Quantitative T2 mapping-based longitudinal assessment of brain injury and therapeutic rescue in the rat following acute organophosphate intoxication.

Code for T2 mapping using 2 functions:

1. Voxel-wise (curvefitting21.m)

2. Regional (curvefitting31.m)- averaging all voxels within a region and then computing T2

Note: MSME (multiple spin multiple echo) dataset is 4 dimensional- 9 slices across 15 echo times (TEs). Segmentations were manually performed on T2-weighted scans

Below is the order of steps for the voxel-wise code (T2mapping_method2_mono.m):

1. Cropping_images.m is a function that performs cropping based on the center of mass algorithm

2. Manually segmented labels are isolated and multiplied with MSME data using function Individual_ROI_mask.m

3. Monoexponential curve fitting is then performed using function curvefitting21.m

4. Coefficients from the fit are then exported into an excel sheet