Differences between revisions 1 and 10 (spanning 9 versions)
⇤ ← Revision 1 as of 2005-09-08 13:28:20 →
Size: 2379
Editor: NickSchmansky
Comment: download and setup of the sample data
← Revision 10 as of 2006-05-24 15:40:58 → ⇥
Size: 2729
Editor: NickSchmansky
Comment: group_study data set not strictly necessary, so download instructions removed
Deletions are marked like this. Additions are marked like this.
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[wiki:Self:FsTutorial top] | [wiki:Self:FsTutorial previous] | [wiki:Self:FsTutorial/Overview next] [wiki:Self:FsTutorial top]
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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 [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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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].		 === Download using the FTP application ===
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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. 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 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
}}}
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The downloaded file can then be deleted. 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
}}}
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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: 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:
 * [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_data-tutorial_subjs.tar.gz buckner_data-tutorial_subjs.tar.gz]

=== 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:
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source $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/scripts/setup_subjects.csh tar xzvf buckner_data-tutorial_subjs.tar.gz
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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: The downloaded .tar.gz file can then be deleted.
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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/group_study/scripts/setup_subjects.csh source $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/scripts/subjects.csh
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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)