FreeSurfer Tutorial
FreeSurfer is brought to you by the Martinos Center for Biomedical Imaging supported by NCRR/P41RR14075 , Massachusetts General Hospital, Boston, MA USA
2008-06-01 20:47
1 FreeSurfer Tutorial Table of Contents
Section Page Overview and course outline 3 Inspection of Freesurfer output 5 Troubleshooting your output 22 Fixing a bad skull strip 26 Making edits to the white matter 34 Correcting pial surfaces 46 Using control points to fix intensity normalization 50 Talairach registration 55 recon-all: morphometry and reconstruction 69 recon-all: process flow table 97 QDEC Group analysis 100 Group analysis: average subject, design matrix, mri_glmfit 125 Group analysis: visualization and inspection 149 Integrating FreeSurfer and FSL’s FEAT 159 Exercise overview 172 Tkmedit reference 176 Tksurfer reference 211 Glossary 227 References 229 Acknowledgments 238
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FreeSurfer Slides 1.
Introduction to Freesurfer - Bruce Fischl 2.
Anatomical Analysis with Freesurfer - Doug Greve 3.
Surface-based Group Analysis - Doug Greve 4.
Applying FreeSurfer Tools to FSL fMRI Analysis - Doug Greve
FreeSurfer Tutorial Overview
The FreeSurfer tools deal with two main types of data: volumetric data volumes of voxels and surface data polygons that tile a surface . This tutorial should familiarize you with FreeSurfer’s volume and surface processing streams, the recommended workflow to execute these, and many of their component tools. The tutorial also describes some of FreeSurfer’s tools for registering volumetric datasets, performing group analysis on morphology data, and integrating FSL Feat output with FreeSurfer overlaying color coded parametric maps onto the cortical surface and visualizing plotted results . After completing the tutorial, 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.
Course Outline
In the following sessions, you will be shown a variety of command strings. Only those that appear between lines should be copy-and-pasted into the terminal for this tutorial. Those commands appear like this:
3 command arg1 arg2
Session 1
Session 1a - Use the volume and surface viewing tools to observe correctly processed output data.
Session 1b - See examples of problematic output data, and learn how to fix the problems.
Extra - Long-form tutorial covering Freesurfer’s morphometry and reconstruction tool recon-all.
Extra - recon-all process-flow reference table.
Session 2
Session 2a - Learn how to conduct a group analysis using Qdec, and to visualize and inspect the results.
Session 2b - Applying FreeSurfer tools to FSL fMRI Analysis FEAT
Extra - Group Analysis tutorial using mri_glmfit from the command line, prior to the release of Qdec.
Extra - Visualization and inspection of group analysis results using tksurfer, prior to release of Qdec.
Additional
Home page: http://surfer.nmr.mgh.harvard.edu
Mailing list: send mail to [email protected] with the following command in the body of your email message: subscribe freesurfer
4 Getting the tutorial data
Listing of all exercises
FreeSurfer tools
Glossary
References
PDF and HTML snapshot
4pp PDFs: intro4pp.pdf, recon4pp.pdf, group4pp.pdf feat4pp.pdf
Acknowledgements
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Inspection of Freesurfer Output
To follow this exercise exactly be sure you’ve downloaded the tutorial data set before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names. If you are using the tutorial data please set the environmental variable TUTORIAL_DATA to the location that you have downloaded the data to here, it has been copied to $FREESURFER_HOME/subjects : tcsh setenv TUTORIAL_DATA $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs
Notice the command to open tcsh. If you are already running the tcsh command shell, then the ’tcsh’ command is not necessary.
In this exercise you will visualize and inspect correctly processed output data so that you can become familiar with what the end product should look like. The exercise will step you through visual inspection of a variety of output, but is not necessarily the recommended procedure to take when trying to verify each subject. Some steps are only necessary to check when there are problems. However it is a good idea for new users to become familiar with what the expected output should look like and how to view it.
First you need to set your SUBJECTS_DIR to the appropriate place: setenv SUBJECTS_DIR $TUTORIAL_DATA cd $SUBJECTS_DIR
* this will set your SUBJECTS_DIR to the location where your tutorial data is if you have defined the variable TUTORIAL_DATA as indicated at the top of this tutorial. If you are not using the tutorial data you should set your SUBJECTS_DIR to the directory in which the subject you will use for this tutorial is located.
Viewing Volumes with Tkmedit
The volumes that are output can be loaded into tkmedit, along with surface outlines and the subcortical segmentation. With one command line you can load in the brainmask.mgz and wm.mgz volumes, the rh.white and lh.white surfaces outlines , and the subcortical segmentation.
6 tkmedit good_output brainmask.mgz lh.white \ -aux T1.mgz -aux-surface rh.white \ -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt
You should see a tkmedit window open up to this: