - http://www.mathworks.com/products/matlab/
- Vistasoft - https://github.com/vistalab/vistasoft
(C) Mezer lab, the Hebrew University of Jerusalem, Israel, Copyright 2023