Diff for "FsTutorial/Data" - Free Surfer Wiki

Differences between revisions 30 and 31

FreeSurfer Tutorial: Sample Data

A public distribution data set is available to run the tutorials. It contains 40+ subjects, and occupies about 18G of disk-space after download and decompression. There are two download methods: using a web browser, or using the wget application. The wget application is recommended, as some web browsers have difficulty downloading files greater than 4GB in size. There are also two tar files associated with the tutorial on the integration of FreeSurfer and FSL/FEAT.

Download using wget

Open a terminal, change to a directory where you know you have at least 18GB of space. The troubleshooting and group study analysis tutorials require the buckner_data-tutorial_subjs.tar.gz download, which is 12GB compressed (18GB decompressed). There is also FSL-FEAT tutorial data. To get these, type:

wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fbert-feat.tgz &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.tgz &

The wget application will handle poor connections, and retry if it is having problems. Notice the commands have the ampersand, so you can run all four commands at once (although the wget output will be hard to decipher). Goto the Installation section below once the files are downloaded (this will likely take several hours).

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). If a popup window appears prompting for a username and password, use 'anonymous' as the username, and your email address as the password.

The troubleshooting and group study analysis tutorials require these downloads:

buckner_data-tutorial_subjs.tar.gz

The FSL-FEAT tutorial require these:

Installation

Once the 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 commands:

tar xzvf buckner_data-tutorial_subjs.tar.gz

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

To setup the environment variable SUBJECTS_DIR to point to the tutorial data, type the following command or include in your .cshrc or .tcshrc file:

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

Note: If you are within the NMR Center, because the default $FREESURFER_HOME is shared, you will not be able to copy your data to $FREESURFER_HOME/subjects. Instead, copy the subject data to a location where you have space, and set the SUBJECTS_DIR environment variable to point to that. You may have to make adjustments throughout the tutorial wherever it refers to $FREESURFER_HOME/subjects (which is equivalent to your $SUBJECTS_DIR).

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

FSL-FEAT Tutorial Data

cd $SUBJECTS_DIR
tar xvfz bert.recon.tgz
cd /place/for/functional/data
tar xvfz fbert-feat.tgz

-Deletions are marked like this.
+Additions are marked like this.
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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 11G of disk-space after download and decompression.  There are two download methods: using a web browser, or using the wget application.  The wget application is recommended, as some web browsers have difficulty downloading files greater than 4GB in size.There are also two tar files associated with the tutorial on the integration of FreeSurfer and FSL/FEAT.
+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 18G of disk-space after download and decompression.  There are two download methods: using a web browser, or using the wget application.  The wget application is recommended, as some web browsers have difficulty downloading files greater than 4GB in size. There are also two tar files associated with the tutorial on the integration of FreeSurfer and FSL/FEAT.
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-Open a terminal, change to a directory where you know you have at least 12GB of space. The troubleshooting and group study analysis tutorials require the '''buckner_data-tutorial_subjs*.tgz''' downloads, which are 6.5GB compressed (11GB decompressed).  There is also FSL-FEAT tutorial data. To get these, type:
+Open a terminal, change to a directory where you know you have at least 18GB of space. The troubleshooting and group study analysis tutorials require the '''buckner_data-tutorial_subjs.tar.gz''' download, which is 12GB compressed (18GB decompressed).  There is also FSL-FEAT tutorial data. To get these, type:
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-wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tgz &

wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs-group_analysis_tutorial_p1.tgz &

wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs-group_analysis_tutorial_p2.tgz &
+wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz &
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+Line 14:
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+## wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs-group_analysis_tutorial_p1.tgz &

## wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs-group_analysis_tutorial_p2.tgz &
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- * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tgz|buckner_data-tutorial_subjs.tgz]]

 * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs-group_analysis_tutorial_p1.tgz|buckner_data-tutorial_subjs-group_analysis_tutorial_p1.tgz]]

 * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs-group_analysis_tutorial_p2.tgz|buckner_data-tutorial_subjs-group_analysis_tutorial_p2.tgz]]
+ * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tgz|buckner_data-tutorial_subjs.tar.gz]]

## * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs-group_analysis_tutorial_p1.tgz|buckner_data-tutorial_subjs-group_analysis_tutorial_p1.tgz]]

## * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs-group_analysis_tutorial_p2.tgz|buckner_data-tutorial_subjs-group_analysis_tutorial_p2.tgz]]
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-tar xzvf buckner_data-tutorial_subjs.tgz

tar xzvf buckner_data-tutorial_subjs-group_analysis_tutorial_p1.tgz

tar xzvf buckner_data-tutorial_subjs-group_analysis_tutorial_p2.tgz
+tar xzvf buckner_data-tutorial_subjs.tar.gz
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+## tar xzvf buckner_data-tutorial_subjs-group_analysis_tutorial_p1.tgz

## tar xzvf buckner_data-tutorial_subjs-group_analysis_tutorial_p2.tgz
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-The downloaded .tgz files can then be deleted.
+The downloaded .tar.gz files can then be deleted.
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-=== Additional group study data ===

There is an additional data set available upon which further group study analysis could be conducted.  It is composed of the 40 subjects from which the tutorial's group study component was created.  The data set is the full Freesurfer reconstruction of the 40 subjects (conducted using stable v3.0.2).  It is 10.5GB compressed, and 18GB decompressed.  It is named '''buckner_data-group_study.tar.gz'''.  Also, there is the file '''buckner_data-raw_dicoms.tar.gz''', which, as indicated by the name, contains the original DICOM files for the subjects.  Be sure to [[http://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_public_distribution.README.txt|read these notes.]]
+## === Additional group study data ===

## There is an additional data set available upon which further group study analysis could be conducted.  It is composed of the 40 subjects from which the tutorial's group study component was created.  The data set is the full Freesurfer reconstruction of the 40 subjects (conducted using stable v3.0.2).  It is 10.5GB compressed, and 18GB decompressed.  It is named '''buckner_data-group_study.tar.gz'''.  Also, there is the file '''buckner_data-raw_dicoms.tar.gz''', which, as indicated by the name, contains the original DICOM files for the ## subjects.  Be sure to #[[http://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_public_distribution.README.txt|read these notes.]]