Diff for "FsTutorial/Jan2009CourseSchedule"

Differences between revisions 1 and 24 (spanning 23 versions)

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	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 - 11:00	Tkmedit/Tksurfer demonstration	demo	Doug Greve	tkmedit,tksurfer
11:00 - 12:30	Interaction with Individual Subject Data	tutorial	staff	FsTutorial	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	FsTutorial/Qdec
5:00 -	FreeSurfer Installation on Personal Laptops (optional)	one-on-one	Nick Schmansky	fswiki	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:
	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	--

FsTutorial/Jan2009CourseSchedule (last edited 2009-12-11 16:12:06 by NickSchmansky)

-  ⇤ ← Revision 1 as of 2008-12-11 20:00:14 → 
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+   ← Revision 24 as of 2008-12-23 16:37:32 → ⇥
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-Deletions are marked like this.
+Additions are marked like this.
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-=== Tuesday January 20: Introduction to FreeSurfer ===
+'''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
-Line 5:
+Line 11:
-|| 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 || ||
+Pre-packets:
 *Unix tutorial
 *Wiki suggested links
 *Stream Page
 *Papers
-Line 21:
+Line 17:
-=== Wednesday January 20: Working with Various Data Types ===
+=== Tuesday, January 20th - Introduction to FreeSurfer ===
-Line 23:
+Line 19:
-|| 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 || 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 - 11:00  || Tkmedit/Tksurfer demonstration || demo || Doug Greve || tkmedit,tksurfer ||  ||
|| 11:00 - 12:30 || Interaction with Individual Subject Data || tutorial || staff || [[FsTutorial]] || 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 || [[FsTutorial/Qdec]] || ||
|| 5:00 - || !FreeSurfer Installation on Personal Laptops (optional) || one-on-one || Nick Schmansky || [[fswiki]] || 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: || || || || ||
|| || 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 || -- || ||