Diff for "FsTutorial/Jan2009CourseSchedule"

Differences between revisions 1 and 49 (spanning 48 versions)

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	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 1. Surrey, 2. O'Reilly	tutorial	Allison Stevens	web links
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	wiki	jacobian?
12:30 - 1:15	lunch
1:15 - 2:30	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
2:45 - 3:00	break
3:00 - 4:00	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 - 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

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	wiki	seg stats spreadsheet tutorial; mris_anatomical_stats; ICV automated (David)
10:45 - 11:00	break
11:00 - 11:15	Troubleshooting Intro	talk	Bruce Fischl	slide	Bruce will give intro to 'scare' tutorial
11:15 - 12:15	Troubleshooting Tutorial	tutorial	staff	wiki	Bruce will give intro; '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	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	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

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

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-Deletions are marked like this.
+Additions are marked like this.
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-#acl AdminGroup:read,write,delete,revert All:
+#acl AdminGroup:read,write,delete,revert KoenVanLeemput:read,write All:
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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; 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
-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 - 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 || ||
|| 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 || [[FsTutorial/OutputData|Interaction with Individual Subject Data]] || tutorial || staff || wiki || jacobian? ||
|| 12:30 - 1:15 || '''lunch''' || || || || ||
|| 1:15 - 2:30 || 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 || ||
|| 2:45 - 3:00 || '''break''' || || || || ||
|| 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 || || ||

=== Wednesday, January 21st - Working with Various Data Types ===

|| Time || Title || Type || Lecturer || Corresponding Materials || To Do/Topics covered ||
|| 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|Troubleshooting Intro]] || talk || Bruce Fischl|| slide || Bruce will give intro to 'scare' tutorial||
|| 11:15 - 12:15 || [[FsTutorial/TroubleshootingData|Troubleshooting Tutorial]] || tutorial || staff || wiki || Bruce will give intro; '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 || ||