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| || 9:00 - 9:20 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.intro.2008.ppt|Introduction to Freesurfer]]|| talk || Bruce Fischl || slide || David making flowchart of overview || | || 9:00 - 9:20 || [[attachment:freesurfer.intro.2008.ppt|Introduction to Freesurfer]]|| talk || Bruce Fischl || slide || David making flowchart of overview || |
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| || 4:30 - 5:00 || Inferring architectonic boundaries from in-vivo MRI || talk || Bruce Fischl || slide || || | || 4:30 - 5:00 || [[attachment:freesurfer.inferring_architectonics.2008.ppt|Inferring architectonic boundaries from in-vivo MRI]] || talk || Bruce Fischl || slide || || |
Deadlines
- December 29th - notify wait-listers of status; notify registrants of payment due date
- January 9th - tutorials/wikis completed
- January 9th - deadline for payment; mail out pre-packets
- January 13th - data must be on all laptops
- January 16th - run through complete
- January ? - paper materials ready for printing
Pre-packets:
- Unix tutorial
- Wiki suggested links
- Stream Page
- Papers
Tuesday, January 20th - Introduction to FreeSurfer
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 |
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 - 11:00 |
Tkmedit/Tksurfer demonstration |
demo |
Doug Greve |
tkmedit,tksurfer |
|
11:00 - 12:30 |
Interaction with Individual Subject Data |
tutorial |
staff |
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 |
|
|
5:00 - |
FreeSurfer Installation on Personal Laptops (optional) |
one-on-one |
Nick Schmansky |
get tarball on machines; router; announce versions we will support |
|
5:00 - |
Start Processing Your Own Data (optional) |
one-on-one |
Allison Stevens |
|
|
Wednesday, January 21st - Working with Various Data Types
Time |
Title |
Type |
Lecturer |
Corresponding Materials |
To Do/Topics covered |
9:00 - 9:45 |
ROI Analysis |
talk |
Doug Greve |
slide |
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 |
slide |
seg stats spreadsheet tutorial; mris_anatomical_stats; ICV automated (David) |
10:45 - 11:00 |
break |
|
|
|
|
11:00 - 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 |
slide |
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 |
slide |
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 |
slide |
quiz handout |
4:30 - 6:00 |
Future Directions of FreeSurfer: |
|
|
|
|
4:30 - 5:00 |
talk |
Bruce Fischl |
slide |
|
|
5:00 - 5:20 |
Combined Volume and Surface Registration |
talk |
Lilla Zollei |
slide |
maybe some children stuff |
5:20 - 5:40 |
Tractography of Underlying Anatomy (TRACULA) |
talk |
Anastasia Yendiki |
slide |
|
5:40 - 6:00 |
Automated segmentation of hippocampal subfields |
talk |
Koen Van Leemput |
slide |
|