[[FsTutorial|top]]

'''Index'''

<<TableOfContents>>

== FreeSurfer Tutorial Datasets ==
## The data set for the Freesurfer tutorials comes in two forms, a "Lightweight" version and a "Full" version.

##  * The "Lightweight" version contains only the files required to run the commands of the !FreeSurfer tutorial. It has all the required input and output data, but lacks the other files that would normally be present when performing a recon. People who just want a quick easy way to run the commands in the tutorial should download this data set.

##  * The "Full" version contains all the files that would normally be present when performing recons. Because of the numerous subjects involved with the tutorials, the full data set is quite large (~60Gigs). People who want to go into more depth than that which is covered in the tutorials should download this data set.

## == Lightweight version ==
## Use the following link to download the lightweight version of the tutorial data:

##  . [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz|tutorial_data.tar.gz]]

## Once the download is complete, uncompress the data file - this usually this can be done by simply double-clicking. In order to do the tutorials, users must define an environment variable called '''TUTORIAL_DATA''' which is set to the location of the extracted data. For example:

## {{{
## $> export TUTORIAL_DATA=/home/username/Downloads/tutorial_data
## $> ls $TUTORIAL_DATA
## buckner_data                    fsfast-functional
## diffusion_recons                fsfast-tutorial.subjects
## diffusion_tutorial              long-tutorial
## }}}
## You are now ready to start the [[Tutorials|Freesurfer tutorials]].

##  == Full version ==
## The size of the data for the freesurfer [[Tutorials|tutorials]] is quite large, so it consists of several sets:

## || '''Download''' || '''Description''' || '''Size''' ||
## || [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data_core.tar.gz|Core Data]]                 || The core tutorial subject data || 16.8 GB ||
## || [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data_functional.tar.gz|Functional Data]]     || The !FsFast functional tutorial data || 18.1 GB ||
## || [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data_diffusion.tar.gz|Diffusion Data]]       || The diffusion and tracula tutorial data || 4.3 GB ||
## || [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data_longitudinal.tar.gz|Longitudinal Data]] || The longitudinal tutorial data || 15.5 GB ||

## If you just want to get started with the basics of !FreeSurfer, you only need to download the core data set. This will allow you to run the following tutorials:

## * [[FsTutorial/OutputData_freeview|Intro to FreeSurfer Output]]
## * [[FsTutorial/TroubleshootingData|Troubleshooting FreeSurfer Output]]
## * [[FsTutorial/GroupAnalysis|Group Analysis via command-line]]
## * [[FsTutorial/QdecGroupAnalysis_freeview|Group Analysis via GUI]]
## * [[FsTutorial/AnatomicalROI|ROI Analysis]]
## * [[FsTutorial/MultiModal_freeview|Multimodal Analysis]]

== Installation ==
The following commands will install the complete tutorial dataset (~8GB) on your machine. Afterwards, you should have a folder called `tutorial_data` in your working directory.

{{{
curl https://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz -o tutorial_data.tar.gz
tar -xzvf tutorial_data.tar.gz
rm tutorial_data.tar.gz
}}}

== Configuration ==

In order to run the tutorials, users must define an environment variable called '''TUTORIAL_DATA''', which must be set to the `tutorial_data` root directory containing the extracted data (i.e. the directories 'buckner_data', 'long-tutorial', 'fsfast-functional', etc.). The tutorials make frequent use of the '''TUTORIAL_DATA''' environment variable and it need to be set properly for any of the tutorials to work. For example:

{{{
export TUTORIAL_DATA=/path/to/your/tutorial/dir
ls $TUTORIAL_DATA

buckner_data                    fsfast-functional
diffusion_recons                fsfast-tutorial.subjects
diffusion_tutorial              long-tutorial
}}}

If you see something similar to the above output, you are now ready to start the [[Tutorials|Freesurfer tutorials]].

----

== FreeSurfer Tutorial Datasets 5.1/5.3 ==

Below are links to the previous versions of the tutorial dataset that correspond to freesurfer version 5.1 and 5.3:

 * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs-5.3.tar.gz|buckner_data-tutorial_subjs-5.3.tar.gz]]
 * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/long-tutoriaL-5.3.tar.gz|long-tutorial-5.3.tar.gz]]
 * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects-5.3.tar.gz|fsfast-tutorial.subjects-5.3.tar.gz]] & [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz|fsfast-functional-5.3.tar.gz]]
 * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_recons-5.3.tar.gz|diffusion_recons-5.3.tar.gz]] & [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_tutorial-5.3.tar.gz|diffusion_tutorial-5.3.tar.gz]]