Diff for "FsTutorial/Jan2009CourseSchedule"

Differences between revisions 6 and 17 (spanning 11 versions)

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	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 - 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	--

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

-  ⇤ ← Revision 6 as of 2008-12-15 17:54:05 → 
  Size: 2800
  Editor: AllisonStevens
  Comment:
+   ← Revision 17 as of 2008-12-17 15:35:26 → ⇥
  Size: 4747
  Editor: AllisonStevens
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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+'''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
-Line 5:
+Line 19:
-|| Time || Title || Type || Lecturer || Relevant Info || To Do/Topics covered ||
|| 8:00 - 8:30 || Unix Tutorial (optional) || tutorial || Allison Stevens || http://www.ee.surrey.ac.uk/Teaching/Unix/ || ||
|| 8:30 - 9:00 || Course Registration || 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 || ||
+|| 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 || [[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 - 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 ||
-Line 12:
+Line 45:
-|| 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 || || ||

=== Wednesday January 21 - Working with Data ===

|| 9:00 - 10:00 || Registration for Multi-Modal Integration || talk || Doug Greve || slide || ||
|| 10:00 - 11:00 || Working with fMRI and Diffusion Data || talk || Doug Greve || slide || ||
|| 11:00 - 12:00 || Working with Different Format Types || talk || Doug Greve || slide || ||
|| 12:00 - 1:00 || '''lunch''' || || || || ||
|| 1:00 - 2:00 || Segmentation/ROI Analysis || talk || Doug Greve || slide || ||
|| 2:00 - 2:30 || Working with !FreeSurfer Stats || talk || Doug Greve || slide || ||
|| 2:30 - 3:00 || Surface-Based Multi-Modal Analysis || talk || Doug Greve || slide || ||
|| 3:00 - 3:15 || Bug Reporting || talk || Doug Greve || slide || ||
+|| 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) ||
-Line 34:
+Line 50:
-|| 3:30 - 4:30 || Question and Answer Session || talk || staff || slide || ||
+|| 3:30 - 4:30 || Question and Answer Session || talk || staff || slide || quiz handout ||
-Line 37:
+Line 53:
-|| || Combined Volume and Surface Registration || talk|| Lilla Zollei || slide || ||
|| || Tractography of Underlying Anatomy (TRACULA) || talk || Anastasia Yendiki || 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 || -- || ||