Differences between revisions 1 and 88 (spanning 87 versions)

FreeSurfer Tutorial and Workshop

Overview

The FreeSurfer tools deal with two main types of data: volumetric data (volumes of voxels) and surface data (polygons that tile a surface). The talks and tutorials should familiarize you with FreeSurfer's volume and surface processing streams, the recommended workflow to execute these, and many of their component tools. The tutorials also describes some of FreeSurfer's tools for registering volumetric datasets, performing group analysis on morphology data, and integrating multi-modal output with FreeSurfer (overlaying color coded parametric maps onto the cortical surface and visualizing plotted results). After completing the tutorials, you should be able to:

perform surface reconstructions;
generate subcortical segmentations;
fix errors encountered during the volume or surface processing;
overlay functional data onto surfaces;
perform group analysis of structural (e.g. thickness) and functional data.

Note: During the tutorial sessions, you will be shown a variety of command strings on the tutorial wiki pages. Only those that appear between lines should be copy-and-pasted into the terminal for this tutorial. Those commands appear like this:

command arg1 arg2

Course Schedule

FreeSurfer Course, April 6 and 7, 2009

MGH, Charlestown Navy Yard, Conference Room A

Monday, April 6th - Introduction / Single Subject / Group Analysis

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

Tuesday, April 7th - 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, Troubleshooting demonstration	tutorial	staff, Allison
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	Future Directions of FreeSurfer:
3:30 - 3:50	Combined Volume and Surface Registration	talk	Lilla Zollei
3:50 - 4:10	TRActs Constrained by UnderLying Anatomy (TRACULA)	talk	Anastasia Yendiki
4:10 - 4:30	Automated segmentation of hippocampal subfields	talk	Koen Van Leemput
4:30 - 5:15	Question and Answer Session, FsQuiz	talk	staff

Additional

Home page: http://surfer.nmr.mgh.harvard.edu
Mailing list: send mail to majordomo@surfer.nmr.mgh.harvard.edu with the following command in the body of your email message: subscribe freesurfer
Getting the tutorial data (necessary only if you are not taking a formal course where data is provided)

-  ⇤ ← Revision 1 as of 2005-08-09 15:39:51 → 
  Size: 720
  Editor: NickSchmansky
  Comment:
+   ← Revision 88 as of 2009-03-20 13:08:24 → ⇥
  Size: 2447
  Editor: NickSchmansky
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-= FreeSurfer Tutorial =
+[[FreeSurferWiki|top]]
 Line 3:
- [wiki:Self:FsTutorial/Overview 1. Tutorial Overview] [[BR]]
 [wiki:Self:FsTutorial/InstallAndSetup 2. Installation and Setup] [[BR]]
 [wiki:Self:FsTutorial/MorphAndRecon 3. Morphometry and Reconstruction] [[BR]]
 [wiki:Self:FsTutorial/GroupAnalysis 4. Group Analysis] [[BR]]
 [wiki:Self:FsTutorial/Visualization 5. Visualization and Inspection of Group Analysis Results] [[BR]]
 [wiki:Self:FsTutorial/FSLFeatFreeSurfer 6. Applying FreeSurfer Tools to FSL fMRI Analysis (FEAT)] [[BR]]
+= FreeSurfer Tutorial and Workshop =
== Overview ==
The !FreeSurfer tools deal with two main types of data: volumetric data (volumes of voxels) and surface data (polygons that tile a surface). The talks and tutorials should familiarize you with !FreeSurfer's volume and surface processing streams, the recommended workflow to execute these, and many of their component tools. The tutorials also describes some of !FreeSurfer's tools for registering volumetric datasets, performing group analysis on morphology data, and integrating multi-modal output with !FreeSurfer (overlaying color coded parametric maps onto the cortical surface and visualizing plotted results). After completing the tutorials, you should be able to:
-Line 10:
+Line 7:
- [wiki:Self:FsTutorial/Exercises Exercise Overview]
+ * perform surface reconstructions;
 * generate subcortical segmentations;
 * fix errors encountered during the volume or surface processing;
 * overlay functional data onto surfaces;
 * perform group analysis of structural (e.g. thickness) and functional data.
-Line 12:
+Line 13:
- [wiki:Self:FsTutorial/FileFormats File Formats]
+Note: During the tutorial sessions, you will be shown a variety of command strings on the tutorial wiki pages.  Only those that appear between lines should be copy-and-pasted into the terminal for this tutorial.  Those commands appear like this:
----
{{{
command arg1 arg2
}}}
----
-Line 14:
+Line 20:
- [wiki:Self:FsTutorial/Tools FreeSurfer Tools]
+== Course Schedule ==
-Line 16:
+Line 22:
- [wiki:Self:FsTutorial/Glossary Glossary]
+## select one of the course schedules, comment-out the others:
##<<Include(FsTutorial/Jan2009CourseSchedule)>>
<<Include(FsTutorial/April2009CourseSchedule)>>
##<<Include(FsTutorial/BrazilCourseSchedule)>>
##<<Include(FsTutorial/FslCourseSchedule)>>

== Additional ==
 * Home page: http://surfer.nmr.mgh.harvard.edu
 * Mailing list: send mail to majordomo@surfer.nmr.mgh.harvard.edu with the following command in the body of your email message: subscribe freesurfer
 * [[FsTutorial/Data|Getting the tutorial data]] (necessary only if you are not taking a formal course where data is provided)
## * [[FsTutorial/Exercises|Listing of all exercises]]
## * [[FsTutorial/Tools|FreeSurfer tools]]
 * [[FsTutorial/Glossary|Glossary]]
 * [[Articles|References]]
## * [[FsTutorial/SnapShot|PDF and HTML snapshot]]
## * 4pp PDFs: [[attachment:intro4pp.pdf]], [[attachment:recon4pp.pdf]], [[attachment:group4pp.pdf]] [[attachment:feat4pp.pdf]]
 * [[FsTutorial/Acknowledgements|Acknowledgements]]
 * [[ConferenceRoomA| Conference Room A]]
 * [[FsTutorial/CourseChecklist| Course checklist (internal)]]