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| #acl AdminGroup:read,write,delete,revert All: | #acl AdminGroup:read,write,delete,revert KoenVanLeemput:read,write AdrianKCLee:read,write PedroOliveira:read All: |
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| === Tuesday January 20: Introduction to FreeSurfer === | === Tuesday, January 20th - Introduction to FreeSurfer === |
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| || 8:30 - 9:15 || Unix Tutorial (optional) || tutorial || Allison Stevens || slide || || 9:30 - 10:30 || Introduction to !FreeSurfer || talk || Doug Greve || slide || || 10:30 - 11:30 || !FreeSurfer Applications || talk || David Salat || slide || || 11:30 - 12:00 || Reliability/Validation of !FreeSurfer || talk || David Salat || slide || || 12:00 - 1:00 || '''lunch''' || || || || || 1:00 - 2:00 || Analyzing the Individual Subject || talk|| Doug Greve || slide || || 1:00 - 2:00 || Tkmedit/Tksurfer demonstration || demo || Doug Greve || tkmedit,tksurfer || || 2:00 - 3:00 || Interaction with Individual Subject Data || tutorial || staff || [[FsTutorial]] || || 3:00 - 4:00 || Group Analysis/GLM || talk || Doug Greve || slide || || 4:00 - 4:15 || QDEC demonstration || demo || Nick Schmansky || qdec || || 4:15 - 4:30 || '''break''' || || || || || 4:30 - 5:15 || Multiple Comparisons || talk || Doug Greve || slide || || 5:15 - 6:00 || Group Analysis Interactive Tutorial || tutorial || staff || [[FsTutorial/Qdec]] || || 6:00 - || !FreeSurfer Installation on Personal Laptops (optional) || one-on-one || Nick Schmansky || [[fswiki]] || || 6:00 - || Start Processing Your Own Data (optional) || one-on-one || Allison Stevens || || |
|| '''Time''' || '''Title''' || '''Type''' || '''Lecturer''' || To Do/Topics covered || || 8:00 - 9:00 || Course Registration || sign-in || staff || glossary link for here and printout for binders || || 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 || Nick give David slide on longitudinal analysis || || 10:30 - 10:45 || '''break''' || || || || || 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? || || 12:30 - 1:15 || '''lunch''' || || || || || 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 || || || 2:45 - 3:00 || '''break''' || || || || || 3:00 - 4:00 || [[FsTutorial/QdecGroupAnalysis|Group Analysis Interactive Tutorial]] || tutorial || staff || || || 4:00 - 5:00 || [[FsTutorial/QdecMultipleComparisons|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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| === Wednesday January 20: Working with Various Data Types === | === Wednesday, January 21st - Working with Various Data Types === |
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| || 9:00 - 10:00 || Registration for Multi-Modal Integration || * Working with fMRI and Diffusion Data * Working with Different Format Types * Segmentation/ROI Analysis * Working with !FreeSurfer Stats * Surface-Based Multi-Modal Analysis * Bug Reporting * Question and Answer Session * Future Directions of !FreeSurfer * Inferring architectonic boundaries from in-vivo MRI - Bruce Fischl * Combined Volume and Surface Registration - Lilla Zollei * Tractography of Underlying Anatomy (TRACULA) - Anastasia Yendiki |
|| Time || Title || Type || Lecturer || To Do/Topics covered || || 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 || [[FsTutorial/AnatomicalROI|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.2009.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 || [[FsTutorial/MultiModal|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.2009.ppt|Inferring architectonic boundaries from in-vivo MRI]] || talk || Bruce Fischl || all talks on Bruce's laptop || || 5:00 - 5:20 || [[attachment:CVS-lzollei.ppt|Combined Volume and Surface Registration]] || talk || Lilla Zollei || || || 5:20 - 5:40 || TRActs Constrained on !UnderLying Anatomy (TRACULA) || talk || Anastasia Yendiki || || || 5:40 - 6:00 || [[attachment:HippocampalSubfields-Koen.ppt|Automated segmentation of hippocampal subfields]] || talk || Koen Van Leemput || || |
Tuesday, January 20th - Introduction to FreeSurfer
Time |
Title |
Type |
Lecturer |
To Do/Topics covered |
8:00 - 9:00 |
Course Registration |
sign-in |
staff |
glossary link for here and printout for binders |
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 |
Nick give David slide on longitudinal analysis |
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 |
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 |
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 |
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 |
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 |
all talks on Bruce's laptop |
|
5:00 - 5:20 |
talk |
Lilla Zollei |
|
|
5:20 - 5:40 |
TRActs Constrained on UnderLying Anatomy (TRACULA) |
talk |
Anastasia Yendiki |
|
5:40 - 6:00 |
talk |
Koen Van Leemput |
|