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| [[FreeSurferWiki|top]] |
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| FreeSurfer is a versatile set of software tools that will help you analyze your structural and functional MRI data of the brain. It is comprised of several components -- user interfaces, graphical displays, and executable commands. | !FreeSurfer is a freely available software package developed by investigators at the [[http://www.nmr.mgh.harvard.edu:|Athinoula A. Martinos Center for Biomedical Imaging]] used for a number of procedures including: |
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| A handy overview of the major processing steps taking place in a standard FreeSurfer workflow are described in this pdf slide presentation: [http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/FSL_anatomical_stream.pdf Building Anatomical Models with Freesurfer]. | 1. Creation of computerized models of the brain from magnetic resonance imaging (MRI) data. [[FsTutorial/MorphAndRecon|link]] |
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| '''MRI Parameters''' | 2. Processing of functional magnetic resonance imaging (fMRI) data. [[FsFastTutorial|link]] |
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| FreeSurfer requires that the MRI data conform to certain parameters. The slice thickness should be 1.3mm and the Field of View should be 25. For best results, each subject should have at least one sagittal structural scan. These scans are averaged and automatically corrected for motion before further processing. | 3. Measuring a number of morphometric properties of the brain including cortical thickness and regional volumes. [[https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl00-cortical-thickness.pdf|link]] |
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| The end result: FreeSurfer will produce a single, high quality 3D structural volume, corresponding 2D surfaces, and automatically segmented subcortical structures for each of your subjects. | 4. Intersubject averaging of structural and functional data using a procedure that aligns individuals based on their cortical folding patterns for optimal alignment of homologous neural regions. [[https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl99-morphing.pdf|link]] |
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| You can also use FreeSurfer to generate an average subject out of all the participants in your study, upon which you can display individual subject data - structural and/or functional. | '''Machine Requirements''' |
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| '''System Requirements''' | To run FreeSurfer, you will need either a PC running Linux or a Macintosh running OS X. FreeSurfer consumes a lot of processor time, memory resources and disk space, so it is recommended to run FreeSurfer on as powerful a machine as you have available. For example, at MGH we typically run Linux CentOS 4 on 2.5GHz dual processor AMD Opterons with 4 to 8 GB of DDR SDRAM, and 250GB of disk space. See SystemRequirements for more info. '''Data Requirements''' The processing procedures for the creation of cortical models require good quality T1 weighted MRI data, such as a Siemens MPRAGE ([[http://www.nmr.mgh.harvard.edu/~andre/|examples of appropriate Siemens scanner protocols]]) or GE SPGR sequence with approximately 1mm^3^ resolution (although a variety of quality data sets can be processed with additional manual intervention). Thickness should not exceed 1.5mm (~1mm^3 is ideal). The best FreeSurfer processing results come from scans having excellent gray/white matter contrast. [[attachment:example_scans.tif|Examples of different quality scans (click to download TIFF image):]] * '''A''' - excellent GM/WM contrast, acquired with MP-RAGE pulse-sequence protocol * '''B''' - very good GM/WM contrast, acquired with MP-RAGE pulse-sequence protocol * '''C''' - good GM/WM contrast, acquired with SPGR pulse-sequence protocol; not as good GM/WM contrast as the MP-RAGE acquisitions; low bandwidth causes some temporal lobe artifacts (brightening of the gray matter) These example scans, captured from FreeSurfer's tkmedit display, are slices from the brainmask.mgz file, created by the -autorecon1 stage of FreeSurfer (requiring about 20 minutes of processing time). This means that some amount of intensity normalization has occurred, but the contrast differences between image examples are easier to see, compared to the original (orig.mgz) volume. Refer to the tutorial sections [[FsTutorial/ControlPoints|'Using Control Points to Fix Intensity Normalization']] and [[FsTutorial/WhiteMatterEdits|'Fixing Common Geometric Inaccuracies in White Matter Surfaces']] for examples of problem areas resulting from scan deficiencies. '''Getting Started''' There is a variety of documentation about the use of FreeSurfer contained in the FreeSurfer wiki including [[DownloadAndInstall|installation of the software]], [[FsTutorial|tutorials]], [[FsTutorial/Data|sample data]], and [[WorkFlows|work flows]] providing step by step guides to performing specific tasks. To get started, we suggest you: 1. Read the introductory material on FreeSurfer from past lectures: * [[attachment:FSL_anatomical_stream.pdf|slides 1 (BF)]] * [[attachment:fsintro.pdf|slides 2 (DG)]] * [[attachment:fsrecon.pdf|slides 3 (DG)]] 2. Read the background material: [[ArticlesSlidesAndPosters|click here]] 3. Install FreeSurfer: [[DownloadAndInstall|click here]] 4. Download the sample data set: [[FsTutorial/Data|click here]] 5. Follow the cortical reconstruction tutorial to create cortical models: [[FsTutorial|click here]] 6. Follow the reconstruction workflow page: [[RecommendedReconstruction|click here]] 7. Peruse the wiki to get a fuller knowledge of all of the available processing procedures in the FreeSurfer software package |
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| An active [[FreeSurferSupport|e-mail list]] is available to answer specific questions about processing procedures. | |
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| There is also a [[UserContributions/FAQ|FAQ]] |
FreeSurfer Beginners Guide
FreeSurfer is a freely available software package developed by investigators at the Athinoula A. Martinos Center for Biomedical Imaging used for a number of procedures including:
Creation of computerized models of the brain from magnetic resonance imaging (MRI) data. link
Processing of functional magnetic resonance imaging (fMRI) data. link
Measuring a number of morphometric properties of the brain including cortical thickness and regional volumes. link
Intersubject averaging of structural and functional data using a procedure that aligns individuals based on their cortical folding patterns for optimal alignment of homologous neural regions. link
Machine Requirements
To run FreeSurfer, you will need either a PC running Linux or a Macintosh running OS X.
FreeSurfer consumes a lot of processor time, memory resources and disk space, so it is recommended to run FreeSurfer on as powerful a machine as you have available. For example, at MGH we typically run Linux CentOS 4 on 2.5GHz dual processor AMD Opterons with 4 to 8 GB of DDR SDRAM, and 250GB of disk space.
See SystemRequirements for more info.
Data Requirements
The processing procedures for the creation of cortical models require good quality T1 weighted MRI data, such as a Siemens MPRAGE (examples of appropriate Siemens scanner protocols) or GE SPGR sequence with approximately 1mm3 resolution (although a variety of quality data sets can be processed with additional manual intervention). Thickness should not exceed 1.5mm (~1mm^3 is ideal). The best FreeSurfer processing results come from scans having excellent gray/white matter contrast.
Examples of different quality scans (click to download TIFF image):
A - excellent GM/WM contrast, acquired with MP-RAGE pulse-sequence protocol
B - very good GM/WM contrast, acquired with MP-RAGE pulse-sequence protocol
C - good GM/WM contrast, acquired with SPGR pulse-sequence protocol; not as good GM/WM contrast as the MP-RAGE acquisitions; low bandwidth causes some temporal lobe artifacts (brightening of the gray matter)
These example scans, captured from FreeSurfer's tkmedit display, are slices from the brainmask.mgz file, created by the -autorecon1 stage of FreeSurfer (requiring about 20 minutes of processing time). This means that some amount of intensity normalization has occurred, but the contrast differences between image examples are easier to see, compared to the original (orig.mgz) volume. Refer to the tutorial sections 'Using Control Points to Fix Intensity Normalization' and 'Fixing Common Geometric Inaccuracies in White Matter Surfaces' for examples of problem areas resulting from scan deficiencies.
Getting Started
There is a variety of documentation about the use of FreeSurfer contained in the FreeSurfer wiki including installation of the software, tutorials, sample data, and work flows providing step by step guides to performing specific tasks. To get started, we suggest you:
Read the introductory material on FreeSurfer from past lectures:
Read the background material: click here
Install FreeSurfer: click here
Download the sample data set: click here
Follow the cortical reconstruction tutorial to create cortical models: click here
Follow the reconstruction workflow page: click here
Peruse the wiki to get a fuller knowledge of all of the available processing procedures in the FreeSurfer software package
An active e-mail list is available to answer specific questions about processing procedures.
There is also a FAQ