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The full data for the [[Tutorials|tutorials]] consists of several data sets: The size of the data for the freesurfer [[Tutorials|tutorials]] is quite large, so it consists of several sets:
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 * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz|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/long-tutorial.tar.gz|long-tutorial.tar.gz]]: the longitudinal tutorial (size: ~16GB uncompressed)
 * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gz|fsfast-tutorial.subjects.tar.gz]] & [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz|fsfast-functional.tar.gz]]: the FS-FAST tutorial data set (size: ~5.6GB uncompressed & ~9.1GB uncompressed, respectively)
 * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_recons.tar.gz|diffusion_recons.tar.gz]] & [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_tutorial.tar.gz|diffusion_tutorial.tar.gz]] - the diffusion and Tracula tutorial data 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 ||
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Also, 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:		 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:
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=== Download using wget ===
The wget application is recommended, as some web browsers have difficulty downloading files greater than 4GB in size. '''Mac OS NOTE:''' Use '''curl -O''' in place of '''wget'''.

Open a terminal, create a directory called {{{tutorial_data}}} where you know you have at least 100GB of space, and {{{cd}}} into that directory. To download, type:

{{{
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/long-tutorial.tar.gz &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gz &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fbert-feat.tgz &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.tgz &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_recons.tar.gz &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_tutorial.tar.gz &
}}}
This download will likely take several hours.

The wget application will handle poor connections, and retry if it is having problems. A failed download can be restarted by adding the -c flag to wget, which will cause it to continue from the point where a partial download stopped. Notice the commands have the ampersand, so you can run all these commands at once (although the wget output will be hard to decipher, so an alternative is to run each without the ampersand in a separate terminal). Go to the Installation section below once the files are downloaded.

## ==== Optional Verification Step ====
## If you want to verify the files transferred correctly using md5sum, the md5sum for each of these downloads can found in files named *.md5sum.txt [[http://surfer.nmr.mgh.harvard.edu/pub/data/|in this directory]] or get them this way:

## {{{
## wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.md5sum.txt &
## wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/long-tutorial.md5sum.txt &
## wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.md5sum.txt &
## wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.md5sum.txt &
## wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fbert-feat.md5sum.txt &
## wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.md5sum.txt &
## wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_recons.md5sum.txt &
## wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_tutorial.md5sum.txt &
## }}}
## You will want to ensure that these md5sum's match what you find when you run md5sum on your own local downloads. If they do not match, the file transfer may have been faulty or there may ## have been a disk error. '''Mac OS NOTE:''' Use '''md5 -r''' to get the same results as '''md5sum'''. More on md5sum can be found [[http://www.techradar.com/us/news/computing/pc/how-## to-verify-your-files-in-linux-with-md5-641436|here]].

=== Installation ===
==== Uncompress the files ====		 == Installation ==
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tar -xzvf <filename>.tar.gz cd /path/to/your/tutorial/dir
tar -xzvf </path/to/downloaded/file.tar.gz>
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Replacing <filename> with the name of the file downloaded. The downloaded .tar.gz files can then be deleted.
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==== Set variables to point FreeSurfer to data ==== == Configuration ==
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Once the download is complete you may uncompress the tar files. 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: In order to run the tutorials, users must define an environment variable called '''TUTORIAL_DATA''' which is set to the 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:
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export TUTORIAL_DATA=/home/username/Downloads/tutorial_data export TUTORIAL_DATA=/path/to/your/tutorial/dir
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You are now ready to start the [[Tutorials|Freesurfer tutorials]].
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{{{
(bash)
export TUTORIAL_DATA=<absolute_path_to_tutorial_data_directory>		 If you see something similar to the above output (you may not have downloaded all the tutorial data sets) you are now ready to start the [[Tutorials|Freesurfer tutorials]].
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(csh)
setenv TUTORIAL_DATA <absolute_path_to_tutorial_data_directory>
}}}
'''Note:''' The tutorial references the {{{TUTORIAL_DATA}}} variable, which is the root directory containing the tutorial data (ie. the directories 'buckner_data', 'long-tutorial', 'fsfast-functional', etc.).		 ----
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Below are links to the previous versions of the tutorial dataset that correspond to freesurfer version 5.1 and 5.3:

top

Index

Contents

  1. FreeSurfer Tutorial Datasets
  2. Installation
  3. Configuration
  4. FreeSurfer Tutorial Datasets 5.1/5.3

FreeSurfer Tutorial Datasets

The size of the data for the freesurfer tutorials is quite large, so it consists of several sets:

Download

Description

Size

Core Data

The core tutorial subject data

16.8 GB

Functional Data

The FsFast functional tutorial data

18.1 GB

Diffusion Data

The diffusion and tracula tutorial data

4.3 GB

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:

Installation

Once the dataset(s) have been downloaded, uncompress and install with the following command run from a terminal window. 

cd /path/to/your/tutorial/dir
tar -xzvf </path/to/downloaded/file.tar.gz>

Configuration

In order to run the tutorials, users must define an environment variable called TUTORIAL_DATA which is set to the 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 may not have downloaded all the tutorial data sets) you are now ready to start the 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:

FsTutorial/Data (last edited 2018-09-30 09:35:54 by AndrewHoopes)