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Please fill out the [[https://docs.google.com/forms/d/1MT90c4G8LwiJfTKZ459U2B48O75SQvzpz9YKGDo_PhQ/viewform|Evaluation]]

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FreeSurfer Tutorial and Workshop

Course Policies

Getting the tutorial data

Please DO NOT try to download the tutorial data during the course! We have copies of this data stored on servers located in the course room. Attempting to download this data from the public link (this link) during the course presents excessive and unnecessary load on our network, and likely will fail due to this load. Please contact a staff member for help in getting this data if needed outside of the course.

About the Course

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 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).

Note: During the tutorial sessions, you will be shown a variety of commands. Only those that appear in a box should be copy-and-pasted into the terminal. They will look like this:

command arg1 arg2

Tip for Mac users: The tutorials often refer to keyboard shortcuts (such as Alt+v) which do not work on a Mac. For a list of equivalent keyboard commands on a Mac, please refer to MacCommands.

Online Question Forum

Videos of Lectures

Throughout the course, you may post questions here (anonymously or not).

You can find videos of the lectures here.

Course Schedule

FreeSurfer Course, March 9-11, 2015

8:00 - 9:00am Registration Desk Open

Monday, March 9th - Introduction / Single Subject Analysis /Troubleshooting

Time

Title

Type

Lecturer

9:00 - 9:30

optional - Unix Tutorial for FreeSurfer Users

talk/tutorial

Ani

9:30 - 9:45

optional - Intro to FreeSurfer Jargon

talk

Ani

9:45 - 10:15

Introduction to Freesurfer

talk

Anastasia Yendiki

10:15 - 10:45

break

10:45 - 11:15

Analyzing the Individual Subject

talk

Lee

11:15 - 11:30

Freeview demonstration

demo

Lee

11:30 - 12:00

Surface-based Analysis: Smoothing & Intersubject Registration

talk

Iman

Tuesday, March 10th - Group Analysis / ROI Analysis / Longitudinal

Time

Title

Type

Lecturer

9:00 - 10:00

Interaction with Individual Subject Data Tutorial

tutorial

staff

10:00 - 10:45

FreeSurfer Troubleshooting

talk

Ani

10:45 - 11:15

break

11:15 - 12:15

Troubleshooting Tutorial

tutorial

staff

12:15 - 1:15

Lunch

--

--

1:15 - 2:15

Quality Checking a Recon

demo

Ani

2:15 - 2:55

Group Analysis

talk

Anastasia Yendiki

2:55 - 3:15

break

3:15 - 3:55

Group Analysis Tutorial

tutorial

staff

3:55 - 4:35

Multiple Comparisons

talk

Anastasia Yendiki

4:35 - 5:00

Multiple Comparisons Tutorial

tutorial

staff

Wednesday, March 11th - Multimodal / Diffusion / Q&A

Time

Title

Type

Lecturer

9:00 - 9:30

Longitudinal FreeSurfer see also: LongitudinalProcessing

talk

Iman

9:30 - 10:00

ROI Analysis

talk

Lee

10:00 - 10:30

ROI Analysis Tutorial

tutorial

staff

10:30 - 11:00

break

11:00 - 11:30

Registration Methods

talk

Iman

11:30 - 12:10

Introduction to Diffusion MRI

talk

Anastasia Yendiki

12:10 - 1:10

Lunch

--

--

1:10 - 2:10

TRActs Constrained by UnderLying Anatomy (TRACULA)

talk

Anastasia Yendiki

2:10 - 3:00

Tracula Tutorial

tutorial

staff

3:00 - 3:30

break

3:30 - 4:30

Multi-Modal Integration

talk

Iman

4:30 - 5:00

Multi-Modal Integration Tutorial

tutorial

staff

Please fill out the Evaluation

Please fill out the Evaluation

Additional Useful Information

During the Course

After the Course

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