Events:HST-563-March2008

Lab date/time/location

• March 19, 2008
• [Direction http://www.spl.harvard.edu/pages/Directions]

Introduction

Background:

The background should provide brief descriptions of the specific imaging technology and image processing techniques (i.e. a few paragraphs) and should reference seminal papers for more detail. Reading References

You should include a list of papers on the specific techniques used in the lab, as well as a few more general background references on the technology (e.g. MR basics) for those that might not have taken HST 561. I will check with Alan Jasanoff (instructor for HST 561) to see if we can post some of his background material. Total reading material can be significant; please send me pdf copies and I will post them in the course locker.

http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1225

http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=294

http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1244

http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1247

Overview/goals of lab exercise

1. Background reading: 1-2 review style papers that cover the basics/fundamentals of the techniques at a general level. This should be enough to understand the lab demonstration. You can just send these to me and I'll post them on the website.

1. Lab demonstration: the 2 hr on-site session at the Surgical Planning Laboratory and Brigham and Women's Hospital.

Computer assisted

1. A small number of questions to answer about the lab demonstration and background reading to test comprehension.

Lab write-up expectations

a five page report with answers to the pre-lab homework and lab exercises.

Pre-lab Exercises

Tutorial

We will take series of tutorials available at http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101

Topics we cover will be

• Data Loading and Visualization
• Data Saving
• Manual Segmentation
• Level-Set Segmentation
• Automatic Brain Segmentation
• Registration
• Diffusion Tensor Imaging Analysis
• Nrrd File Format
• Dicom to Nrrd Conversion
• Functional Magnetic Resonace Imaging Analysis

Homework problems

Please read either one of the following literature before the class.

Lab Exercises

The lab exercise should be thought of as the take-home portion of the lab which forms the bulk of the lab-writeup (the finished document that gets graded). It should include some sort of data processing, perhaps including a walk-through/example of the image processing technique, code writing (preferable in matlab or other widely-known software package), and questions to probe understanding of the material. I’m sure this section will vary the most from lab to lab, but it should at least include a series of questions that can be answered (and graded!).

Description of data/process

This section should link the student to the data (e.g. found in course locker) and have simple instructions about what to do with the data (e.g. FFT the data series). Questions can be interspersed.

Questions

Questions can be actual problems (e.g. remove the shot noise from image A) or more open-ended discussion questions (e.g. what are the advantages/disadvantages of signal averaging?)