Time

Title

Type

Lecturer

Corresponding Materials

To Do/Topics covered

8:00 - 8:30

Unix Tutorial for FreeSurfer (optional)

tutorial

Allison Stevens

http://www.ee.surrey.ac.uk/Teaching/Unix/ http://docstore.mik.ua/orelly/linux/lnut/index.htm

8:30 - 9:00

Course Registration

sign-in

staff

--

binders with slides, acquisition parameters? relevant papers? nametags, coffee

9:00 - 9:20

Introduction to FreeSurfer

talk

Bruce Fischl

slide

David making flowchart of overview

9:20 - 10:00

FreeSurfer Applications

talk

David Salat

slide

10:00 - 10:30

Reliability/Validation of FreeSurfer

talk

David Salat

slide

10:30 - 10:45

break

10:45 - 11:45

Analyzing the Individual Subject

talk

Doug Greve

slide

example of good data; update on the typical failure modes (Sita editing tutorial); detail on directories (Allison has a slide); aseg stats surface based vs. voxel based

10:45 - 11:45

Tkmedit/Tksurfer demonstration

demo

Doug Greve

tkmedit,tksurfer

11:45 - 12:30

Interaction with Individual Subject Data

tutorial

staff

FsTutorial

jacobian?

12:30 - 1:15

lunch

1:15 - 2:15

Group Analysis/GLM

talk

Doug Greve

slide

mapping labels; loading functional on surface and in volume; Brodmann's areas

2:15 - 2:30

QDEC demonstration

demo

Nick Schmansky

qdec

2:30 - 2:45

break

2:45 - 3:30

Multiple Comparisons

talk

Doug Greve

slide

find old tutorial and spruce up

3:30 - 5:00

Group Analysis Interactive Tutorial

tutorial

staff

FsTutorial/Qdec

5:00 -

FreeSurfer Installation on Personal Laptops (optional)

one-on-one

Nick Schmansky

fswiki

get tarball on machines; router; announce versions we will support

5:00 -

Start Processing Your Own Data (optional)

one-on-one

Allison Stevens

Time

Title

Type

Lecturer

Corresponding Materials

To Do/Topics covered

9:00 - 10:00

Registration for Multi-Modal Integration

talk

Doug Greve

slide

tkregister2 tutorial (Doug); bbregister wiki (Doug)

10:00 - 11:00

Working with fMRI and Diffusion Data

talk

Doug Greve

slide

David dt_recon wiki; label2label; ask someone for SPM directions; wmparc (add to wiki); how to load DTI data (add to wiki)

11:00 - 12:00

Working with Different Format Types

talk

Doug Greve

slide

FSL, FSFAST, SPM; extraction

12:00 - 1:00

lunch

1:00 - 2:00

Segmentation/ROI Analysis

talk

Doug Greve

slide

how to draw labels and how to get stats from labels (tutorial); aseg editing in tkmedit in wiki; parcellation edits? how divide label in thirds; CMA papers; your own atlas; thickness

2:00 - 2:30

Working with FreeSurfer Stats

talk

Doug Greve

slide

seg stats spreadsheet tutorial; mris_anatomical_stats; ICV automated (David & Doug)

2:30 - 3:00

Surface-Based Multi-Modal Analysis

talk

Doug Greve

slide

wiki of secret commands

3:00 - 3:15

Bug Reporting/Troubleshooting

talk

Nick Schmansky/Allison Stevens

slide

bugr; Allison has slide on bug reporting; version differences maybe; defect_seg (Sita wiki)

3:15 - 3:30

break

3:30 - 4:30

Question and Answer Session

talk

staff

slide

quiz handout

4:30 - 6:00

Future Directions of FreeSurfer:

Inferring architectonic boundaries from in-vivo MRI

talk

Bruce Fischl

slide

Combined Volume and Surface Registration

talk

Lilla Zollei

slide

maybe some children stuff

Tractography of Underlying Anatomy (TRACULA)

talk

Anastasia Yendiki

slide

Automated segmentation of hippocampal subfields

talk

Koen Van Leemput

slide

Freeview

demo

Allison Stevens

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