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| The full data for the [[Tutorials|tutorials]] consists of several data sets: | ## The size of the data for the freesurfer [[Tutorials|tutorials]] is quite large, so it consists of several sets: |
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| * [[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.tar.gz|diffusion_tutorial.tar.gz]] - the diffusion and Tracula tutorial data 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 || |
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| ## 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: | |
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| 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]] |
## * [[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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| Once the dataset(s) have been downloaded, uncompress and install with the following command run from a terminal window. | 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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| tar -xzvf <filename>.tar.gz | 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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| Replacing <filename> with the name of the file downloaded. The downloaded .tar.gz files can then be deleted. | |
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| == Set variables to point FreeSurfer to data == | == Configuration == |
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| 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.). For example: | 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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| export TUTORIAL_DATA=/home/username/Downloads/tutorial_data | export TUTORIAL_DATA=/path/to/your/tutorial/dir |
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| 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]]. | If you see something similar to the above output, you are now ready to start the [[Tutorials|Freesurfer tutorials]]. |
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| Below are links to the previous versions of the tutorial dataset that correspond to freesurfer version 5.1 and 5.3: |
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: