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| == FreeSurfer Tutorial: Sample Data == | '''Index''' |
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| The data for the [[FsTutorial| tutorials]] consists of several data sets: * buckner_data-tutorial_subjs.tar.gz ~16GB uncompressed - the main 'recon-all' stream subject data processing * long-tutorial.tar.gz ~16GB uncompressed - the longitudinal tutorial * fsfast-tutorial.subjects.tar.gz ~5.6GB uncompressed and fsfast-functional.tar.gz ~9.1GB uncompressed - the FS-FAST tutorial data set * diffusion_recons.tar.gz and diffusion_tutorial.tar.gz - the diffusion and CVS tutorial data sets * fbert-feat.tgz and bert.recon.tgz - tutorial on the integration of FreeSurfer and FSL/FEAT |
<<TableOfContents>> |
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| 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'''. === Download using wget === |
== 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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| Open a terminal, change to a directory where you know you have at least 100GB of space. To download, type: | ## * 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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| 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/diffusion_recons.tar.gz & wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_tutorial.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 & }}}torial_subjs-group_analysis_tutorial_p2.tgz & 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 were a partial download stopped. Notice the commands have the ampersand, so you can run all three 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). Goto the Installation section below once the files are downloaded (this will likely take several hours). If you want to verify the md5sum, the md5sum for each of these files is found in files named *.md5sum.txt in this directory {{{ http://surfer.nmr.mgh.harvard.edu/pub/data/ |
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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| === Installation === | == Configuration == |
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| Once the files are downloaded, move the file(s) to the $FREESURFER_HOME/subjects directory, and uncompress and install with the following commands: | 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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| tar xzvf <filename>.tar.gz | 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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| Replacing of course <filename> with the name of each file downloaded. The downloaded .tar.gz files can then be deleted. | If you see something similar to the above output, you are now ready to start the [[Tutorials|Freesurfer tutorials]]. |
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| 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: {{{ setenv TUTORIAL_DATA $FREESURFER_HOME/subjects source $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/scripts/subjects.csh }}} |
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| '''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 TUTORIAL_DATA and SUBJECTS_DIR environment variables to point to that. You may have to make adjustments throughout the tutorial wherever it refers to $FREESURFER_HOME/subjects (which is equivalent to your $SUBJECTS_DIR). | == FreeSurfer Tutorial Datasets 5.1/5.3 == |
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| 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.). | 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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| ## === 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.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: