Diff for "FsTutorial/April2011CourseSchedule"

Differences between revisions 5 and 46 (spanning 41 versions)

FreeSurfer Course, April 4 - 6, 2011

MGH, Charlestown Navy Yard, Building 149, Conference Room A

Monday, April 4th - Introduction / Single Subject / MRI / Longitudinal/ Troubleshooting

Time	Title	Type	Lecturer
8:00 - 8:30	optional - Unix Tutorial for FreeSurfer Users online practice	tutorial	Allison Stevens
8:30 - 9:00	optional - Intro to FreeSurfer Jargon	talk	Allison Stevens
8:30 - 9:00	Course Registration	sign-in	staff
9:00 - 9:30	Introduction to Freesurfer	talk	Bruce Fischl
9:30 - 10:30	Analyzing the Individual Subject	talk	Doug Greve
10:30 - 10:45	break
10:45 - 11:15	Tkmedit/Tksurfer demonstration	demo	Doug Greve
11:15 - 11:45	Interaction with Individual Subject Data Tutorial	tutorial	staff
11:45- 12:15	Failure Modes	talk	Bruce Fischl
12:15 - 1:15	Lunch (Suggestions)	--	--
12:45 - 1:15	Optional Lunch Talk- A Non-physicist's Intro to MR SpinBench	talk	Dylan Tisdall
1:15 - 2:15	Troubleshooting Demonstration, Troubleshooting Tutorial	tutorial	staff, Allison
2:15 - 2:45	Surface-based Smoothing/Surface-based Registration	talk	Doug Greve
2:45 - 3:15	FreeSurfer Applications	talk	David Salat
3:15 - 3:30	break
3:30 - 4:15	Registration Methods	talk	Lilla Zollei
4:15 - 4:45	Longitudinal FreeSurfer see also: LongitudinalProcessing	talk	Martin Reuter
4:45 - 5:30	Longitudinal Tutorial	tutorial	staff
5:30 -	optional - FreeSurfer Installation on Personal Laptops	one-on-one	staff
5:30 -	optional - Start Processing Your Own Data	one-on-one	staff

Boston Beer Works location information here and here.
Meet us at 6:25pm at the front of Building 149 (the entrance on the opposite side of the building from where the Course is held).
If you miss us, we are taking the 6:30pm MGH/Navy Yard shuttle to North Station (the next one departs at 6:45pm). From there, you cross the street and go down Canal Street. Boston Beer Works will be on your right.

Tuesday, April 5th - Group Analysis/ ROIs / Registration / Diffusion

Time	Title	Type	Lecturer
9:00 - 10:00	Group Analysis / GLM / Multiple Comparisons	talk	Mert Sabuncu
10:00 - 10:30	QDEC demonstration	demo	Nick Schmansky
10:30 - 10:45	break
10:45 - 11:45	Group Analysis / Multiple Comparisons - mri_glmfit Tutorial	tutorial	staff
10:45 - 11:45	Group Analysis - qdec Tutorial	tutorial	staff
11:45 - 12:45	Lunch	--	--
12:15 - 12:45	Optional Lunch Talk- MRI Acquisition Methods for Morphometry	talk	Andre van der Kouwe
12:45 - 1:45	ROI Analysis	talk	Doug Greve
1:45 - 2:15	ROI Analysis Tutorial	tutorial	staff
2:15 - 3:15	Introduction to Diffusion MRI	talk	Anastasia Yendiki
3:15 - 3:30	break
3:30 - 4:15	Diffusion Processing Tutorial	tutorial	staff
4:15 - 4:45	TRActs Constrained by UnderLying Anatomy (TRACULA)	talk	Anastasia Yendiki
4:45 - 5:30	Tracula Tutorial	tutorial	staff
5:30 - 6:00	optional - Quality Checking a Recon	demo	Allison Stevens

Wednesday, April 6th - Multi-Modal / Future Directions / fMRI / Q&A

9:00 - 10:00	Basics of fMRI Analysis	talk	Doug Greve
10:00 - 10:15	break
10:15 - 11:30	FSFAST	talk	Doug Greve
11:30 - 12:30	FSFAST Tutorial	tutorial	staff
12:30 - 1:30	Lunch	--	--
1:00 - 1:30	Optional Lunch Talk- Motion-compensated neuroanatomical imaging	talk	Dylan Tisdall
1:30 - 2:00	Accuracy, Reliability and Validation	talk	David Salat
2:00 - 2:20	Future Directions: Inferring architectonic boundaries from in-vivo MRI	talk	Bruce Fischl
2:20 - 2:45	break & Evaluation
2:45 - 3:45	Multi-Modal Integration	talk	Doug Greve
3:45 - 4:30	Multi-Modal Integration Tutorial	tutorial	staff
4:30 - 5:00	Question and Answer Session, FsQuiz	talk	staff

FsTutorial/April2011CourseSchedule (last edited 2011-04-06 12:35:21 by AllisonStevens)

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-=== FreeSurfer Course, April 4 and 5, 2010 ===
+=== FreeSurfer Course, April 4 - 6, 2011 ===
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+||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' ||
||8:00 - 8:30 ||'''optional -''' [[http://surfer.nmr.mgh.harvard.edu/pub/docs/unix_tutorial_FS_course.ppt|Unix Tutorial for FreeSurfer Users]] [[http://www.ee.surrey.ac.uk/Teaching/Unix|online practice]] ||tutorial ||Allison Stevens ||
||8:30 - 9:00 ||'''optional -''' [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsjargon.ppt|Intro to FreeSurfer Jargon|&do=get]] ||talk ||Allison Stevens ||
||8:30 - 9:00 ||'''Course Registration''' ||sign-in ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/staff2011.jpg|staff]] ||
||9:00 - 9:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.intro.ppt|Introduction to Freesurfer]] ||talk ||Bruce Fischl ||
||9:30 - 10:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.ppt|Analyzing the Individual Subject]] ||talk ||Doug Greve ||
||10:30 - 10:45 ||'''break''' || || ||
||10:45 - 11:15 ||Tkmedit/Tksurfer demonstration ||demo ||Doug Greve ||
||11:15 - 11:45 ||[[FsTutorial/OutputData|Interaction with Individual Subject Data Tutorial]] ||tutorial ||staff ||
||11:45- 12:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.failure_modes.ppt|Failure Modes|&do=get]] ||talk ||Bruce Fischl ||
||12:15 - 1:15 ||'''Lunch''' [[attachment:lunch_map.jpg|  (Suggestions)]]||-- ||-- ||
||''12:45 - 1:15'' ||''Optional Lunch Talk''- '' [[http://surfer.nmr.mgh.harvard.edu/pub/docs/mri_basics.pdf|A Non-physicist's Intro to MR|&do=get]] [[http://www.heartvista.com/SpinBench|SpinBench]]'' ||''talk'' ||''Dylan Tisdall'' ||
||1:15 - 2:15 ||Troubleshooting Demonstration, [[FsTutorial/TroubleshootingData|Troubleshooting Tutorial]] ||tutorial ||staff, Allison ||
||2:15 - 2:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.surface-based-analysis.ppt|Surface-based Smoothing/Surface-based Registration|&do=get]] ||talk ||Doug Greve ||
||2:45 - 3:15 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.applications.2011.ppt|FreeSurfer Applications|&do=get]] ||talk || David Salat ||
||3:15 - 3:30 ||'''break''' || || ||
||3:30 - 4:15 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.registration.ppt|Registration Methods|&do=get]] || talk || Lilla Zollei ||
||4:15 - 4:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.longitudinal.ppt|Longitudinal FreeSurfer|&do=get]] ''see also:'' LongitudinalProcessing ||talk ||Martin Reuter ||
||4:45 - 5:30 ||[[FsTutorial/LongitudinalTutorial|Longitudinal Tutorial]] ||tutorial ||staff ||
||5:30 - ||'''optional -''' [[DownloadAndInstall|FreeSurfer Installation on Personal Laptops]] ||one-on-one || staff ||
||5:30 - ||'''optional -''' [[http://surfer.nmr.mgh.harvard.edu/pub/docs/runningyourdata.ppt|Start Processing Your Own Data|&do=get]] ||one-on-one || staff ||
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-|| '''Time''' || '''Title''' || '''Type''' || '''Lecturer''' ||
|| 8:00 - 8:30 || '''optional -''' [[http://surfer.nmr.mgh.harvard.edu/pub/docs/unix_tutorial_FS_course.ppt|Unix Tutorial for FreeSurfer Users|&do=get]] [[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 ||
|| 8:30 - 9:00 || '''optional -''' Intro to !FreeSurfer Jargon || talk || Allison Stevens ||
|| 8:30 - 9:00 || '''Course Registration''' || sign-in || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/boston_fs_course_jan2009.jpg|staff|&do=get]] ||
|| 9:00 - 9:30 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.intro.ppt|Introduction to Freesurfer|&do=get]]|| talk || Bruce Fischl ||
|| 9:30 - 10:30 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.ppt|Analyzing the Individual Subject|&do=get]] || talk|| Doug Greve ||
|| 10:30 - 10:45 || '''break''' || || ||
|| 10:45 - 11:15  || Tkmedit/Tksurfer demonstration || demo || Doug Greve ||
|| 11:15 - 11:45 || [[FsTutorial/OutputData|Interaction with Individual Subject Data Tutorial]] || tutorial || staff ||
|| 11:45 - 12:15 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.surface-based-analysis.ppt|Surface-based Smoothing/Surface-based Registration|&do=get]] || talk || Doug Greve ||
|| 12:15 - 1:15 || '''Lunch''' || -- || -- ||
|| ''12:30 - 1:00'' || ''Optional Lunch Talk''- '' [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.applications.ppt|FreeSurfer Applications|&do=get]]'' || ''talk'' || ''David Salat''||
|| 1:15 - 1:45 ||  [[http://surfer.nmr.mgh.harvard.edu/pub/docs/mri_acquisition.ppt|Intro to MR|&do=get]] || talk || Dylan Tisdall ||
|| 1:45 - 2:30 ||  [[http://surfer.nmr.mgh.harvard.edu/pub/docs/mri_acquisition.ppt|MRI Acquisition Methods for Morphometry|&do=get]] || talk || Andre van der Kouwe ||
|| 2:30 - 2:45 || '''break''' || || ||
|| 2:45 - 3:15 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.longitudinal.ppt|Longitudinal FreeSurfer|&do=get]] ''see also:'' LongitudinalProcessing|| talk || Martin Reuter ||
|| 3:15 - 4:00 || Longitudinal tutorial; checking recon-all.log of failed subject; how to report bugs/ask questions on list; <<BR>>*anything that needs to be done to finish use case || tutorial || staff ||
|| 4:00 - 4:30 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.failure_modes.ppt|Failure Modes|&do=get]] || talk || Bruce Fischl||
|| 4:30 - 5:30 || Troubleshooting Demonstration, [[FsTutorial/TroubleshootingData|Troubleshooting Tutorial]]|| tutorial || staff, Allison ||
|| 5:30 - || '''optional -''' [[DownloadAndInstall|FreeSurfer Installation on Personal Laptops]] || one-on-one || Nick Schmansky  ||
|| 5:30 - || '''optional -''' [[http://surfer.nmr.mgh.harvard.edu/pub/docs/runningyourdata.ppt|Start Processing Your Own Data|&do=get]]|| one-on-one || Allison Stevens ||
+'''Boston Beer Works location information [[http://www.beerworks.net/html/locations_canal.html|here]] and [[http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=112+Canal+Street+Boston,+MA+02114&aq=&sll=37.0625,-95.677068&sspn=44.25371,54.228516&ie=UTF8&hq=&hnear=112+Canal+St,+Boston,+Massachusetts+02114&ll=42.367359,-71.058776&spn=0.010131,0.013239&z=16|here]].'''<<BR>>
Meet us at 6:25pm at the front of Building 149 (the entrance on the opposite side of the building from where the Course is held). <<BR>>
If you miss us, we are taking the 6:30pm MGH/Navy Yard shuttle to North Station (the next one departs at 6:45pm). From there, you cross the street and go down Canal Street. Boston Beer Works will be on your right.
-Line 30:
+Line 33:
-|| '''Time''' || '''Title''' || '''Type''' || '''Lecturer''' ||
|| 8:15 - 9:00 || Quality Checking a Recon || demo || Allison Stevens ||
|| 9:00 - 10:00 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.groupanalysis.ppt|Group Analysis / GLM / Multiple Comparisons|&do=get]] || talk || Mert Sabuncu ||
|| 10:00 - 11:00 || [[FsTutorial/GroupAnalysis|Group Analysis / Multiple Comparisons - mri_glmfit Tutorial]] || tutorial || staff ||
|| 11:00 - 11:15 || '''break''' || || ||
|| 11:15 - 11:45 || QDEC demonstration || demo || Nick Schmansky ||
|| 11:45 - 12:30 || [[FsTutorial/QdecGroupAnalysis|Group Analysis - qdec Tutorial]] || tutorial || staff ||
|| 12:30 - 1:30 || '''Lunch''' || -- || -- ||
|| ''12:45 - 1:15'' || ''Optional Lunch Talk''- ''Which What to Register'' || ''talk'' || ''Lilla Zollei''||
|| 1:30 - 2:30 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.ppt|ROI Analysis|&do=get]] || talk || Doug Greve ||
|| 2:30 - 3:00 || [[FsTutorial/AnatomicalROI|ROI Analysis Tutorial]] || tutorial || staff ||
|| 3:00 - 3:30 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/CVS-lzollei.ppt|Combined Volume and Surface Registration|&do=get]] || talk || Lilla Zollei ||
|| 3:30 - 3:45 || '''break''' || || ||
|| 3:45 - 4:15 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.dt_recon-intro.ppt|Introduction to Diffusion Processing|&do=get]] || talk || Lilla Zollei ||
|| 4:15 - 5:15 || Diffusion Tutorial || tutorial || staff ||
|| 5:15 - 5:35 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt|TRActs Constrained by UnderLying Anatomy (TRACULA)|&do=get]] || talk || Anastasia Yendiki ||
|| 5:35 - || '''optional -''' [[DownloadAndInstall|FreeSurfer Installation on Personal Laptops]] || one-on-one || Nick Schmansky  ||
|| 5:35 - || '''optional -''' [[http://surfer.nmr.mgh.harvard.edu/pub/docs/runningyourdata.ppt|Start Processing Your Own Data|&do=get]]|| one-on-one || Allison Stevens ||
+||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' ||
||9:00 - 10:00 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.groupanalysis.ppt|Group Analysis / GLM / Multiple Comparisons]] ||talk ||Mert Sabuncu ||
||10:00 - 10:30 ||QDEC demonstration ||demo ||Nick Schmansky ||
||10:30 - 10:45 ||'''break''' || || ||
||10:45 - 11:45 ||[[FsTutorial/GroupAnalysis|Group Analysis / Multiple Comparisons - mri_glmfit Tutorial]] ||tutorial ||staff ||
||10:45 - 11:45 ||[[FsTutorial/QdecGroupAnalysis|Group Analysis - qdec Tutorial]] ||tutorial ||staff ||
||11:45 - 12:45 ||'''Lunch''' ||-- ||-- ||
||''12:15 - 12:45'' ||''Optional Lunch Talk''- ''[[http://surfer.nmr.mgh.harvard.edu/pub/docs/mri_acquisition.ppt|MRI Acquisition Methods for Morphometry|&do=get]]'' ||''talk'' ||''Andre van der Kouwe'' ||
||12:45 - 1:45  ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.ppt|ROI Analysis|&do=get]] ||talk ||Doug Greve ||
||1:45 - 2:15 ||[[FsTutorial/AnatomicalROI|ROI Analysis Tutorial]] ||tutorial ||staff ||
||2:15 - 3:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/dmri,fs.ppt|Introduction to Diffusion MRI|&do=get]] ||talk ||Anastasia Yendiki ||
||3:15 - 3:30 ||'''break''' || || ||
||3:30 - 4:15 ||[[FsTutorial/Diffusion|Diffusion Processing Tutorial]] ||tutorial ||staff ||
||4:15 - 4:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt|TRActs Constrained by UnderLying Anatomy (TRACULA)|&do=get]] ||talk ||Anastasia Yendiki ||
||4:45 - 5:30 ||[[FsTutorial/Tracula|Tracula Tutorial]] ||tutorial ||staff ||
||5:30 - 6:00 ||'''optional -''' Quality Checking a Recon ||demo ||Allison Stevens ||
 Line 51:
-|| 8:30 - 9:45 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal-integration.ppt|Multi-Modal Integration|&do=get]] || talk || Doug Greve ||
|| 9:45 - 10:45 || [[FsTutorial/MultiModal|Multi-Modal Integration Tutorial]] || tutorial || staff ||
|| 10:45 - 11:00 || '''break''' || || ||
|| 11:00 - 11:30 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.reliability.ppt|Accuracy, Reliability and Validation|&do=get]] || talk || David Salat ||
|| 11:30 - 12:30 || '''Lunch''' || -- || -- ||
|| 12:10 - 12:30 || ''Optional Lunch Talk''- ''[[http://surfer.nmr.mgh.harvard.edu/pub/docs/tisdall_moco.pdf|Motion-compensated neuroanatomical imaging|&do=get]]'' || ''talk'' || ''Dylan Tisdall'' ||
|| 12:30 - 12:50 || Future Directions: [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.inferring_architectonics.ppt|Inferring architectonic boundaries from in-vivo MRI|&do=get]] || talk || Bruce Fischl ||
|| 12:50 - 2:15 || FSFAST || talk || Doug Greve ||
|| 2:15 - 2:30 || '''break''' || || ||
|| 2:30 - 3:30 || FSFAST || talk || Doug Greve ||
|| 3:30 - 4:30 || FSFAST || tutorial || staff ||
|| 4:30 - 5:15 || Question and Answer Session, FsQuiz || talk || staff ||
+||9:00 - 10:00 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fmri.april2011.pdf|Basics of fMRI Analysis|&do=get]] ||talk ||Doug Greve ||
||10:00 - 10:15 ||'''break''' || || ||
||10:15 - 11:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsfast.april2011.ppt|FSFAST|&do=get]] ||talk ||Doug Greve ||
||11:30 - 12:30 ||[[FsFastTutorialV5.1|FSFAST Tutorial]] ||tutorial ||staff ||
||12:30 - 1:30 ||'''Lunch''' ||-- ||-- ||
||''1:00 - 1:30'' ||''Optional Lunch Talk''- ''[[http://surfer.nmr.mgh.harvard.edu/pub/docs/motion_correction.pdf|Motion-compensated neuroanatomical imaging|&do=get]]'' ||''talk'' ||''Dylan Tisdall'' ||
||1:30 - 2:00 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.reliability.ppt|Accuracy, Reliability and Validation|&do=get]] ||talk ||David Salat ||
||2:00 - 2:20 ||Future Directions: [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.inferring_architectonics.ppt|Inferring architectonic boundaries from in-vivo MRI|&do=get]] ||talk ||Bruce Fischl ||
||2:20 - 2:45 ||'''break''' & [[https://spreadsheets.google.com/viewform?formkey=dGlVV3Bzb296bnBWN3lBc3l5U3lPUGc6MA|Evaluation]] || || ||
||2:45 - 3:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal-integration.ppt|Multi-Modal Integration|&do=get]] ||talk ||Doug Greve ||
||3:45 - 4:30 ||[[FsTutorial/MultiModal|Multi-Modal Integration Tutorial]] ||tutorial ||staff ||
||4:30 - 5:00 ||Question and Answer Session, FsQuiz ||talk ||staff ||

##'''The !FreeSurfer Evaluation is [[https://spreadsheets.google.com/viewform?formkey=dHM0ZWFSY0owUVoyQmpMR3NTWUt2SHc6MA|here]]!'''