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| To begin doing the tutorials open a terminal window and source freesurfer. Then create an environment variable called '''TUTORIAL_DATA''' and set it to the location of the extracted file from above. If you {{{ls $TUTORIAL_DATA}}} you should see the directories extracted in step #2. The example below shows how you would perform these steps on a Mac OSX system. The only difference for your system would be the actual paths: | To begin doing the tutorials open a terminal window and source freesurfer. Then create an environment variable called '''TUTORIAL_DATA''' and set it to the location of the extracted file from above. The '''TUTORIAL_DATA''' environment variable is required for all tutorials. The example below shows the commands to type AFTER sourcing freesurfer. If you {{{ls $TUTORIAL_DATA}}} you should see the directories extracted in step #2 and you may now begin the [[FsTutorial|freesurfer tutorials]]. |
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$> export FREESURFER_HOME=/Applications/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.sh |
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Here is an example of what the terminal window should look like: |
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Second The data for the [[FsTutorial| tutorials]] consists of several data sets: * buckner_data-tutorial_subjs.tar.gz: the main 'recon-all' stream subject data processing (size: ~16GB uncompressed)[[ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.md5sum.txt|Here is the md5sum]]. * long-tutorial.tar.gz: the longitudinal tutorial (size: ~16GB uncompressed) * fsfast-tutorial.subjects.tar.gz & fsfast-functional.tar.gz: the FS-FAST tutorial data set (size: ~5.6GB uncompressed & ~9.1GB uncompressed, respectively) * diffusion_recons.tar.gz & diffusion_tutorial.tar.gz - the diffusion and Tracula tutorial data sets * fbert-feat.tgz & bert.recon.tgz - tutorial on the integration of !FreeSurfer and FSL/FEAT If you only want to get started with the basics of !FreeSurfer, you need only download the buckner_data set. This will allow you to do the following tutorials: |
FreeSurfer Tutorial Data set
This page describes the setup process for running the freesurfer tutorials. These instructions apply to users who want to run the tutorials on their personal machine, users who are attending and upcoming freesurfer course, or as a guide for an administrator setting up a freesurfer course.
1. Install freesurfer
The first step is to install freesurfer on your personal machine. To install freesurfer, follow the instructions on the download and installation page. Important Note: The tutorials require users to have the "development version" of freesurfer installed. So when it comes time so select the version for download do NOT select version 5.3, download the "development version" instead, which can be found on this page.
2. Download tutorial data
Before continuing, please ensure you have a functioning freesurfer installation by running the commands on the testing freesurfer installation page. It would be pointless to continue otherwise. If you are having issues running the commands, please follow the instructions on the Setup and Configuaration page.
Once you have a functioning freesurfer installation, it is time to download the freesurfer tutorial data set. When the download completes you will want to extract its contents. This can be done on most operating systems by simply double-clicking the file. Remember the location of this directory. It is used throughout all of the tutorials. The file should extract a directory called tutorial_data and its content should look as follows:
3. Configure your system
To begin doing the tutorials open a terminal window and source freesurfer. Then create an environment variable called TUTORIAL_DATA and set it to the location of the extracted file from above. The TUTORIAL_DATA environment variable is required for all tutorials. The example below shows the commands to type AFTER sourcing freesurfer. If you ls $TUTORIAL_DATA you should see the directories extracted in step #2 and you may now begin the freesurfer tutorials.
$> export TUTORIAL_DATA=/Users/localzeke/Downloads/tutorial_data $> ls $TUTORIAL_DATA buckner_data fsfast-functional diffusion_recons fsfast-tutorial.subjects diffusion_tutorial long-tutorial
