|
Size: 2029
Comment:
|
Size: 4212
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| == FreeSurfer Tutorial Dataset == | == FreeSurfer Tutorial Data set == |
| Line 3: | Line 3: |
| The [[FsTutorial|freesurfer course]] is a 3-4 workshop held around 2x per year in the Boston area. It is a collection of talks, demos and tutorials designed to help users become more accustomed to using freesurfer for the analyzing and processing of their MRI data. | The [[FsTutorial|freesurfer course]] is a 3-4 workshop usually held 2x per year in the Boston area. It is a collection of talks, demos and tutorials designed to help users become more accustomed to using freesurfer for the analyzing and processing of their MRI data. |
| Line 5: | Line 5: |
| The sample data sets used during the course is provided so that users may go thru these tutorials on their own without the need of attending a freesurfer course. It also can be used by freesurfer course participants so that they may be abvle to use their own computer during the course, instead of the own provided at the course location. Downloading the tutorial data set and configuring your system should be fairly straight forward and is described in the instructions below. | The tutorial data set used during the course is provided to the public so that users may go thru these tutorials on their own without the need of attending a freesurfer course. It may also be used by freesurfer course participants so that they can use their own computer during the course, instead of the one provided to them at the course. Configuring your system so so that it may be used to perform these tutorials should be a fairly straightforward process and is described below: === 1. Download freesurfer === To install freesurfer, follow the instructions on [[https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall|the download and installation page]]. '''''IMPORTANT NOTE''''' The tutorials use the latest "development version" of freesurfer. So when it comes time so select the version for download do NOT select version 5.3, download the "development version" instead, which can be found [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/|on this page]]. === 2. Download tutorial data === Please ensure you have a functioning freesurfer installation by running the commands on the [[https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer| testing freesurfer installation]] page, as is would be pointless to continue otherwise. If you are having issues running the commands, please follow the instructions on the [[https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration|Setup and Configuaration page]]. Once you have a functioning freesurfer installation, it is time to download the [[ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz|freesurfer tutorial data set]]. Once the download completes you will want to extract its contents. This can be done on most operating systems by simply double-clicking the file. '''''Remember the location of this directory. It is used throughtout all of the tutorials.''''' The file should extract a directory called '''tutorial_data''' and its content should look as follows: {{attachment:Screen Shot 2015-08-24 at 2.55.20 PM.png}} === 3. Configure your system === To begin doing the tutorials you start by opening a terminal window and sourcing freesurfer. Then you need to create an environment variable called '''TUTORIAL_DATA''' and set it to the location of the extracted file from above. If you {{{ls $TUTORIAL_DATA}}} you should see the directories extracted in step #2. The example below shows how you would perform these steps on a Mac OSX system. The only difference for your system would be the actual paths: {{{ $> export FREESURFER_HOME=/Applications/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.sh $> export TUTORIAL_DATA=/Users/localzeke/Downloads/tutorial_data $> ls $TUTORIAL_DATA buckner_data fsfast-functional diffusion_recons fsfast-tutorial.subjects diffusion_tutorial long-tutorial }}} Here is an example of what the terminal window should look like: {{attachment:Screen Shot 2015-08-24 at 4.56.51 PM.png}} |
| Line 10: | Line 45: |
| * Click the following link: ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz |
|
| Line 13: | Line 46: |
| * On Mac OSX platforms use 'curl -O' {{{curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz}}} * On Linux platforms use 'wget' {{{wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz}}} |
Second |
FreeSurfer Tutorial Data set
The freesurfer course is a 3-4 workshop usually held 2x per year in the Boston area. It is a collection of talks, demos and tutorials designed to help users become more accustomed to using freesurfer for the analyzing and processing of their MRI data.
The tutorial data set used during the course is provided to the public so that users may go thru these tutorials on their own without the need of attending a freesurfer course. It may also be used by freesurfer course participants so that they can use their own computer during the course, instead of the one provided to them at the course.
Configuring your system so so that it may be used to perform these tutorials should be a fairly straightforward process and is described below:
1. Download freesurfer
To install freesurfer, follow the instructions on the download and installation page. IMPORTANT NOTE The tutorials use the latest "development version" of freesurfer. So when it comes time so select the version for download do NOT select version 5.3, download the "development version" instead, which can be found on this page.
2. Download tutorial data
Please ensure you have a functioning freesurfer installation by running the commands on the testing freesurfer installation page, as is would be pointless to continue otherwise. If you are having issues running the commands, please follow the instructions on the Setup and Configuaration page.
Once you have a functioning freesurfer installation, it is time to download the freesurfer tutorial data set. Once the download completes you will want to extract its contents. This can be done on most operating systems by simply double-clicking the file. Remember the location of this directory. It is used throughtout all of the tutorials. The file should extract a directory called tutorial_data and its content should look as follows:
3. Configure your system
To begin doing the tutorials you start by opening a terminal window and sourcing freesurfer. Then you need to create an environment variable called TUTORIAL_DATA and set it to the location of the extracted file from above. If you ls $TUTORIAL_DATA you should see the directories extracted in step #2. The example below shows how you would perform these steps on a Mac OSX system. The only difference for your system would be the actual paths:
$> export FREESURFER_HOME=/Applications/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.sh $> export TUTORIAL_DATA=/Users/localzeke/Downloads/tutorial_data $> ls $TUTORIAL_DATA buckner_data fsfast-functional diffusion_recons fsfast-tutorial.subjects diffusion_tutorial long-tutorial
Here is an example of what the terminal window should look like:
Second
The 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)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
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: