[Edit: fix spelling.]
I have worked with MRI images, but not with perfusion images. I have also worked with fitting compartmental models. But not with Simbiology.
See Zollner et al, 2021 for a good description of analysis procedures. Zollner et al assume the user has certain non-Matlab software packages. Even if you don't have those packages, Zollner's chapter is useful.
To avoid re-inventing the wheel, check out the Matlab file exchange submissions for MRI imaging and for perfusion model fitting. For example, MP3 Medical Imaging Toolbox; 4D medical image de-noising; 4D data exploration; View4D; and two packages by excellent authors who have helped many of us on Matlab Answers: Image Manipulation Toolbox by @DGM and Image Segmentation Tutorial by @Image Analyst.
References:
Good luck with your research.
