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A [http://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_public_distribution.README.txt public distribution data set] is available to run the tutorials. It contains 40 subjects, and occupies about 20G of disk-space after download and uncompression. The data set is divided into two files: the data for the troubleshooting examples (9.5GB), and the data for the group study analysis (18GB). There are two download methods: using a web browser, or using the ftp application.

=== Download using the web browser ===
Some web browsers seem to have difficulty downloading files greater than 4GB in size, but if you would like to attempt the download using your browser, then the two files are listed next (click on the .tar.gz filename to download).

The troubleshooting tutorials, in the section [wiki:Self:FsTutorial/MorphAndRecon Morphometry and Reconstruction], require this download:
 * [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_data-tutorial_subjs.tar.gz buckner_data-tutorial_subjs.tar.gz]

The group study [wiki:Self:FsTutorial/GroupAnalysis analysis] and [wiki:Self:FsTutorial/Visualization visualization] tutorials require this download:
 * [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_data-group_study.tar.gz buckner_data-group_study.tar.gz] 		A [http://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_public_distribution.README.txt public distribution data set] is available to run the tutorials. It contains 40+ subjects, and occupies about 10G of disk-space after download and uncompression. There are two download methods: using a web browser, or using the ftp application. The ftp application is recommended, as some web browsers have difficulty downloading files greater than 4GB in size.
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If you have trouble downloading the files in your web browser, then use an ftp application directly. Type '''ftp surfer.nmr.mgh.harvard.edu'''. Login as '''anonymous''' and use your email address as the password. At your terminal, type '''ftp surfer.nmr.mgh.harvard.edu'''. Login as '''anonymous''' and use your email address as the password.
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The troubleshooting tutorials, in the section [wiki:Self:FsTutorial/MorphAndRecon Morphometry and Reconstruction], require the '''buckner_data-tutorial_subjs.tar.gz''' download, which is 4.5GB compressed: The troubleshooting and group study analysis tutorials require the '''buckner_data-tutorial_subjs.tar.gz''' download, which is 6.5GB compressed:
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}}}

The group study [wiki:Self:FsTutorial/GroupAnalysis analysis] and [wiki:Self:FsTutorial/Visualization visualization] tutorials require the '''buckner_data-group_study.tar.gz''' download, which is about 10GB compressed:
{{{
ftp> get buckner_data-group_study.tar.gz
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=== Download using the web browser ===
Some web browsers seem to have difficulty downloading files greater than 4GB in size, but if you would like to attempt the download using your browser, then the one necessary file is listed next (click on the .tar.gz filename to download).

The troubleshooting and group study analysis tutorials require this download:
 * [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_data-tutorial_subjs.tar.gz buckner_data-tutorial_subjs.tar.gz]
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Once a file is downloaded, move the file(s) to the $FREESURFER_HOME/subjects directory, and uncompress and install with the following command: Once a file is downloaded (via either ftp or web browser), move the file(s) to the $FREESURFER_HOME/subjects directory, and uncompress and install with the following command:
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tar xzvf buckner_data-<dataset>.tar.gz tar xzvf buckner_data-tutorial_subjs.tar.gz
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where <dataset> is either '''tutorial_subjs''' or '''group_study'''.
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To setup the environment variable SUBJECTS_DIR to point to the troubleshooting tutorial data (for use in the tutorial section [wiki:Self:FsTutorial/MorphAndRecon Morphometry and Reconstruction]), type the following command or include in your .cshrc or .tcshrc file: To setup the environment variable SUBJECTS_DIR to point to the tutorial data (for use in the tutorial section [wiki:Self:FsTutorial/MorphAndRecon Morphometry and Reconstruction]), type the following command or include in your .cshrc or .tcshrc file:
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source $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/scripts/setup_subjects.csh source $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/scripts/subjects.csh
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To setup the environment variables SUBJECTS_DIR and SUBJECTS to point to the group study tutorial data (for use in the tutorial sections group study [wiki:Self:FsTutorial/GroupAnalysis analysis] and [wiki:Self:FsTutorial/Visualization visualization]), type the following command or include in your .cshrc or .tcshrc file:
{{{
source $FREESURFER_HOME/subjects/buckner_data/group_study/scripts/setup_subjects.csh
}}}

You can only source one '''setup_subjects.csh''' file at a time. The tutorial will also instruct you to set the SUBJECTS_DIR when appropriate. 		The tutorial will also instruct you to set the SUBJECTS_DIR when appropriate.

[wiki:FsTutorial top]

FreeSurfer Tutorial: Sample Data

A [http://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_public_distribution.README.txt public distribution data set] is available to run the tutorials. It contains 40+ subjects, and occupies about 10G of disk-space after download and uncompression. There are two download methods: using a web browser, or using the ftp application. The ftp application is recommended, as some web browsers have difficulty downloading files greater than 4GB in size.

Download using the FTP application

At your terminal, type ftp surfer.nmr.mgh.harvard.edu. Login as anonymous and use your email address as the password.

Example login: 

$ ftp surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu (132.183.202.158).
220 surfer.nmr.mgh.harvard.edu FTP server (Version wu-2.6.2-15.7x.legacy) ready.
Name (surfer.nmr.mgh.harvard.edu:fsurfer): anonymous
331 Guest login ok, send your complete e-mail address as password.
Password:
230 Guest login ok, access restrictions apply.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp>

The tutorial datasets are found in the pub/dist directory: 

ftp> cd pub/dist

The troubleshooting and group study analysis tutorials require the buckner_data-tutorial_subjs.tar.gz download, which is 6.5GB compressed: 

ftp> get buckner_data-tutorial_subjs.tar.gz

Now exit the ftp application: 

ftp> quit

Download using the web browser

Some web browsers seem to have difficulty downloading files greater than 4GB in size, but if you would like to attempt the download using your browser, then the one necessary file is listed next (click on the .tar.gz filename to download).

The troubleshooting and group study analysis tutorials require this download:

Installation

Once a file is downloaded (via either ftp or web browser), move the file(s) to the $FREESURFER_HOME/subjects directory, and uncompress and install with the following command: 

tar xzvf buckner_data-tutorial_subjs.tar.gz

The downloaded .tar.gz file can then be deleted.

To setup the environment variable SUBJECTS_DIR to point to the tutorial data (for use in the tutorial section [wiki:FsTutorial/MorphAndRecon Morphometry and Reconstruction]), type the following command or include in your .cshrc or .tcshrc file: 

source $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/scripts/subjects.csh

The tutorial will also instruct you to set the SUBJECTS_DIR when appropriate.

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