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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 11G of disk-space after download and decompression. There are two download methods: using a web browser, or using the ftp application. The ftp 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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| === Download using the FTP application === | === Download using wget === |
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| At your terminal, type '''ftp surfer.nmr.mgh.harvard.edu'''. Login as '''anonymous''' and use your email address as the password. | 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 http://magick.mit.edu/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 & }}} ## 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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| 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 and group study analysis tutorials require the '''buckner_data-tutorial_subjs.tar.gz''' download, which is 6.5GB compressed (11GB decompressed): {{{ ftp> get buckner_data-tutorial_subjs.tar.gz }}} To get the FSL-FEAT tutorial data {{{ ftp> get fbert-feat.tar.gz ftp> get bert.recon.tar.gz }}} Now exit the ftp application: {{{ ftp> quit }}} |
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 three 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 one necessary file is 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 and group study analysis tutorials 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: * [[http://magick.mit.edu/buckner_data-tutorial_subjs.tar.gz|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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| The FSL-FEAT tutorial require this download: * [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fbert-feat.tar.gz fbert-feat.tar.gz] * [ftp://surfer.nmr.mgh.harvard.edu/pub/dist/bert.recon.tar.gz bert.recon.tar.gz] |
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]] ## === Mirror Site === ## M. Pearrow has kindly provided a [[http://magick.mit.edu/buckner_data-tutorial_subjs.tar.gz|mirror site of the data]] at MIT. |
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| 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 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-tutorial_subjs-group_analysis_tutorial_p1.tgz ## tar xzvf buckner_data-tutorial_subjs-group_analysis_tutorial_p2.tgz |
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| The downloaded .tar.gz file can then be deleted. | The downloaded .tar.gz files can then be deleted. |
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| '''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). |
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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.]] |
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| tar xvfz bert.recon.tar.gz | tar xvfz bert.recon.tgz |
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| tar xvtz bertf-feat.tar.gz | tar xvfz fbert-feat.tgz |
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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 http://magick.mit.edu/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 three 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.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