Folder Data.zip contains 3D MRI data of three patients (P1 P2 P3) who suffer from renal artery stenosis (RAS). This disease causes a narrowing of the arteries feeding the kidney which in the long term starves the kidneys of oxygen leading to tissue damage a reduced kidney function and ultimately also a reduction in kidney size.
Patients can have RAS affecting both kidneys (bilateral) or just one of their kidneys (unilateral).
Some patients can be treated by revascularisation therapy which involves placing a stent in the narrowed artery in an attempt to open it up and restore blood flow to the kidneys. However in some cases the damage to the kidney is irreversible and the treatment will not result in an improved function. When a kidney does respond to treatment an increase in kidney size is often apparent. If a kidney does not respond the size may remain the same or decrease further.
In these cases patient 1 received a unilateral stent in the right renal artery patient 2 received bilateral stents and patient 3 received a unilateral stent in the left renal artery. The folder Data.zip contains images taken immediately before treatment and a follow-up scan 4 months after treatment for each of the 3 patients. The images were acquired with a 3D MRI sequence with voxel size 1.5625 mm x 1.5625 mm x 2 mm (i.e. a slice thickness of 2 mm).
Assignment
1. Search the literature to review methods that have been used to estimate volumes on 3D data
2. Select modify or design a method to estimate the volume of each of the kidneys before and after treatment
3. Use your measurements to determine which kidneys have responded to treatment which have stayed the same and which have continued to deteriorate. Response is measured here by kidney volume.
4. Determine the precision in the measurements your method produces through inter- and/or intra-observer analysis and use this information to support your conclusions.
5. Report your results in the form of a journal article with a maximum of 2500 words. The article should be structured in the usual format:
Abstract of less than 250 words (not included in the word count)
Introduction: Discuss medical image analysis methods that are used for this type of problem in the literature as well as their performance and explain why you chose a particular method or why you developed a new one. Finish by clearly stating your objectives.
Methods: Describe the method that you used to derive the results. The methods have to be explained in sufficient detail to allow a reader to reproduce the results independently.
Results: Report the results obtained from the procedures described in the methods section.
Discussion: Explain how the data presented in the results section justify the conclusion as stated in the conclusion section. Discuss any issues encountered during analysis that may affect the validity of the conclusions. What have you learned from applying the methods and what changes would you suggest for future applications?
Conclusions: provide a concise summary of the main conclusions (which kidneys have responded)
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