Diff for "FsTutorial/Data" - Free Surfer Wiki

Differences between revisions 85 and 95 (spanning 10 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 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:

cd /path/to/your/tutorial/dir
tar -xzvf /path/to/downloaded/data.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 85 as of 2017-03-30 17:49:35 → 
  Size: 5299
  Editor: ZekeKaufman
  Comment:
+   ← Revision 95 as of 2018-09-29 19:06:44 → ⇥
  Size: 4974
  Editor: AndrewHoopes
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 31:
-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 ||
-Line 38:
+Line 39:
-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:
 Line 48:
-=== Installation ===
==== Uncompress the files ====
Once the dataset(s) have been downloaded, uncompress and install with the following command run from a terminal window.
+== Installation ==
Once the dataset(s) have been downloaded, uncompress and install with the following command:
-Line 53:
+Line 52:
-tar -xzvf <filename>.tar.gz
+cd /path/to/your/tutorial/dir
tar -xzvf /path/to/downloaded/data.tar.gz
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-Replacing <filename> with the name of the file downloaded.  The downloaded .tar.gz files can then be deleted.
-Line 57:
+Line 56:
-==== Set variables to point FreeSurfer to data ====
+== Configuration ==
-Line 59:
+Line 58:
-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:
-Line 62:
+Line 61:
-export TUTORIAL_DATA=/home/username/Downloads/tutorial_data
+export TUTORIAL_DATA=/path/to/your/tutorial/dir
-Line 64:
+Line 63:
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-You are now ready to start the [[Tutorials|Freesurfer tutorials]].
-Line 70:
+Line 69:
-{{{
(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]].
-Line 74:
+Line 71:
-(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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+Line 74:
+Below are links to the previous versions of the tutorial dataset that correspond to freesurfer version 5.1 and 5.3: