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A public distribution data set is available to run the tutorials. It contains 40 subjects, and occupies about 21G of disk-space. The data set is divided into two files: the data for the troubleshooting examples (7GB), and the data for the group study analysis (14GB). A public distribution data set is available to run the tutorials. It contains 40 subjects, and occupies about 20G of disk-space after downloaded and uncompressed. The data set is divided into two files: the data for the troubleshooting examples (6GB), and the data for the group study analysis (14GB).
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The files are available from the [ftp://surfer.nmr.mgh.harvard.edu/pub/dist distribution site], and are called
[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_data-tutorial_subjs.tar.gz buckner_data-tutorial_subjs.tar.gz] and
[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_data-group_study.tar.gz buckner_data-group_study.tar.gz].
The files can be obtained via anonymous ftp. Use '''ftp surfer.nmr.mgh.harvard.edu'''. Login as '''anonymous''' and use your email addresses as the password.
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The troubleshooting tutorials, in the section [wiki:Self:FsTutorial/MorphAndRecon Morphometry and Reconstruction], require the [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_data-tutorial_subjs.tar.gz buckner_data-tutorial_subjs.tar.gz] download.

The group study [wiki:Self:FsTutorial/GroupAnalysis analysis] and [wiki:Self:FsTutorial/Visualization visualization] tutorials require the [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_data-group_study.tar.gz buckner_data-group_study.tar.gz] download.

Once a file is downloaded, move the file to the $FREESURFER_HOME/subjects directory, and uncompress and install with the following command:
Example login:
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tar xzvf buckner_data-XXXXXX.tar.gz $ 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>
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where XXXXXX is either '''tutorial_subjs''' or '''group_study'''. The tutorial datasets are found in the pub/dist directory:
{{{
ftp> cd pub/dist
}}}

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:
{{{
ftp> get buckner_data-tutorial_subjs.tar.gz
}}}

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 6.5GB compressed:
{{{
ftp> get buckner_data-group_study.tar.gz
}}}

Now exit the ftp application:
{{{
ftp> quit
}}}

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

{{{
tar xzvf buckner_data-<dataset>.tar.gz
}}}

where <dataset> is either '''tutorial_subjs''' or '''group_study'''.
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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.

[wiki:FsTutorial top] | [wiki:FsTutorial previous] | [wiki:FsTutorial/Overview next]

FreeSurfer Tutorial: Sample Data

A public distribution data set is available to run the tutorials. It contains 40 subjects, and occupies about 20G of disk-space after downloaded and uncompressed. The data set is divided into two files: the data for the troubleshooting examples (6GB), and the data for the group study analysis (14GB).

The files can be obtained via anonymous ftp. Use ftp surfer.nmr.mgh.harvard.edu. Login as anonymous and use your email addresses 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 tutorials, in the section [wiki:FsTutorial/MorphAndRecon Morphometry and Reconstruction], require the buckner_data-tutorial_subjs.tar.gz download, which is 4.5GB compressed:

ftp> get buckner_data-tutorial_subjs.tar.gz

The group study [wiki:FsTutorial/GroupAnalysis analysis] and [wiki:FsTutorial/Visualization visualization] tutorials require the buckner_data-group_study.tar.gz download, which is about 6.5GB compressed:

ftp> get buckner_data-group_study.tar.gz

Now exit the ftp application:

ftp> quit

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

tar xzvf buckner_data-<dataset>.tar.gz

where <dataset> is either tutorial_subjs or group_study.

The downloaded file can then be deleted.

To setup the environment variable SUBJECTS_DIR to point to the troubleshooting 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/setup_subjects.csh

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:FsTutorial/GroupAnalysis analysis] and [wiki: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.

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