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| [wiki:Self:FsTutorial top] | [wiki:Self:FsTutorial previous] | [wiki:Self:FsTutorial/Overview next] | [[FsTutorial|top]] |
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| == FreeSurfer Tutorial: Sample Data == | '''Index''' |
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| A 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 (6GB), and the data for the group study analysis (14GB). | <<TableOfContents>> |
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| The files can be obtained via anonymous ftp. Use '''ftp surfer.nmr.mgh.harvard.edu'''. Login as '''anonymous''' and use your email addresses as the password. | == 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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| Example login: | ## * 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. ## * 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 size of the data for the freesurfer [[Tutorials|tutorials]] is quite large, so it consists of several sets: ## || '''Download''' || '''Description''' || '''Size''' || ## || [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data_core.tar.gz|Core Data]] || The core tutorial subject data || 16.8 GB || ## || [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data_functional.tar.gz|Functional Data]] || The !FsFast functional tutorial data || 18.1 GB || ## || [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data_diffusion.tar.gz|Diffusion Data]] || The diffusion and tracula tutorial data || 4.3 GB || ## || [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data_longitudinal.tar.gz|Longitudinal Data]] || The longitudinal tutorial data || 15.5 GB || ## If you just want to get started with the basics of !FreeSurfer, you only need to download the core data set. This will allow you to run 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 == The following commands will install the complete tutorial dataset (~8GB) on your machine. Afterwards, you should have a folder called `tutorial_data` in your working directory. |
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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> |
curl https://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz -o tutorial_data.tar.gz tar -xzvf tutorial_data.tar.gz rm tutorial_data.tar.gz |
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| The tutorial datasets are found in the pub/dist directory: | == Configuration == In order to run the tutorials, users must define an environment variable called '''TUTORIAL_DATA''', which must be set to the `tutorial_data` 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: |
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| ftp> cd pub/dist | export TUTORIAL_DATA=/path/to/your/tutorial/dir ls $TUTORIAL_DATA buckner_data fsfast-functional diffusion_recons fsfast-tutorial.subjects diffusion_tutorial long-tutorial |
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| 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 }}} |
If you see something similar to the above output, you are now ready to start the [[Tutorials|Freesurfer tutorials]]. |
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| 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 }}} |
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| Now exit the ftp application: {{{ ftp> quit }}} |
== FreeSurfer Tutorial Datasets 5.1/5.3 == |
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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: | 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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| {{{ tar xzvf buckner_data-<dataset>.tar.gz }}} where <dataset> is either '''tutorial_subjs''' or '''group_study'''. The downloaded 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: {{{ source $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/scripts/setup_subjects.csh }}} 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: {{{ source $FREESURFER_HOME/subjects/buckner_data/group_study/scripts/setup_subjects.csh }}} 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. |
* [[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
Installation
The following commands will install the complete tutorial dataset (~8GB) on your machine. Afterwards, you should have a folder called tutorial_data in your working directory.
curl https://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz -o tutorial_data.tar.gz tar -xzvf tutorial_data.tar.gz rm tutorial_data.tar.gz
Configuration
In order to run the tutorials, users must define an environment variable called TUTORIAL_DATA, which must be set to the tutorial_data 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=/path/to/your/tutorial/dir 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 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: