I am using FSL and MRTrix to process DICOM data to .nii files to use in a PDE based approach to modelling glioblastoma.  To compare our experiments with patient data, I need to create a tumour mask and define a region of tumour, presumably by an intensity threshold in the volume of the tumour. I know this must have been done many times and wonder if anyone has experience with a toolbox or application that has already been written for this purpose. Thank you.