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| *January 16th - run through complete | *January 16th - run through complete |
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|| Time || Title || Type || Lecturer || Corresponding Materials || 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 [[http://www.ee.surrey.ac.uk/Teaching/Unix|1. Surrey]], [[http://docstore.mik.ua/orelly/linux/lnut/index.htm|2. O'Reilly]] || tutorial || Allison Stevens || web links || || || 9:00 - 9:20 || [[attachment:freesurfer.intro.2008.ppt|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 || || |
|| '''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 [[http://www.ee.surrey.ac.uk/Teaching/Unix|1. Surrey]], [[http://docstore.mik.ua/orelly/linux/lnut/index.htm|2. O'Reilly]] || tutorial || Allison Stevens || || || 9:00 - 9:20 || [[attachment:freesurfer.intro.2008.ppt|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 || || |
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|| 10:45 - 11:45 || [[attachment:freesurfer.recon.2007.ppt|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 || [[FsTutorial/OutputData|Interaction with Individual Subject Data]] || tutorial || staff || wiki || jacobian? || |
|| 10:45 - 11:45 || [[attachment:freesurfer.recon.2007.ppt|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 || [[FsTutorial/OutputData|Interaction with Individual Subject Data]] || tutorial || staff || jacobian? || |
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|| 1:15 - 2:30 || [[attachment:freesurfer.groupanalysis.ppt|Group Analysis / GLM / Multiple Comparisons]] || talk || Doug Greve || slide || mapping labels; loading functional on surface and in volume; Brodmann's areas || || 2:30 - 2:45 || QDEC demonstration || demo || Nick Schmansky || qdec || || |
|| 1:15 - 2:30 || [[attachment:freesurfer.groupanalysis.ppt|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 || || |
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|| 3:00 - 4:00 || [[FsTutorial/QdecGroupAnalysis|Group Analysis Interactive Tutorial]] || tutorial || staff || wiki || || || 4:00 - 5:00 || Multiple Comparisons || tutorial || staff || wiki || find old tutorial and spruce up || || 5:00 - || '''optional -''' [[DownloadAndInstall|FreeSurfer Installation on Personal Laptops]] || tutorial || Nick Schmansky || wiki || get tarball on external usb harddisks; router; announce versions we will support || || 5:00 - || '''optional -''' Start Processing Your Own Data || tutorial || Allison Stevens || || || |
|| 3:00 - 4:00 || [[FsTutorial/QdecGroupAnalysis|Group Analysis Interactive Tutorial]] || tutorial || staff || || || 4:00 - 5:00 || Multiple Comparisons || tutorial || staff || find old tutorial and spruce up || || 5:00 - || '''optional -''' [[DownloadAndInstall|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 || || |
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|| 9:00 - 9:45 || [[attachment:fs.roi.ppt|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 || wiki || seg stats spreadsheet tutorial; mris_anatomical_stats; ICV automated (David) || || 10:45 - 11:00 || '''break''' || || || || || || 11:00 - 11:15 || [[attachment:freesurfer.failure_modes.2008.ppt|Failure Modes]] || talk || Bruce Fischl|| slide || Bruce will give intro to 'scare' tutorial|| || 11:15 - 12:15 || [[FsTutorial/TroubleshootingData|Troubleshooting]] || tutorial || staff || wiki || 'scare' tutorial, defect_seg, bugr|| || 12:15 - 1:00 || '''lunch''' || || || || || || 1:00 - 2:15 || [[attachment:fs.multimodal-integration.ppt|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 || wiki || 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 || exam questions || || 4:30 - 6:00 || Future Directions of !FreeSurfer: || || || || || || 4:30 - 5:00 || [[attachment:freesurfer.inferring_architectonics.2008.ppt|Inferring architectonic boundaries from in-vivo MRI]] || 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 || || |
|| 9:00 - 9:45 || [[attachment:fs.roi.ppt|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 || [[attachment:freesurfer.failure_modes.2008.ppt|Failure Modes]] || talk || Bruce Fischl|| Bruce will give intro to 'scare' tutorial|| || 11:15 - 12:15 || [[FsTutorial/TroubleshootingData|Troubleshooting]] || tutorial || staff || 'scare' tutorial, defect_seg, bugr|| || 12:15 - 1:00 || '''lunch''' || || || || || 1:00 - 2:15 || [[attachment:fs.multimodal-integration.ppt|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 || [[attachment:freesurfer.inferring_architectonics.2008.ppt|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 || || 5:20 - 5:40 || Tractography of Underlying Anatomy (TRACULA) || talk || Anastasia Yendiki || || || 5:40 - 6:00 || Automated segmentation of hippocampal subfields || talk || Koen Van Leemput || || |
Deadlines
- December 29th - notify wait-listers of status; notify registrants of payment due date
- January 9th - tutorials/wikis completed; release new stable freesurfer
- 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 |
|
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 |
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 |
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 |
tutorial |
staff |
jacobian? |
||
12:30 - 1:15 |
lunch |
|
|
|
|
1:15 - 2:30 |
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 |
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 |
Corresponding Materials |
To Do/Topics covered |
9:00 - 9:45 |
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 |
talk |
Bruce Fischl |
Bruce will give intro to 'scare' tutorial |
||
11:15 - 12:15 |
tutorial |
staff |
'scare' tutorial, defect_seg, bugr |
||
12:15 - 1:00 |
lunch |
|
|
|
|
1:00 - 2:15 |
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 |
talk |
Bruce Fischl |
|
||
5:00 - 5:20 |
Combined Volume and Surface Registration |
talk |
Lilla Zollei |
maybe some children stuff |
|
5:20 - 5:40 |
Tractography of Underlying Anatomy (TRACULA) |
talk |
Anastasia Yendiki |
|
|
5:40 - 6:00 |
Automated segmentation of hippocampal subfields |
talk |
Koen Van Leemput |
|