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| The [[FsTutorial|freesurfer course]] is a 3-4 workshop usually held 2x per year in the Boston area. It is a collection of talks, demos and tutorials designed to help users become more accustomed to using freesurfer for the analyzing and processing of their MRI data. | Follow the instructions below for running the [[FsTutorial|FreeSurfer tutorials]]. These instruction are valid for both Mac OSX and Linux platforms (!FreeSurfer is not available on Windows platform). |
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| The tutorial data set used during the course is provided to the public so that users may go thru these tutorials on their own without the need of attending a freesurfer course. It may also be used by freesurfer course participants so that they can use their own computer during the course, instead of the one provided to them at the course. | ''Please note, some experience with the command line (Terminal) is required to successfully install and run !FreeSurfer. If you do not have previous experience with the command line, and you are setting up your computer in preparation for the !FreeSurfer course, it is probably best to simply attempt to install !FreeSurfer, and download the tutorial data onto your machine, then wait till after the first !FreeSurfer course presentation [[http://surfer.nmr.mgh.harvard.edu/pub/docs/unix_jargon_ani.ppt|Unix Tutorial for FreeSurfer Users]] until you start running the tutorials on your own machine.'' |
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| Configuring your system so so that it may be used to perform these tutorials should be a fairly straightforward process and is described below: | === 1. Install FreeSurfer === |
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| === 1. Download freesurfer === | The first step is to install !FreeSurfer on your personal machine. To install !FreeSurfer, follow the instructions on [[https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall|the download and installation page]]. |
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| To install freesurfer, follow the instructions on [[https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall|the download and installation page]]. '''''Important Note:''''' When it comes time to download freesurfer do NOT download the most recent version (v5.3). The tutorials use the latest "development version" of freesurfer so download that version instead, which can be found [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/|on this page]]. |
''Please note, the tutorials require users to have the "development version" of !FreeSurfer installed. So when it comes time to select the version for download do NOT select version 5.3, download the "development version" instead, which can be found [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/|on this page]].'' |
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| Please ensure you have a functioning freesurfer installation by running the commands on the [[https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer| testing freesurfer installation]] page, as is would be pointless to continue otherwise. If you are having issues running the commands, please follow the instructions on the [[https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration|Setup and Configuaration page]]. | Once !FreeSurfer is installed, it is time to download the tutorial data set: |
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| [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz|tutorial_data.tar.gz]]. | |
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| Once you have a functioning freesurfer installation, you can download the data set and begin the tutorials. The tutorial data set is a 3 Gigabyte compressed tarball. It can be downloaded using [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz|this link]]. Once the download completes you will want to extract its contents. This can be done on most operating systems by simply double-clicking the file. The file should extract a directory called '''tutorial_data''' and its content should look as follows: | '''''REMEMBER THE LOCATION OF THE EXTRACTED CONTENTS''''', you will need to set an an environment variable called '''TUTORIAL_DATA''', set to this this directory, in order to do the tutorials. Its content should look as follows: |
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| {{attachment:Screen Shot 2015-08-24 at 2.55.20 PM.png}} |
{{attachment:finder.png}} |
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| Configuring your !FreeSurfer installation for the tutorials requires one simple step, sourcing !FreeSurfer and setting the '''TUTORIAL_DATA''' environment variable (setting it to the location of the extracted file from above). Continuing with the example from above, the steps below show the commands to type AFTER sourcing !FreeSurfer. If you type the {{{ls $TUTORIAL_DATA}}} command and see the directories extracted in step #2, you are ready to begin the [[FsTutorial|FreeSurfer tutorials]]. | |
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| {{{ $> <source freesurfer> $> export TUTORIAL_DATA=/Users/localzeke/Downloads/tutorial_data $> ls $TUTORIAL_DATA buckner_data fsfast-functional diffusion_recons fsfast-tutorial.subjects diffusion_tutorial long-tutorial }}} |
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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: |
{{attachment:Screen Shot 2015-08-24 at 4.56.51 PM.png}} |
FreeSurfer Tutorial Data set
Follow the instructions below for running the FreeSurfer tutorials. These instruction are valid for both Mac OSX and Linux platforms (FreeSurfer is not available on Windows platform).
Please note, some experience with the command line (Terminal) is required to successfully install and run FreeSurfer. If you do not have previous experience with the command line, and you are setting up your computer in preparation for the FreeSurfer course, it is probably best to simply attempt to install FreeSurfer, and download the tutorial data onto your machine, then wait till after the first FreeSurfer course presentation Unix Tutorial for FreeSurfer Users until you start running the tutorials on your own machine.
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.
Please note, the tutorials require users to have the "development version" of FreeSurfer installed. So when it comes time to 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
Once FreeSurfer is installed, it is time to download the tutorial data set:
REMEMBER THE LOCATION OF THE EXTRACTED CONTENTS, you will need to set an an environment variable called TUTORIAL_DATA, set to this this directory, in order to do the tutorials. Its content should look as follows:
3. Configure your system
Configuring your FreeSurfer installation for the tutorials requires one simple step, sourcing FreeSurfer and setting the TUTORIAL_DATA environment variable (setting it to the location of the extracted file from above). Continuing with the example from above, the steps below show the commands to type AFTER sourcing FreeSurfer. If you type the ls $TUTORIAL_DATA command and see the directories extracted in step #2, you are ready to begin the FreeSurfer tutorials.
$> <source freesurfer> $> export TUTORIAL_DATA=/Users/localzeke/Downloads/tutorial_data $> ls $TUTORIAL_DATA buckner_data fsfast-functional diffusion_recons fsfast-tutorial.subjects diffusion_tutorial long-tutorial
