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| '''Index''' <<TableOfContents>> |
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| ## The data set for the Freesurfer tutorials comes in two forms, a "Lightweight" version and a "Full" version. | |
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| 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 |
## * 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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| 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]] |
## * 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. |
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| === 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'''. |
## == Lightweight version == ## Use the following link to download the lightweight version of the tutorial data: |
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| Open a terminal, change to a directory where you know you have at least 100GB of space. To download, type: | ## . [[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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| 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 & |
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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| This download will likely take several hours. | == Configuration == |
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| 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. ==== Optional Verification Step ==== 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: |
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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| 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 & |
export TUTORIAL_DATA=/path/to/your/tutorial/dir ls $TUTORIAL_DATA buckner_data fsfast-functional diffusion_recons fsfast-tutorial.subjects diffusion_tutorial long-tutorial |
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| You will want to ensure that these md5sum's match what you find when you run md5sum on your own local downloads. If they do not match, the file transfer may have been faulty or there may have been a disk error. '''Mac OS NOTE:''' Use '''md5 -r''' to get the same results as '''md5sum'''. More on md5sum can be found [[http://www.techradar.com/us/news/computing/pc/how-to-verify-your-files-in-linux-with-md5-641436|here]]. | If you see something similar to the above output, you are now ready to start the [[Tutorials|Freesurfer tutorials]]. |
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| === Installation === ==== Uncompress the files ==== Once the datasets have been downloaded, move them to the {{{$FREESURFER_HOME/subjects}}} directory, and uncompress and install with the following command run from a terminal window. You'll have to {{{cd} $FREESURFER_HOME/subjects}}} first if you haven't already: |
---- |
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| {{{ tar xzvf <filename>.tar.gz }}} |
== FreeSurfer Tutorial Datasets 5.1/5.3 == |
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| Replacing <filename> with the name of each file downloaded. The downloaded .tar.gz files can then be deleted. | 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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| ==== Set variables to point FreeSurfer to data ==== 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/ }}} '''Note for 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 variable, 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 }}} |
* [[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: