HST 563

Lab #: Title

Lab creators


This is a template for the HST 563 lab websites. The HST 563 labs are intended to include a practical, on-site imaging experience (2 hrs, Wednesday, 4-6 PM) with a demonstration of the imaging technology, followed by a lab write-up, involving some questions/exercises (e.g. image processing of canned data-sets). The website should provide all of the materials, or at least links, needed to prepare for the lab practical and complete the lab exercises. Hopefully the practical and the exercises work synergistically and provide a comprehensive understanding of the material! Data files for the lab exercises will be loaded to the mit Athena course locker: http://web.mit.edu/hst.563/and available for download. Please consider this template as a loose format and fill in the parts that you feel are necessary for your particular lab. Iíve tried to follow the format used previously in HST 583 (see e.g. http://web.mit.edu/~jmelcher/www/HST583/Lab3_handout2006.htm) As you develop the content, send me the material and I will package it into a website. Thanks for all of your help; I hope this will be a successful and helpful course. ~ Scott Raymond


Contents: outline of the website

I. Introduction

††††††††††† Background

††††††††††† Reading References

††††††††††† Overview/goals of lab exercise

††††††††††† Lab write-up expectations

II. Pre-lab Exercises

††††††††††† Tutorial

††††††††††† Homework problems

III. Lab Exercises

††††††††††† Description of data/process

††††††††††† Questions


I. Introduction


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. ďa five page report with answers to the pre-lab homework and lab exercises.Ē Students like to know explicitly what the finished product should look like (at least I do!).

II. Pre-lab Exercises

Pre-lab exercises should include any problem-sets or software training that will be needed to fully maximize the on-site imaging experience.


A tutorial would be applicable if there is a specific software package used for the lab exercise (e.g. freesurfer). We can simply link to your pre-developed tutorial, or work to build a small tutorial.

Homework problems

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

III. 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. Iím 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 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?)