Deadlines

Pre-packets:

Tuesday, January 20th - Introduction to FreeSurfer

Time

Title

Type

Lecturer

To Do/Topics covered

8:00 - 9:00

Course Registration

sign-in

staff

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

8:00 - 8:30

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

tutorial

Allison Stevens

9:00 - 9:20

Introduction to Freesurfer

talk

Bruce Fischl

David making flowchart of overview

9:20 - 10:00

FreeSurfer Applications

talk

David Salat

10:00 - 10:30

Reliability/Validation of FreeSurfer

talk

David Salat

10:30 - 10:45

break

10:45 - 11:45

Analyzing the Individual Subject

talk

Doug Greve

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 - 11:00

Tkmedit/Tksurfer demonstration

demo

Doug Greve

11:00 - 12:30

Interaction with Individual Subject Data

tutorial

staff

jacobian?

12:30 - 1:15

lunch

1:15 - 2:30

Group Analysis / GLM / Multiple Comparisons

talk

Doug Greve

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

2:30 - 2:45

QDEC demonstration

demo

Nick Schmansky

2:45 - 3:00

break

3:00 - 4:00

Group Analysis Interactive Tutorial

tutorial

staff

4:00 - 5:00

Multiple Comparisons

tutorial

staff

find old tutorial and spruce up

5:00 -

optional - FreeSurfer Installation on Personal Laptops

tutorial

Nick Schmansky

get tarball on external usb harddisks; router; announce versions we will support

5:00 -

optional - Start Processing Your Own Data

tutorial

Allison Stevens

Wednesday, January 21st - Working with Various Data Types

Time

Title

Type

Lecturer

To Do/Topics covered

9:00 - 9:45

ROI Analysis

talk

Doug Greve

Extracting ROI measures from anatomial data (stats files). Exporting ROI stats; ICV; Creating your own labels; mapping labels between subjects; 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

9:45 - 10:45

ROI Analysis

tutorial

staff

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

10:45 - 11:00

break

11:00 - 11:15

Failure Modes

talk

Bruce Fischl

Bruce will give intro to 'scare' tutorial

11:15 - 12:15

Troubleshooting

tutorial

staff

'scare' tutorial, defect_seg, bugr

12:15 - 1:00

lunch

1:00 - 2:15

Multi-Modal Integration: ROI and Surface-based Analysis

talk

Doug Greve

Cross-modal registration; Application to fMRI: HRF and activation maps in ROI and surface. DTI: integration with WM Parc. tkregister2 tutorial (Doug); bbregister wiki (Doug)

2:15 - 3:15

Multi-Modal Integration

tutorial

staff

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

3:15 - 3:30

break

3:30 - 4:30

Question and Answer Session

talk

staff

exam questions

4:30 - 6:00

Future Directions of FreeSurfer:

4:30 - 5:00

Inferring architectonic boundaries from in-vivo MRI

talk

Bruce Fischl

5:00 - 5:20

Combined Volume and Surface Registration

talk

Lilla Zollei

maybe some children stuff (my pet goat)

5:20 - 5:40

TRActs Constrained on UnderLying Anatomy (TRACULA)

talk

Anastasia Yendiki

5:40 - 6:00

Automated segmentation of hippocampal subfields

talk

Koen Van Leemput