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.

Overview/goals of lab exercise

A brief description of the lab practical and exercise. It would be good to formulate the didactic goals of the lab, i.e. learn techniques of rigid coregistration. This will help in the formulation of the lab.

Lab write-up expectations

A succinct description of what the students should turn in, i.e. “a five page report with answers to the pre-lab homework and lab exercises.” Students like to know explicitly what the finished product should look like (at least I do!).

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

It might be nice to work through a few simple problems on fundamental ideas (e.g. FFT) before on-site imaging.

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?)