T1S0_To_WF

This repository contains the analysis pipeline and relevant scripts used in the study: "Mapping a Reproducible Water Fraction and T1 using MP2RAGE and Variable Flip Angle Quantitative MRI Protocols*".

Overview:

The pipeline estimates Water Fraction (WF) maps from quantitative MRI (qMRI) data, using two acquisition protocols for T1 mapping - Variable Flip Angle (VFA) and MP2RAGE.

The repository includes:

• T1S0_to_WF.m - an exmaple script demonstrating the full pipeline
• Reporisoties of T1 and S0 estimation for both VFA and MP2RAGE
• PD estimation functions
• calibratePDmap.m - WF calculation function

Example Data:

• T1 and S0 maps
• Brain mask
• Segmentation
• Expected WF and CSF segmentation (from WF calculation function)

Dependencies:

The scripts rely on functions and tools from the following repositories (make sure they are installed and added to your MATLAB path):

• mrQ - https://github.com/mezera/mrQ/tree/master
• MP2RAGE-related-scripts - https://github.com/JosePMarques/MP2RAGE-related-scripts/tree/master
• Vistasoft - https://github.com/vistalab/vistasoft
• SPM8 - https://github.com/spm/spm8

(*Add citation once the paper will be published)