Diff for "FsTutorial/Jan2009CourseSchedule"

Differences between revisions 54 and 115 (spanning 61 versions)

Tuesday, January 20th - Introduction / Single Subject / Group Analysis

Time	Title	Type	Lecturer
8:00 - 9:00	Course Registration	sign-in	staff
8:00 - 8:30	optional - Unix Tutorial for FreeSurfer 1. Surrey, 2. O'Reilly	tutorial	Allison Stevens
9:00 - 9:20	Introduction to Freesurfer	talk	Bruce Fischl
9:20 - 10:00	FreeSurfer Applications	talk	David Salat
10:00 - 10:30	Accuracy, Reliability and Validation	talk	David Salat
10:30 - 10:45	break
10:45 - 11:45	Analyzing the Individual Subject	talk	Doug Greve
11:45 - 12:30	lunch		Barack Obama
12:30 - 1:00	Tkmedit/Tksurfer demonstration	demo	Doug Greve
1:00 - 1:30	Interaction with Individual Subject Data	tutorial	staff
1:30 - 2:45	Group Analysis / GLM / Multiple Comparisons	talk	Doug Greve
2:45 - 3:00	QDEC demonstration	demo	Nick Schmansky
3:00 - 3:15	break
3:15 - 4:15	Group Analysis / Multiple Comparisons - mri_glmfit	tutorial	staff
4:15 - 5:00	Group Analysis - qdec	tutorial	staff
5:00 -	optional - FreeSurfer Installation on Personal Laptops	one-on-one	Nick Schmansky
5:00 -	optional - Start Processing Your Own Data	one-on-one	Allison Stevens

Wednesday, January 21st - ROIs / Troubleshooting / Multi-Modal / QA / Future Directions

Time	Title	Type	Lecturer
9:00 - 10:00	ROI Analysis	talk	Doug Greve
10:00 - 10:45	ROI Analysis	tutorial	staff
10:45 - 11:00	break
11:00 - 11:15	Failure Modes	talk	Bruce Fischl
11:15 - 12:15	Troubleshooting	tutorial	staff
12:15 - 1:00	lunch
1:00 - 2:15	Multi-Modal Integration: ROI and Surface-based Analysis	talk	Doug Greve
2:15 - 3:15	Multi-Modal Integration	tutorial	staff
3:15 - 3:30	break
3:30 - 4:30	Question and Answer Session, FsQuiz	talk	staff
4:30 - 6:00	Future Directions of FreeSurfer:
4:30 - 5:00	Inferring architectonic boundaries from in-vivo MRI	talk	Bruce Fischl
5:00 - 5:20	Combined Volume and Surface Registration	talk	Lilla Zollei
5:20 - 5:40	TRActs Constrained by UnderLying Anatomy (TRACULA)	talk	Anastasia Yendiki
5:40 - 6:00	Automated segmentation of hippocampal subfields	talk	Koen Van Leemput

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

-  ⇤ ← Revision 54 as of 2009-01-08 16:12:09 → 
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-'''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
+=== Tuesday, January 20th - Introduction / Single Subject / Group Analysis ===
-Line 11:
+Line 5:
-Pre-packets:
 *Unix tutorial
 *Wiki suggested links
 *Stream Page
 *Papers
+|| '''Time''' || '''Title''' || '''Type''' || '''Lecturer''' ||
|| 8:00 - 9:00 || Course Registration || sign-in || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/boston_fs_course_jan2009.jpg|staff|&do=get]] ||
|| 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 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.intro.2009.ppt|Introduction to Freesurfer|&do=get]]|| talk || Bruce Fischl ||
|| 9:20 - 10:00 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.applications.2009.ppt|FreeSurfer Applications|&do=get]] || talk || David Salat ||
|| 10:00 - 10:30 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.reliability.2009.ppt|Accuracy, Reliability and Validation|&do=get]] || talk || David Salat ||
|| 10:30 - 10:45 || '''break''' || || ||
|| 10:45 - 11:45 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.ppt|Analyzing the Individual Subject|&do=get]] || talk|| Doug Greve ||
|| 11:45 - 12:30 || '''lunch''' || || [[http://www.cbsnews.com/stories/2009/01/08/national/inauguration09/main4707733.shtml | Barack Obama]] ||
|| 12:30 - 1:00  || Tkmedit/Tksurfer demonstration || demo || Doug Greve ||
|| 1:00 - 1:30 || [[FsTutorial/OutputData|Interaction with Individual Subject Data]] || tutorial || staff ||
|| 1:30 - 2:45 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.groupanalysis.ppt|Group Analysis / GLM / Multiple Comparisons|&do=get]] || talk || Doug Greve ||
|| 2:45 - 3:00 || QDEC demonstration || demo || Nick Schmansky ||
|| 3:00 - 3:15 || '''break''' || || ||
|| 3:15 - 4:15 || [[FsTutorial/GroupAnalysis|Group Analysis / Multiple Comparisons - mri_glmfit]] || tutorial || staff ||
|| 4:15 - 5:00 || [[FsTutorial/QdecGroupAnalysis|Group Analysis - qdec]] || tutorial || staff ||
|| 5:00 - || '''optional -''' [[DownloadAndInstall|FreeSurfer Installation on Personal Laptops]] || one-on-one || Nick Schmansky  ||
|| 5:00 - || '''optional -''' Start Processing Your Own Data || one-on-one || Allison Stevens ||
-Line 17:
+Line 24:
-=== Tuesday, January 20th - Introduction to FreeSurfer ===
+=== Wednesday, January 21st - ROIs / Troubleshooting / Multi-Modal / QA / Future Directions ===
-Line 19:
+Line 26:
-|| 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 || [[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? ||
|| 12:30 - 1:15 || '''lunch''' || || || || ||
|| 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 || ||
|| 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|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 || ||
+|| '''Time''' || '''Title''' || '''Type''' || '''Lecturer''' ||
|| 9:00 - 10:00 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.ppt|ROI Analysis|&do=get]] || talk || Doug Greve ||
|| 10:00 - 10:45 || [[FsTutorial/AnatomicalROI|ROI Analysis]] || tutorial || staff ||
|| 10:45 - 11:00 || '''break''' || || ||
|| 11:00 - 11:15 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.failure_modes.2009.ppt|Failure Modes|&do=get]] || talk || Bruce Fischl||
|| 11:15 - 12:15 || [[FsTutorial/TroubleshootingData|Troubleshooting]] || tutorial || staff ||
|| 12:15 - 1:00 || '''lunch''' || || ||
|| 1:00 - 2:15 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal-integration.ppt|Multi-Modal Integration: ROI and Surface-based Analysis|&do=get]] || talk || Doug Greve ||
|| 2:15 - 3:15 || [[FsTutorial/MultiModal|Multi-Modal Integration]] || tutorial || staff ||
|| 3:15 - 3:30 || '''break''' || || ||
|| 3:30 - 4:30 || Question and Answer Session, FsQuiz || talk || staff ||
|| 4:30 - 6:00 || Future Directions of !FreeSurfer: || || ||
|| 4:30 - 5:00 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.inferring_architectonics.2009.ppt|Inferring architectonic boundaries from in-vivo MRI|&do=get]] || talk || Bruce Fischl ||
|| 5:00 - 5:20 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/CVS-lzollei.ppt|Combined Volume and Surface Registration|&do=get]] || talk || Lilla Zollei ||
|| 5:20 - 5:40 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt|TRActs Constrained by UnderLying Anatomy (TRACULA)|&do=get]] || talk || Anastasia Yendiki ||
|| 5:40 - 6:00 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/HippocampalSubfields-Koen.ppt|Automated segmentation of hippocampal subfields|&do=get]] || talk || Koen Van Leemput ||