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| [wiki:Self:FsTutorial top] | [[FsTutorial|top]] |
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| == FreeSurfer Tutorial: Sample Data == | == FreeSurfer Tutorial Datasets == |
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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 uncompression. 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. | The data for the [[FsTutorial| tutorials]] consists of several data sets: * buckner_data-tutorial_subjs.tar.gz: the main 'recon-all' stream subject data processing (size: ~16GB uncompressed)[[ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.md5sum.txt|Here is the md5sum]]. * long-tutorial.tar.gz: the longitudinal tutorial (size: ~16GB uncompressed) * fsfast-tutorial.subjects.tar.gz & fsfast-functional.tar.gz: the FS-FAST tutorial data set (size: ~5.6GB uncompressed & ~9.1GB uncompressed, respectively) * diffusion_recons.tar.gz & diffusion_tutorial.tar.gz - the diffusion and Tracula tutorial data sets * fbert-feat.tgz & bert.recon.tgz - tutorial on the integration of FreeSurfer and FSL/FEAT |
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| === Download using the FTP application === | If you only want to get started with the basics of !FreeSurfer, you need only download the bucker_data set. This will allow you to do the following tutorials: *[[FsTutorial/OutputData_freeview|Intro to FreeSurfer Output]] *[[FsTutorial/TroubleshootingData|Troubleshooting FreeSurfer Output]] *[[FsTutorial/GroupAnalysis|Group Analysis via command-line]] *[[FsTutorial/QdecGroupAnalysis_freeview|Group Analysis via GUI]] *[[FsTutorial/AnatomicalROI|ROI Analysis]] *[[FsTutorial/MultiModal_freeview|Multimodal Analysis]] |
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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. | === Download using wget === 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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| 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/fbert-feat.tgz & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.tgz & 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 & }}} This download will likely take several hours. 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). Go to the Installation section below once the files are downloaded. If you want to verify the files transferred correctly using md5sum, the md5sum for each of these downloads can found in files named *.md5sum.txt [[http://surfer.nmr.mgh.harvard.edu/pub/data/|in this directory]] or get them this way: |
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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> |
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/long-tutorial.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fbert-feat.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_recons.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_tutorial.md5sum.txt & |
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| 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 uncompressed): {{{ ftp> get buckner_data-tutorial_subjs.tar.gz }}} Now exit the ftp application: {{{ ftp> quit }}} === 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). 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] |
You will want to ensure that these md5sum's match what you find when you run md5sum on your own local downloads. If they do not match, the file transfer may have been faulty or there may have been a disk error. '''Mac OS NOTE:''' Use '''md5 -r''' to get the same results as '''md5sum'''. More on md5sum can be found [[http://www.techradar.com/us/news/computing/pc/how-to-verify-your-files-in-linux-with-md5-641436|here]. |
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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 datasets have been downloaded, move them to the $FREESURFER_HOME/subjects directory, and uncompress and install with the following command run from a terminal window (you'll have to {{{cd}}} to $FREESURFER_HOME/subjects first if you haven't already): |
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| tar xzvf buckner_data-tutorial_subjs.tar.gz | tar xzvf <filename>.tar.gz |
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| The downloaded .tar.gz file can then be deleted. | Replacing <filename> with the name of each file downloaded. The downloaded .tar.gz files can then be deleted. |
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| To setup the environment variable SUBJECTS_DIR to point to the 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 commands every time you open a new terminal window. Alternatively, you can include the below commands in your .cshrc or .tcshrc file so these variables are automatically set every time you open a new terminal window: |
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| source $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/scripts/subjects.csh | setenv TUTORIAL_DATA $FREESURFER_HOME/subjects setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs/ |
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| The tutorial will also instruct you to set the SUBJECTS_DIR when appropriate. | '''Martinos Center employees:''' Because the default $FREESURFER_HOME is shared, you will not be able to copy your data to $FREESURFER_HOME/subjects when doing so on a Martinos Center workstation. 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 location. 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 uncompressed. 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.] |
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 }}} |
FreeSurfer Tutorial Datasets
The data for the tutorials consists of several data sets:
buckner_data-tutorial_subjs.tar.gz: the main 'recon-all' stream subject data processing (size: ~16GB uncompressed)Here is the md5sum.
- long-tutorial.tar.gz: the longitudinal tutorial (size: ~16GB uncompressed)
fsfast-tutorial.subjects.tar.gz & fsfast-functional.tar.gz: the FS-FAST tutorial data set (size: ~5.6GB uncompressed & ~9.1GB uncompressed, respectively)
diffusion_recons.tar.gz & diffusion_tutorial.tar.gz - the diffusion and Tracula tutorial data sets
fbert-feat.tgz & bert.recon.tgz - tutorial on the integration of FreeSurfer and FSL/FEAT
If you only want to get started with the basics of FreeSurfer, you need only download the bucker_data set. This will allow you to do the following tutorials:
Download using wget
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.
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/fbert-feat.tgz & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.tgz & 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 &
This download will likely take several hours.
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). Go to the Installation section below once the files are downloaded.
If you want to verify the files transferred correctly using md5sum, the md5sum for each of these downloads can found in files named *.md5sum.txt in this directory or get them this way:
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/long-tutorial.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fbert-feat.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_recons.md5sum.txt & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_tutorial.md5sum.txt &
You will want to ensure that these md5sum's match what you find when you run md5sum on your own local downloads. If they do not match, the file transfer may have been faulty or there may have been a disk error. Mac OS NOTE: Use md5 -r to get the same results as md5sum. More on md5sum can be found [[http://www.techradar.com/us/news/computing/pc/how-to-verify-your-files-in-linux-with-md5-641436|here].
Installation
Once the datasets have been downloaded, move them to the $FREESURFER_HOME/subjects directory, and uncompress and install with the following command run from a terminal window (you'll have to cd to $FREESURFER_HOME/subjects first if you haven't already):
tar xzvf <filename>.tar.gz
Replacing <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 commands every time you open a new terminal window. Alternatively, you can include the below commands in your .cshrc or .tcshrc file so these variables are automatically set every time you open a new terminal window:
setenv TUTORIAL_DATA $FREESURFER_HOME/subjects setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs/
Martinos Center employees: Because the default $FREESURFER_HOME is shared, you will not be able to copy your data to $FREESURFER_HOME/subjects when doing so on a Martinos Center workstation. 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 location. 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