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| [wiki:Self:FsTutorial top] | [[FsTutorial|top]] |
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| == FreeSurfer Tutorial: Sample Data == | '''Index''' |
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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. | <<TableOfContents>> |
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| === Download using the FTP application === | == FreeSurfer Tutorial Datasets == ## The data set for the Freesurfer tutorials comes in two forms, a "Lightweight" version and a "Full" version. |
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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. | ## * The "Lightweight" version contains only the files required to run the commands of the !FreeSurfer tutorial. It has all the required input and output data, but lacks the other files that would normally be present when performing a recon. People who just want a quick easy way to run the commands in the tutorial should download this data set. |
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| Example login: | ## * The "Full" version contains all the files that would normally be present when performing recons. Because of the numerous subjects involved with the tutorials, the full data set is quite large (~60Gigs). People who want to go into more depth than that which is covered in the tutorials should download this data set. ## == Lightweight version == ## Use the following link to download the lightweight version of the tutorial data: ## . [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz|tutorial_data.tar.gz]] ## Once the download is complete, uncompress the data file - this usually this can be done by simply double-clicking. In order to do the tutorials, users must define an environment variable called '''TUTORIAL_DATA''' which is set to the location of the extracted data. For example: ## {{{ ## $> export TUTORIAL_DATA=/home/username/Downloads/tutorial_data ## $> ls $TUTORIAL_DATA ## buckner_data fsfast-functional ## diffusion_recons fsfast-tutorial.subjects ## diffusion_tutorial long-tutorial ## }}} ## You are now ready to start the [[Tutorials|Freesurfer tutorials]]. ## == Full version == The full data for the [[Tutorials|tutorials]] consists of several data sets: * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz|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/long-tutorial.tar.gz|long-tutorial.tar.gz]]: the longitudinal tutorial (size: ~16GB uncompressed) * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gz|fsfast-tutorial.subjects.tar.gz]] & [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz|fsfast-functional.tar.gz]]: the FS-FAST tutorial data set (size: ~5.6GB uncompressed & ~9.1GB uncompressed, respectively) * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_recons.tar.gz|diffusion_recons.tar.gz]] & [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_tutorial_v6.tar.gz|diffusion_tutorial.tar.gz]] - the diffusion and Tracula tutorial data sets Also, if you only want to get started with the basics of !FreeSurfer, you need only download the buckner_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]] == Installation == Once the dataset(s) have been downloaded, uncompress and install with the following command run from a terminal window. |
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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 }}} Replacing <filename> with the name of the file downloaded. The downloaded .tar.gz files can then be deleted. == Configuration == In order to do the tutorials, users must define an environment variable called '''TUTORIAL_DATA''' which is set to the root directory containing the extracted data (i.e. the directories 'buckner_data', 'long-tutorial', 'fsfast-functional', etc.). The tutorials make frequent use of the '''TUTORIAL_DATA''' environment variable and it need to be set properly for any of the tutorials to work. For example: {{{ export TUTORIAL_DATA=/home/username/Downloads/tutorial_data ls $TUTORIAL_DATA buckner_data fsfast-functional diffusion_recons fsfast-tutorial.subjects diffusion_tutorial long-tutorial |
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| The tutorial datasets are found in the pub/dist directory: {{{ ftp> cd pub/dist }}} |
If you see something similar to the above output (you may not have downloaded all the tutorial data sets) you are now ready to start the [[Tutorials|Freesurfer tutorials]]. |
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| 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 }}} |
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| Now exit the ftp application: {{{ ftp> quit }}} |
== FreeSurfer Tutorial Datasets 5.1/5.3 == |
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| === 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). |
Below are links to the previous versions of the tutorial dataset that correspond to freesurfer version 5.1 and 5.3: |
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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 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] === 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 command: {{{ tar xzvf buckner_data-tutorial_subjs.tar.gz }}} The downloaded .tar.gz file 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 at 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 === {{{ cd $SUBJECTS_DIR tar xvfz bert.recon.tar.gz cd /place/for/functional/data tar xvfz fbert-feat.tar.gz }}} |
* [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs-5.3.tar.gz|buckner_data-tutorial_subjs-5.3.tar.gz]] * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/long-tutoriaL-5.3.tar.gz|long-tutorial-5.3.tar.gz]] * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects-5.3.tar.gz|fsfast-tutorial.subjects-5.3.tar.gz]] & [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz|fsfast-functional-5.3.tar.gz]] * [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_recons-5.3.tar.gz|diffusion_recons-5.3.tar.gz]] & [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_tutorial-5.3.tar.gz|diffusion_tutorial-5.3.tar.gz]] |
Index
Contents
FreeSurfer Tutorial Datasets
The full 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).
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
Also, if you only want to get started with the basics of FreeSurfer, you need only download the buckner_data set. This will allow you to do the following tutorials:
Installation
Once the dataset(s) have been downloaded, uncompress and install with the following command run from a terminal window.
tar -xzvf <filename>.tar.gz
Replacing <filename> with the name of the file downloaded. The downloaded .tar.gz files can then be deleted.
Configuration
In order to do the tutorials, users must define an environment variable called TUTORIAL_DATA which is set to the root directory containing the extracted data (i.e. the directories 'buckner_data', 'long-tutorial', 'fsfast-functional', etc.). The tutorials make frequent use of the TUTORIAL_DATA environment variable and it need to be set properly for any of the tutorials to work. For example:
export TUTORIAL_DATA=/home/username/Downloads/tutorial_data ls $TUTORIAL_DATA buckner_data fsfast-functional diffusion_recons fsfast-tutorial.subjects diffusion_tutorial long-tutorial
If you see something similar to the above output (you may not have downloaded all the tutorial data sets) you are now ready to start the Freesurfer tutorials.
FreeSurfer Tutorial Datasets 5.1/5.3
Below are links to the previous versions of the tutorial dataset that correspond to freesurfer version 5.1 and 5.3: