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## == 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.
== Course Evaluation ==
Please fill out our course evaluation [[https://spreadsheets.google.com/viewform?hl=en&formkey=dGNqMkJaeE52Z0o0b0tvWmJGN3dWckE6MA|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, February 1 and 2, 2010

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

Monday, February 1st - Introduction / Single Subject / ROIs /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 - 10:30

Analyzing the Individual Subject

talk

Bruce Fischl

10:30 - 10:45

break

10:45 - 11:15

Tkmedit/Tksurfer demonstration

demo

Doug Greve

11:15 - 11:45

Interaction with Individual Subject Data Tutorial

tutorial

staff

11:45 - 12:15

Surface-based Smoothing/Surface-based Registration

talk

Doug Greve

12:15 - 12:45

Working lunch Optional talk - Introduction to Diffusion Processing

talk

Lilla Zollei

12:45 - 1:15

Working lunch Optional talk - MRI Acquisition Methods for Morphometry

talk

Andre van der Kouwe

1:15 - 2:15

ROI Analysis

talk

Doug Greve

2:15 - 2:45

ROI Analysis Tutorial

tutorial

staff

2:45 - 3:00

break

3:00 - 3:45

Group Analysis / GLM / Multiple Comparisons

talk

Mert Sabuncu

3:45 - 4:45

Group Analysis / Multiple Comparisons - mri_glmfit Tutorial

tutorial

staff

4:45 - 5:00

QDEC demonstration

demo

Nick Schmansky

5:00 - 5:45

Group Analysis - qdec Tutorial

tutorial

staff

5:45 -

optional - FreeSurfer Installation on Personal Laptops

one-on-one

Nick Schmansky

5:45 -

optional - Start Processing Your Own Data

one-on-one

Allison Stevens

Tuesday, February 2nd - Troubleshooting / Multi-Modal / Q&A / Future Directions

Time

Title

Type

Lecturer

9:00 - 9:30

Accuracy, Reliability and Validation

talk

David Salat

9:30 - 10:00

Longitudinal FreeSurfer see also: LongitudinalProcessing

talk

Martin Reuter

10:00 - 10:45

FreeSurfer Applications

talk

David Salat

10:45 - 11:00

break

11:00 - 11:30

Failure Modes

talk

Bruce Fischl

11:30 - 12:30

Troubleshooting Tutorial, Troubleshooting Demonstration

tutorial

staff, Allison

12:30 - 1:00

Working lunch Optional demo - Step-by-Step Through a Recon

demo

TBD

1:00 - 1:30

Working lunch Optional talk - Combined Gray Matter/White Matter Analysis of the Aging Brain

talk

David Salat

1:30 - 2:45

Multi-Modal Integration

talk

Doug Greve

2:45 - 3:45

Multi-Modal Integration Tutorial

tutorial

staff

3:45 - 4:00

break

4:00 - 5:00

Future Directions of FreeSurfer:

4:00 - 4:20

Combined Volume and Surface Registration

talk

Lilla Zollei

4:20 - 4:40

TRActs Constrained by UnderLying Anatomy (TRACULA)

talk

Anastasia Yendiki

4:40 - 5:00

Inferring architectonic boundaries from in-vivo MRI

talk

Bruce Fischl

5:00 - 5:30

Question and Answer Session, FsQuiz

talk

staff

Additional

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