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| || 8:00 - 8:30 || Unix Tutorial (optional) || tutorial || Allison Stevens || http://www.ee.surrey.ac.uk/Teaching/Unix/ http://docstore.mik.ua/orelly/linux/lnut/index.htm || || | || 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 || || |
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| || 10:45 - 11:45 || Analyzing the Individual Subject || talk|| Doug Greve || slide || update on the typical failure modes; 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 || draw labels || |
|| 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 || || |
| Line 41: | Line 41: |
| || 9:00 - 10:00 || Registration for Multi-Modal Integration || talk || Doug Greve || slide || tkregister2 wiki; bbregister || || 10:00 - 11:00 || Working with fMRI and Diffusion Data || talk || Doug Greve || slide || David dt_recon wiki; seg stats slide/wiki; label2label; mris_anatomical_stats; ask someone for SPM directions; wmparc (add to wiki); how to load DTI data || |
|| 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) || |
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| || 1:00 - 2:00 || Segmentation/ROI Analysis || talk || Doug Greve || slide || ICV automated; how to draw labels and how to get stats from labels; example of good data; 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 || how to put in table || |
|| 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) || |
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| || 3:00 - 3:15 || Bug Reporting || talk || Doug Greve || slide || bugr; Allison has slide || | || 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) || |
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| || 3:30 - 4:30 || Question and Answer Session || talk || staff || slide || quiz questions || | || 3:30 - 4:30 || Question and Answer Session || talk || staff || slide || quiz handout || |
Deadlines
- December 19th - 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 |
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 |
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 - 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 |
-- |
|