Differences between revisions 9 and 28 (spanning 19 versions)

FreeSurfer Tutorial and Workshop

Cape Town, South Africa

11-12 February 2010

Centre for High Performance Computing (CHPC), map

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 describe 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

Question / Suggestion Box

During the course, if you have questions or suggestions, please follow this link to submit them (anonymously, or not). We will process them during the course and give feedback at the end.

Course Evaluation

Please fill out our course evaluation here. You can fill it in throughout the remainder of the course but you can't save your answers and finish it later so be sure to submit it before you leave. If you started it but cannot finish it until later, enter any random 4 digit number at the top of the survey and hit submit. When you are at home, fill out a new form (skipping questions you already answered) but put that same 4 digit number in at the top so we can tie your answers together.

Course Schedule

Thursday, February 11th - 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
8:45 - 9:00	optional - Intro to FreeSurfer Jargon	talk	Allison Stevens
8:30 - 9:00	Course Registration	sign-in
9:00 - 9:30	Introduction to Freesurfer	talk	David Salat
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	MRI Acquisition Methods for Morphometry	talk	Andre van der Kouwe
12:15 - 12:30	break
12:30 - 13:00	Working lunch Optional talk - Combined Gray Matter/White Matter Analysis of the Aging Brain	talk	David Salat
13:00 - 13:30	lunch
13:30 - 14:15	FreeSurfer Applications	talk	David Salat
14:15 - 14:45	Surface-based Smoothing/Surface-based Registration	talk	Doug Greve
14:45 - 15:00	break
15:00 - 15:45	Group Analysis / GLM / Multiple Comparisons	talk	Doug Greve
15:45 - 16:00	QDEC demonstration	demo	Doug Greve
16:00 - 17:00	Group Analysis / Multiple Comparisons - mri_glmfit Tutorial	tutorial	staff
17:00 - 17:45	Group Analysis - qdec Tutorial	tutorial	staff

Friday, February 12th - ROIs / Troubleshooting / Multi-Modal / Q&A

Time	Title	Type	Lecturer
9:00 - 9:30	Accuracy, Reliability and Validation	talk	David Salat
9:30 - 10:30	ROI Analysis	talk	Doug Greve
10:30 - 11:00	ROI Analysis Tutorial	tutorial	staff
11:00 - 11:30	break
11:30 - 12:00	Failure Modes	talk	Allison Stevens
12:00 - 12:30	How to QA a Recon, Troubleshooting Tutorial demonstration	demo	Allison
12:30 - 13:15	lunch
13:15 - 14:15	Troubleshooting Tutorial	tutorial	staff
14:15 - 15:30	Multi-Modal Integration	talk	Doug Greve
15:30 - 15:45	break
15:45 - 16:45	Multi-Modal Integration Tutorial	tutorial	staff
16:45 - 17:30	Designing Event-related Experiments for fMRI	talk	Doug Greve

FsTutorial/CapeTown2010CourseSchedule (last edited 2010-02-11 11:43:38 by AllisonStevens)

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-=== FreeSurfer Course, 11-12 February 2010 ===
+= FreeSurfer Tutorial and Workshop =
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+=== 11-12 February 2010 ===
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+Line 8:
+== 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 describe 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
}}}
----

== Question / Suggestion Box ==
During the course, if you have questions or suggestions, [[http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/questions.cgi|please follow this link]] to submit them (anonymously, or not).  We will process them during the course and give feedback at the end. 

== Course Evaluation ==
Please fill out our course evaluation [[https://spreadsheets.google.com/viewform?hl=en&formkey=dGI5U21qSU1RdDZQbE1GclNPalpsemc6MA|here]]. You can fill it in throughout the remainder of the course but you can't save your answers and finish it later so be sure to submit it before you leave. If you started it but cannot finish it until later, enter any random 4 digit number at the top of the survey and hit submit. When you are at home, fill out a new form (skipping questions you already answered) but put that same 4 digit number in at the top so we can tie your answers together.

== Course Schedule ==
-Line 9:
+Line 35:
-|| 8:00 - 8:30 || '''optional -''' [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/unix_tutorial.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 ||
+|| 8:00 - 8:30 || '''optional -''' [[http://www.bme.uct.ac.za/freesurfer/unix_tutorial.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 ||
|| 8:45 - 9:00 || '''optional -''' Intro to FreeSurfer Jargon || talk || Allison Stevens ||
-Line 11:
+Line 38:
-|| 9:00 - 9:30 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.intro.2009.ppt|Introduction to Freesurfer|&do=get]]|| talk || David Salat||
|| 9:30 - 10:30 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.ppt|Analyzing the Individual Subject|&do=get]] || talk|| Doug Greve||
+|| 9:00 - 9:30 || [[http://www.bme.uct.ac.za/freesurfer/freesurfer.intro.ppt|Introduction to Freesurfer|&do=get]]|| talk || David Salat||
|| 9:30 - 10:30 || [[http://www.bme.uct.ac.za/freesurfer/fsrecon.ppt|Analyzing the Individual Subject|&do=get]] || talk|| Doug Greve||
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+Line 42:
-|| 11:15 - 11:45 || [[FsTutorial/OutputData|Interaction with Individual Subject Data]] || tutorial || staff ||
|| 11:45 - 12:15 || MRI Acquisition Methods for Morphometry || talk || Andre van der Kouwe  ||
+|| 11:15 - 11:45 || [[FsTutorial/OutputData|Interaction with Individual Subject Data Tutorial]] || tutorial || staff ||
|| 11:45 - 12:15 || [[http://www.bme.uct.ac.za/freesurfer/mri_acquisition.ppt|MRI Acquisition Methods for Morphometry|&do=get]] || talk || Andre van der Kouwe  ||
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-|| 12:30 - 1:00 || '''Working lunch''' Optional talk - Combined Gray Matter/White Matter Analysis of the Aging Brain || talk || David Salat ||
|| 1:00 - 1:30 || '''lunch''' || || ||
|| 1:30 - 2:15 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.applications.2009.ppt|FreeSurfer Applications|&do=get]] || talk || David Salat ||
|| 2:15 - 2:45 || [[ftp://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 - 3:00 || '''break''' || || ||
|| 3:00 - 3:45 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.groupanalysis.ppt|Group Analysis / GLM / Multiple Comparisons|&do=get]] || talk || Doug Greve ||
|| 3:45 - 4:00 || QDEC demonstration || demo || Doug Greve ||
|| 4:00 - 5:00 || [[FsTutorial/GroupAnalysis|Group Analysis / Multiple Comparisons - mri_glmfit]] || tutorial || staff ||
|| 5:00 - 5:45 || [[FsTutorial/QdecGroupAnalysis|Group Analysis - qdec]] || tutorial || staff ||
+|| 12:30 - 13:00 || '''Working lunch''' Optional talk - Combined Gray Matter/White Matter Analysis of the Aging Brain || talk || David Salat ||
|| 13:00 - 13:30 || '''lunch''' || || ||
|| 13:30 - 14:15 || [[http://www.bme.uct.ac.za/freesurfer/freesurfer.applications.ppt|FreeSurfer Applications|&do=get]] || talk || David Salat ||
|| 14:15 - 14:45 || [[http://www.bme.uct.ac.za/freesurfer/fs.surface-based-analysis.ppt|Surface-based Smoothing/Surface-based Registration|&do=get]] || talk || Doug Greve ||
|| 14:45 - 15:00 || '''break''' || || ||
|| 15:00 - 15:45 || [[http://www.bme.uct.ac.za/freesurfer/freesurfer.groupanalysis.ppt|Group Analysis / GLM / Multiple Comparisons|&do=get]] || talk || Doug Greve ||
|| 15:45 - 16:00 || QDEC demonstration || demo || Doug Greve ||
|| 16:00 - 17:00 || [[FsTutorial/GroupAnalysis|Group Analysis / Multiple Comparisons - mri_glmfit Tutorial]] || tutorial || staff ||
|| 17:00 - 17:45 || [[FsTutorial/QdecGroupAnalysis|Group Analysis - qdec Tutorial]] || tutorial || staff ||
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+Line 58:
-|| 9:00 - 9:30 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.reliability.2009.ppt|Accuracy, Reliability and Validation|&do=get]] || talk || David Salat ||
|| 9:30 - 10:30 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.ppt|ROI Analysis|&do=get]] || talk || Doug Greve ||
|| 10:30 - 11:00 || [[FsTutorial/AnatomicalROI|ROI Analysis]] || tutorial || staff ||
+|| 9:00 - 9:30 || [[http://www.bme.uct.ac.za/freesurfer/freesurfer.reliability.ppt|Accuracy, Reliability and Validation|&do=get]] || talk || David Salat ||
|| 9:30 - 10:30 || [[http://www.bme.uct.ac.za/freesurfer/fs.roi.ppt|ROI Analysis|&do=get]] || talk || Doug Greve ||
|| 10:30 - 11:00 || [[FsTutorial/AnatomicalROI|ROI Analysis Tutorial]] || tutorial || staff ||
-Line 35:
+Line 62:
-|| 11:30 - 12:00 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.failure_modes.2009.ppt|Failure Modes|&do=get]] || talk || Allison Stevens||
|| 12:00 - 12:30 || Step-by-Step Through a Recon, Troubleshooting Tutorial demonstration || demo || Allison ||
|| 12:30 - 1:30 || [[FsTutorial/TroubleshootingData|Troubleshooting]] || tutorial || staff ||
|| 1:30 - 2:00 || '''lunch''' || ||  ||
|| 2:00 - 3:15 || [[ftp://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal-integration.ppt|Multi-Modal Integration|&do=get]] || talk || Doug Greve ||
|| 3:15 - 4:15 || [[FsTutorial/MultiModal|Multi-Modal Integration]] || tutorial || staff ||
|| 4:15 - 4:30 || '''break''' || || ||
|| 4:30 - 5:15 || fMRI || talk || Doug Greve ||
+|| 11:30 - 12:00 || [[http://www.bme.uct.ac.za/freesurfer/freesurfer.failure_modes.ppt|Failure Modes|&do=get]] || talk || Allison Stevens||
|| 12:00 - 12:30 || How to QA a Recon, Troubleshooting Tutorial demonstration || demo || Allison ||
|| 12:30 - 13:15 || '''lunch''' || ||  ||
|| 13:15 - 14:15 || [[FsTutorial/TroubleshootingData|Troubleshooting Tutorial]] || tutorial || staff ||
|| 14:15 - 15:30 || [[http://www.bme.uct.ac.za/freesurfer/fs.multimodal-integration.ppt|Multi-Modal Integration|&do=get]] || talk || Doug Greve ||
|| 15:30 - 15:45 || '''break''' || || ||
|| 15:45 - 16:45 || [[FsTutorial/MultiModal|Multi-Modal Integration Tutorial]] || tutorial || staff ||
|| 16:45 - 17:30 || [[http://www.bme.uct.ac.za/freesurfer/event-related.pdf|Designing Event-related Experiments for fMRI|&do=get]] || talk || Doug Greve ||