References
tumor, IDH
TUMOR
A flowchart detailing every component of the pipeline is described in this report. The user first inputs a pair of contours, T1s, and metabolite maps. All images from the second scan are registered to the first scan either in Velocity (Varian Medical Systems) or within the program using SimpleITK. After approval of registration, if metabolite maps have varying coverage in the vicinity around the tumor, then the quality map for the lower coverage scan is applied to both scans to maintain coverage across both metabolite maps. Overlap statistics between the two contours are then calculated, and difference maps are generated for each axial slice based on the new, modified metabolite maps. After this step, 2D and 3D renderings of the contours can be generated. The steps within the dashed box must be repeated for each pair of contours within a cohort of patients. The final step is to generate Kaplan–Meier curves for OS and PFS for each overlap statistic, stratifying the groups by the median value of the statistic of interest. A log-rank test is performed on each pair of Kaplan-Meier curves to determine if the overlap statistic used is a statistically significant biomarker of survival.An example of the 2D and 3D visualization generated by the pipeline for a given subject. ((An example of a patient whose Cho/NAA ≥ 2x contour volume increased by almost 400%. The top row shows their pre-RT Cho/NAA ≥ 2x contour and Cho/NAA map overlaid on the T1, as well as a 3D visualization of the Cho/NAA ≥ 2x contour. The bottom row shows their mid-RT contour, Cho/NAA map, and T1. The right-hand side shows the overlap statistics calculated for the two contours displayed. This patient did not have an IDH mutation and was not MGMT promoter hypermethylated, and experienced progression 8.3 months after resection.