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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 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. |
The data for the [[FsTutorial| tutorials]] consists of several data sets: * buckner_data-tutorial_subjs.tar.gz ~16GB - the main 'recon-all' stream subject data processing * long-tutorial.tar.gz ~16GB - the longitudinal tutorial * fsfast-tutorial.subjects.tar.gz ~5GB and fsfast-functional.tar.gz - the FS-FAST tutorial data set * diffusion_recons.tar.gz and diffusion_tutorial.tar.gz - the diffusion and CVS tutorial data sets * fbert-feat.tgz and bert.recon.tgz - tutorial on the integration of FreeSurfer and FSL/FEAT |
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| 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'''. | |
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| 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: | Open a terminal, change to a directory where you know you have at least 100GB 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/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 & |
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}}}torial_subjs-group_analysis_tutorial_p2.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 were a partial download stopped. Notice the commands have the ampersand, so you can run all three 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 {{{ http://surfer.nmr.mgh.harvard.edu/pub/data/ |
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## wget http://magick.mit.edu/buckner_data-tutorial_subjs.tar.gz & ## 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 & 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). '''Mac OS NOTE:''' use '''curl -O''' in place of '''wget'''. Goto the Installation section below once the files are downloaded (this will likely take several hours). The md5sum for buckner_data-tutorial_subjs.tar.gz is: {{{ 691078b7353d989826d65cdea477b3d4 }}} === 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: * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz|buckner_data-tutorial_subjs.tar.gz]] ## * [[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]] 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 commands: | 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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| tar xzvf buckner_data-tutorial_subjs.tar.gz | tar xzvf <filename>.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 .tar.gz files can then be deleted. | Replacing of course <filename> with the name of each file downloaded. The downloaded .tar.gz files can then be deleted. |
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| setenv TUTORIAL_DATA $FREESURFER_HOME/subjects | |
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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). | '''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). |
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| The tutorial will also instruct you to set the SUBJECTS_DIR when appropriate. | 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.). |
FreeSurfer Tutorial: Sample Data
The data for the tutorials consists of several data sets:
- buckner_data-tutorial_subjs.tar.gz ~16GB - the main 'recon-all' stream subject data processing
- long-tutorial.tar.gz ~16GB - the longitudinal tutorial
- fsfast-tutorial.subjects.tar.gz ~5GB and fsfast-functional.tar.gz - the FS-FAST tutorial data set
- diffusion_recons.tar.gz and diffusion_tutorial.tar.gz - the diffusion and CVS tutorial data sets
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. 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/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 &
torial_subjs-group_analysis_tutorial_p2.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 were a partial download stopped. Notice the commands have the ampersand, so you can run all three 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
http://surfer.nmr.mgh.harvard.edu/pub/data/
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 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 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