Diff for "FsTutorial/Data" - Free Surfer Wiki

Differences between revisions 9 and 93 (spanning 84 versions)

Index

Contents

FreeSurfer Tutorial Datasets
Installation
Configuration
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 only want to get started with the basics of FreeSurfer, you need only 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:

-  ⇤ ← Revision 9 as of 2006-05-24 14:25:57 → 
  Size: 4031
  Editor: NickSchmansky
  Comment:
+   ← Revision 93 as of 2018-09-29 19:05:32 → ⇥
  Size: 5003
  Editor: AndrewHoopes
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-[wiki:Self:FsTutorial top]
+[[FsTutorial|top]]
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-== FreeSurfer Tutorial: Sample Data ==
+'''Index'''
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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.
+<<TableOfContents>>
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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 two files are listed next (click on the .tar.gz filename to download).
+== FreeSurfer Tutorial Datasets ==
## The data set for the Freesurfer tutorials comes in two forms, a "Lightweight" version and a "Full" version.
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-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 "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.
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+Line 12:
-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]
+##  * 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.
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+Line 14:
-=== Download using the FTP application ===
+## == Lightweight version ==
## Use the following link to download the lightweight version of the tutorial data:
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+Line 17:
-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.
+##  . [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz|tutorial_data.tar.gz]]
-Line 20:
+Line 19:
-Example login:
+## 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 only want to get started with the basics of !FreeSurfer, you need only 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 ==
Once the dataset(s) have been downloaded, uncompress and install with the following command run from a terminal window.
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+Line 52:
-$ 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>
+cd /path/to/your/tutorial/dir
tar -xzvf </path/to/downloaded/file.tar.gz>
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+Line 56:
-The tutorial datasets are found in the pub/dist directory:
+== 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:
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+Line 61:
-ftp> cd pub/dist
+export TUTORIAL_DATA=/path/to/your/tutorial/dir
ls $TUTORIAL_DATA

buckner_data                    fsfast-functional
diffusion_recons                fsfast-tutorial.subjects
diffusion_tutorial              long-tutorial
-Line 40:
+Line 69:
-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
}}}
+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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+Line 71:
-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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+Line 73:
-Now exit the ftp application:
{{{
ftp> quit
}}}
+== FreeSurfer Tutorial Datasets 5.1/5.3 ==
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+Line 75:
-=== Installation ===
+Below are links to the previous versions of the tutorial dataset that correspond to freesurfer version 5.1 and 5.3:
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+Line 77:
-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 .tar.gz 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:Self: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: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.
+ * [[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]]