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| [wiki:Self:FsTutorial top] | [wiki:Self:FsTutorial previous] | [wiki:Self:FsTutorial/Overview next] | [[FsTutorial|top]] |
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| 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 data for the [[FsTutorial| tutorials]] consists of several data sets: * buckner_data-tutorial_subjs.tar.gz ~16GB uncompressed - the main 'recon-all' stream subject data processing * long-tutorial.tar.gz ~16GB uncompressed - the longitudinal tutorial * fsfast-tutorial.subjects.tar.gz ~5.6GB uncompressed and fsfast-functional.tar.gz ~9.1GB uncompressed - the FS-FAST tutorial data set * diffusion_recons.tar.gz and diffusion_tutorial.tar.gz - the diffusion and CVS tutorial data sets * Tracula_tutorial_data.tar.gz - Tracula tutorial dataset * fbert-feat.tgz and bert.recon.tgz - tutorial on the integration of FreeSurfer and FSL/FEAT |
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| 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. | The wget application is recommended, as some web browsers have difficulty downloading files greater than 4GB in size. '''Mac OS NOTE:''' use '''curl -O''' in place of '''wget'''. === Download using wget === |
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| Example login: | Open a terminal, change to a directory where you know you have at least 100GB of space. To download, 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/long-tutorial.tar.gz & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gz & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_recons.tar.gz & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_tutorial.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. A failed download can be restarted by adding the -c flag to wget, which will cause it to continue from the point where a partial download stopped. Notice the commands have the ampersand, so you can run all these commands at once (although the wget output will be hard to decipher, so an alternative is to run each without the ampersand in a separate terminal). Goto the Installation section below once the files are downloaded (this will likely take several hours). If you want to verify the md5sum, the md5sum for each of these files is found in files named *.md5sum.txt [[http://surfer.nmr.mgh.harvard.edu/pub/data/|in this directory]]. === Installation === Once the files are downloaded, move the file(s) to the $FREESURFER_HOME/subjects directory, and uncompress and install with the following commands: |
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| $ 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> |
tar xzvf <filename>.tar.gz |
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| The tutorial datasets are found in the pub/dist directory: | Replacing of course <filename> with the name of each file downloaded. 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: |
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| ftp> cd pub/dist | setenv TUTORIAL_DATA $FREESURFER_HOME/subjects setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs/ |
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| 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: | '''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 TUTORIAL_DATA and SUBJECTS_DIR environment variables 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. The tutorial references the TUTORIAL_DATA var, which is the root directory containing the tutorial data (ie. the directories 'buckner_data', 'long-tutorial', 'fsfast-functional', etc.). ## === 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.]] === FSL-FEAT Tutorial Data === |
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| ftp> get buckner_data-tutorial_subjs.tar.gz | cd $SUBJECTS_DIR tar xvfz bert.recon.tgz cd /place/for/functional/data tar xvfz fbert-feat.tgz |
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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'''. 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: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. |
FreeSurfer Tutorial: Sample Data
The data for the tutorials consists of several data sets:
- buckner_data-tutorial_subjs.tar.gz ~16GB uncompressed - the main 'recon-all' stream subject data processing
- long-tutorial.tar.gz ~16GB uncompressed - the longitudinal tutorial
- fsfast-tutorial.subjects.tar.gz ~5.6GB uncompressed and fsfast-functional.tar.gz ~9.1GB uncompressed - the FS-FAST tutorial data set
- diffusion_recons.tar.gz and diffusion_tutorial.tar.gz - the diffusion and CVS tutorial data sets
- Tracula_tutorial_data.tar.gz - Tracula tutorial dataset
fbert-feat.tgz and bert.recon.tgz - tutorial on the integration of FreeSurfer and FSL/FEAT
The wget application is recommended, as some web browsers have difficulty downloading files greater than 4GB in size. Mac OS NOTE: use curl -O in place of wget.
Download using wget
Open a terminal, change to a directory where you know you have at least 100GB of space. To download, 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/long-tutorial.tar.gz & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gz & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_recons.tar.gz & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_tutorial.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. A failed download can be restarted by adding the -c flag to wget, which will cause it to continue from the point where a partial download stopped. Notice the commands have the ampersand, so you can run all these commands at once (although the wget output will be hard to decipher, so an alternative is to run each without the ampersand in a separate terminal). Goto the Installation section below once the files are downloaded (this will likely take several hours). If you want to verify the md5sum, the md5sum for each of these files is found in files named *.md5sum.txt in this directory.
Installation
Once the files are downloaded, move the file(s) to the $FREESURFER_HOME/subjects directory, and uncompress and install with the following commands:
tar xzvf <filename>.tar.gz
Replacing of course <filename> with the name of each file downloaded. 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:
setenv TUTORIAL_DATA $FREESURFER_HOME/subjects setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs/
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 TUTORIAL_DATA and SUBJECTS_DIR environment variables 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. The tutorial references the TUTORIAL_DATA var, which is the root directory containing the tutorial data (ie. the directories 'buckner_data', 'long-tutorial', 'fsfast-functional', etc.).
FSL-FEAT Tutorial Data
cd $SUBJECTS_DIR tar xvfz bert.recon.tgz cd /place/for/functional/data tar xvfz fbert-feat.tgz