1. FreeSurfer Tutorial
FreeSurfer is brought to you by the Martinos Center for Biomedical Imaging supported by NCRR/P41RR14075 , Massachusetts General Hospital, Boston, MA USA
2012-03-27 15:02 1. FSL/FreeSurfer Course: FreeSurfer Lectures and Tutorials 1.1. May 17 and 18, 2012
1.1.1. Auckland, New Zealand
FSL Course Timetable
1.1.2. Thursday, May 17th - Introduction
Time Title Type Lecturer 5:30 - 6:15 Introduction to Freesurfer talk Nick Schmansky
1.1.3. Friday, May 18th - Applications / Troubleshooting / Group Analysis / FS-Feat Integration Time Title Type Lecturer 9:00 - 9:20 FreeSurfer Applications talk Lilla Zollei 9:20 - 9:45 Freesurfer-FEAT Integration talk Lilla Zollei 9:45 - Analyzing the Individual Subject talk Louis Vinke 10:30 10:30 - tea and coffee 11:00 11:00 - Analyzing the Individual Subject cont. & demo Louis Vinke 11:30 Tkmedit/Tksurfer demonstration 11:30 - Inspection of Freesurfer Output tutorial staff 12:00 12:00 - Troubleshooting tutorial staff 12:30 12:30 - lunch 2:00 2:00 - 2:30 Troubleshooting cont. tutorial staff 2:30 - 3:10 Group Analysis / GLM / Multiple Comparisons talk Lilla Zollei Nick 3:10 - 3:30 QDEC demonstration demo Schmansky 3:30 - 4:00 tea and coffee 4:00 - 5:00 Group Analysis - qdec tutorial staff 5:00 - 5:30 Freesurfer-FEAT Integration tutorial staff 5:30 - 6:15 Future Directions of FreeSurfer talk Lilla Zollei
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1. Inspection of Freesurfer Output
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 take you through a variety of output, but is not necessarily the recommended procedure to take when trying to verify each subject. Some outputs are only necessary to check when there are problems or for a particular type of study. 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.
1.1. Preparations 1.1.1. If You're at an Organized Course
If you are taking one of the formally organized courses, everything has been set up for you on the provided laptop. The only thing you will need to do is run the following commands in every new terminal window aka shell you open throughout this tutorial. Copy and paste the commands below to get started: setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs cd $SUBJECTS_DIR
To copy: Highlight the command in the box above, right click and select copy (or use keyboard shortcut Ctrl+c), then use the middle button of your mouse to click inside the terminal window (this will paste the command). Press enter to run the command.
These two commands set the SUBJECTS_DIR variable to the directory where the data is stored and then navigates into this directory. You can now skip ahead to the tutorial below the gray line .
1.1.2. If You're not at an Organized Course
If you are NOT taking one of the formally organized courses, then 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. These are the commands that you need to run before getting started: tcsh source your_freesurfer_dir/SetUpFreeSurfer.csh setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs cd $SUBJECTS_DIR
Notice the command to open tcsh. If you are already running the tcsh command shell, then the ’tcsh’ command is not necessary. If you are not using the tutorial data you should set your SUBJECTS_DIR to the directory in which the recon s of the subject s you will use for this tutorial are located. 1.2. Viewing Volumes with Tkmedit
Output volumes 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. Copy and paste the command below inside the terminal window: tkmedit good_output brainmask.mgz \ -aux T1.mgz -surfs -aseg
Some notes on the above command line:
good_output : name of subject brainmask.mgz : skull-stripped volume primarily used for troubleshooting found in $SUBJECTS_DIR/good_output/mri . -aux T1.mgz : pre-skull-stripped volume loaded as 2nd volume in $SUBJECTS_DIR/good_output/mri -surfs : loads all surfaces orig, white, and pial, for left and right hemispheres -aseg : loads automatic volume segmentation called aseg.mgz
You should see a tkmedit window open: