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## == Course Evaluation ==
## Please fill out our course evaluation [[http://spreadsheets.google.com/viewform?formkey=cHJlMFNVZDFNeDltbUE0RkNhaTBuWFE6MA..|here]]. You can fill it in throughout the course.
 == Course Evaluation ==
Please fill out our course evaluation [[http://spreadsheets.google.com/viewform?formkey=dHhBeGpVT3NUMUwtQzdWZW1FOWRCM0E6MA..|here]]. You can fill it in throughout the remainder of the course but you can't save your answers and finish it later so be sure to submit it before you leave.

top

FreeSurfer Tutorial and Workshop

Overview

The FreeSurfer tools deal with two main types of data: volumetric data (volumes of voxels) and surface data (polygons that tile a surface). The talks and tutorials should familiarize you with FreeSurfer's volume and surface processing streams, the recommended workflow to execute these, and many of their component tools. The tutorials also describe some of FreeSurfer's tools for registering volumetric datasets, performing group analysis on morphology data, and integrating multi-modal output with FreeSurfer (overlaying color coded parametric maps onto the cortical surface and visualizing plotted results). After completing the tutorials, you should be able to:

  • perform surface reconstructions;
  • generate subcortical segmentations;
  • fix errors encountered during the volume or surface processing;
  • overlay functional data onto surfaces;
  • perform group analysis of structural (e.g. thickness) and functional data.

Note: During the tutorial sessions, you will be shown a variety of command strings on the tutorial wiki pages. Only those that appear between lines should be copy-and-pasted into the terminal for this tutorial. Those commands appear like this:


command arg1 arg2


Laptop damage policy: If liquid is spilled on a provided laptop, then you are liable for payment of the repair costs!

Question / Suggestion Box

During the course, if you have questions or suggestions, please follow this link to submit them (anonymously, or not). We will process them during the course and give feedback at the end.

  • == Course Evaluation ==

Please fill out our course evaluation here. You can fill it in throughout the remainder of the course but you can't save your answers and finish it later so be sure to submit it before you leave.

Course Schedule

FreeSurfer Course, September 17 and 18, 2009

MGH, Charlestown Navy Yard, Building 149, Conference Room A

Thursday, September 17th - Introduction / Single Subject / Group Analysis

Time

Title

Type

Lecturer

8:00 - 8:30

optional - Unix Tutorial for FreeSurfer Users 1. Surrey, 2. O'Reilly

tutorial

Allison Stevens

8:30 - 9:00

Course Registration

sign-in

staff

9:00 - 9:30

Introduction to Freesurfer

talk

Bruce Fischl

9:30 - 10:00

Accuracy, Reliability and Validation

talk

David Salat

10:00 - 10:15

break

10:15 - 11:15

Analyzing the Individual Subject

talk

Bruce Fischl

11:15 - 11:45

Tkmedit/Tksurfer demonstration

demo

Doug Greve

11:45 - 12:15

Interaction with Individual Subject Data

tutorial

staff

12:15 - 1:00

lunch

1:00 - 1:30

FreeSurfer Applications

talk

David Salat

1:30 - 2:00

Surface-based Smoothing/Surface-based Registration

talk

Doug Greve

2:00 - 2:15

break

2:15 - 3:00

Group Analysis / GLM / Multiple Comparisons

talk

Doug Greve

3:00 - 4:00

Group Analysis / Multiple Comparisons - mri_glmfit

tutorial

staff

4:00 - 4:15

QDEC demonstration

demo

Nick Schmansky

4:15 - 5:00

Group Analysis - qdec

tutorial

staff

5:00 - 5:30

Longitudinal FreeSurfer

talk

Martin Reuter

5:30 -

optional - FreeSurfer Installation on Personal Laptops

one-on-one

Nick Schmansky

5:30 -

optional - Start Processing Your Own Data

one-on-one

Allison Stevens

Friday, September 18th - ROIs / Troubleshooting / Multi-Modal / QA / Future Directions

Time

Title

Type

Lecturer

9:00 - 10:00

ROI Analysis

talk

Doug Greve

10:00 - 10:45

ROI Analysis

tutorial

staff

10:45 - 11:00

break

11:00 - 11:15

Failure Modes

talk

Bruce Fischl

11:15 - 12:15

Troubleshooting, Troubleshooting demonstration

tutorial

staff, Allison

12:15 - 1:00

Working lunch Optional talk - Introduction to Diffusion Processing

talk

Lilla Zollei and David Salat

1:00 - 2:15

Multi-Modal Integration: ROI and Surface-based Analysis

talk

Doug Greve

2:15 - 3:15

Multi-Modal Integration

tutorial

staff

3:15 - 3:30

break

3:30 - 4:30

Future Directions of FreeSurfer:

3:30 - 3:50

Combined Volume and Surface Registration

talk

Lilla Zollei

3:50 - 4:10

TRActs Constrained by UnderLying Anatomy (TRACULA)

talk

Anastasia Yendiki

4:10 - 4:30

Inferring architectonic boundaries from in-vivo MRI

talk

Bruce Fischl

4:30 - 5:15

Question and Answer Session, FsQuiz

talk

staff

Additional

FsTutorial (last edited 2022-11-28 14:32:26 by LiamrSennott)