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| [wiki:Self:FsTutorial top] | [[FsTutorial|top]] |
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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. | 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. === Download using wget === 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: {{{ 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/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). |
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| 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). | 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. |
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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 troubleshooting and group study analysis tutorials require these downloads: * [[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]] |
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| 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] === Download using the FTP application === 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. 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 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 }}} 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 }}} |
The FSL-FEAT tutorial require these: * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/fbert-feat.tgz|fbert-feat.tgz]] * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.tgz|bert.recon.tgz]] |
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| Once a file is downloaded, move the file(s) to the $FREESURFER_HOME/subjects directory, and uncompress and install with the following command: | 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: |
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| tar xzvf buckner_data-<dataset>.tar.gz | 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 |
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| where <dataset> is either '''tutorial_subjs''' or '''group_study'''. | The downloaded .tgz files can then be deleted. |
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| 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: |
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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| source $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/scripts/setup_subjects.csh | source $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/scripts/subjects.csh |
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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: | '''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. === 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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| source $FREESURFER_HOME/subjects/buckner_data/group_study/scripts/setup_subjects.csh | cd $SUBJECTS_DIR tar xvfz bert.recon.tgz cd /place/for/functional/data tar xvfz fbert-feat.tgz |
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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
A 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.
Download using wget
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:
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/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:
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.tgz tar xzvf buckner_data-tutorial_subjs-group_analysis_tutorial_p1.tgz tar xzvf buckner_data-tutorial_subjs-group_analysis_tutorial_p2.tgz
The downloaded .tgz 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.
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 read these notes.
FSL-FEAT Tutorial Data
cd $SUBJECTS_DIR tar xvfz bert.recon.tgz cd /place/for/functional/data tar xvfz fbert-feat.tgz