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FreeSurfer & FSL

Authors: Ayaan Khan & Aryan Kondapalli


Introduction to Freesurfer

Typical 3D neuroimaging data utilizes voxels that can either represent anatomical features or functional activity. However, voxels are not efficient and effective when wanting to analyze partial volumes or regions, as they are not able to distinctly distinguish between regions in activity data images. As a result, FreeSurfer is a tool that can be utilized to overcome this challenge. FreeSurfer is a software tool that analyzes cortical and subcortical anatomy and condenses multiple points of information into a single interface to be used for analysis. Freesurfer is a neuroimaging package for the analysis and visualization of neuroimaging data. It is an open-source neuroimaging toolkit for processing, analyzing, and visualizing human brain MRI images. It is meant to make this analysis easy as it is able to preprocess large sums of data all at once. Freesurfer is used especially for cortical and subcortical anatomy analysis. Additionally, FreeSurfer can preprocess data sets and do the preprocessing steps with simple commands and even all at once. This makes preprocessing far easier and can be more efficient and accurate for analysis later. However, it is slow because it takes 6-24 hours for a single subject image, so there are features like parallel that can be used to run multiple subject data at a time and shorten the overall time for preprocessing and analysis.  For more info go to


The Function of Freesurfer

Freesurfer is used for the creation of computerized models of the brain from MRI data. It is especially useful in the processing of fMRI data. Freesurfer can measure a number of morphometric properties of the brain including cortical thickness, the width of gray matter in the human cortex, and regional volumes. FreeSurfer essentially creates a computerized model of the brain from MRI data, through preprocessing of data including fMRI data. Through its processing, one can measure different brain properties including cortical thickness and regional volumes. Cortical thickness is the measure of the width of gray matter thickness, and regional volumes are volumes of different size regions of the brain like diff. Subcortex. Another FreeSurfer function is to be a single interface through which users can combine and average structural and functional data. This means they can vary between different surface overlays of the brain as seen in the image. Users can also compare two different subject brains which are highly useful in analysis. Freesurfer can also perform inter-subject averaging of structural and functional data and uses a procedure that aligns individuals based on their cortical folding patterns for the optimal alignment of homologous neural regions.



Input, Analysis, and Preprocessing with Freesurfer

Freesurfer takes in input data from multiple sources in order to create condensed 3D Images with multiple features. It analyzes a weighted 3D image to create different anatomical images. Each voxel is converted into 2D triangles with each vertex containing information like volume, thickness, and activity levels. MRI is preprocessed and a final image is created in a number of steps. First, FreeSurfer removes the skull from the brain volume in the image. Second, gray-white matter segmentation occurs to divide and identify different cortex regions. Third, the boundaries of the different boundaries are determined and outlined. Lastly, this prepped image is inflated to a sphere and then compared to a template sphere called the fsAverage that determines and aligns different parts of the brain. 


Freesurfer Tool #1: FreeView

Freeview is a visualization tool on Freesurfer. It can load multiple volumes at once and can be used to visualize high-resolution data as well as tractography splines. Additionally, it allows you to create and edit new volumes in layers upon the original anatomical scan volume. Modification of images such as the color of certain brain sections, opacity, outline thickness and outline color. It is a viewing interface to view all the different surface overlays or image files that FreeSurfer creates. You can add multiple images on top of each other kind of like different layers. FreeView offers multiple options for each image including changing the color of the outline, changing the color of sections, changing opacity, or changing the outline thickness.  For more info go to


Freesurfer Tool #2: Tracula

Tracula is a tool for automatic reconstruction of a set of major white-matter pathways from diffusion-weighted MRI data. Prior distributions on the neighboring anatomical structures of each white-matter pathway are derived from a set of manually annotated training subjects. Additionally, Tracula also uses prior knowledge on the relative positions of white-matter pathways with respect to their surrounding anatomical structures to accomplish this. It helps reconstruct a pathway of interest in a novel subject. For reference, diffusion-weighted MRI,  a neuroimaging technique that utilizes the diffusion of water to determine anatomical structure of the brain, especially in white-matter regions. Tracula uses previous knowledge of white-matter pathways and an individual's diffusion data to determine the 3D pathway image, somewhat similar to the inflation and fsAverage data set technique that FreeSurfer uses. Tracula also preprocesses diffusion data and correlates the diffusion-weighted and anatomical images to make it easier for comparison and analysis since both images are tied together to one subject. Additionally, it collects and provides statistics of diffusion measures for each trajectory pathway, as well as providing a visual representation of the results and image as seen in the picture to the right of the text. This is just one type of neuroimaging processing tool that FreeSurfer is compatible with. For more info go to


Compatible Neuroimaging Techniques

There are multiple neuroimaging techniques that are compatible with FreeSurfer. The fMRI tool is called FreeSurfer Functional Analysis Stream or FS-FAST. It provides fMRI data analysis and is easily integrable into FreeSurfer. Tracula, as I mentioned before, utilizes Diffusion MRI data to reconstruct white-matter pathways by processing diffusion data. Finally PETsurfer allowed for the analysis of PET or positron emission tomography data. The various neuroimaging techniques that FreeSurfer is compatible with highlights how versatile of a tool it really is and why it can be an important aspect of neuroimaging as a whole. 


Freesurfer Installation Tutorials for MacOS & Windows Machines

Introduction to FSL

FMRIB Software Library, FSL, is a comprehensive analysis library of programs such as Magnetic Resonance Imaging (MRI), Functional Magnetic Resonance Imaging (FMRI), and Diffusion Tensor Imaging (DTI) brain imaging data. FSL is a software library containing image analysis tools for structural, functional, and diffusion MRI brain imaging data. FSL is available with precompiled binaries and source code for PC and Apple computers(both Windows and Linux). For more info go to


The Function of FSL

FSL, FMRIB Software Library, is a comprehensive library of analysis tools for functional, structural, and diffusion MRI brain imaging data, written mainly by members of the Analysis Group, FMRIB, Oxford. There are many different tools FSL uses to attain the highest level they can. Some of those tools are FEAT, which is used in FMRI for model-based analysis, FLIRT and FNIRT, which are used in structural MRI for linear and nonlinear registration, FAST, which is used in structural MRI for tissue-type segmentation, and FIRST, which is used in structural MRI for segmentation of subcortical structures.


Magnetic Resonance Imaging (MRI)

MRI, magnetic resonance imaging, is a medical imaging technique used in radiology to form pictures of the physiological and anatomical processes of the body. It can be used to help diagnose or monitor treatment for a variety of conditions within the chest, abdomen, and pelvis. It can diagnose anything from torn ligaments to tumors. MRI scanners use strong magnetic fields, gradients, and radio waves to generate images of the organs in the body. PET and CT scans are different from MRI because MRI does not have anything to do with X-rays or radiation ionization. Compared to CT, MRI provides better contrast in images of soft-tissues and organs in the brain. However, MRI may be perceived as less comfortable by patients due to the longer and louder measurements with the subject in a long, confined, excluded tube where they reside. 

Functional Magnetic Resonance Imaging

Functional Magnetic Resonance Imaging, fMRI, is a scan that measures and maps the brain's activity. This technique relies on the fact that cerebral blood flow and neuronal activation are coupled together. It measures how active brain regions are over time and the BOLD response. BOLD stands for Blood Oxygenation Level-Dependent Imaging. It measures the ratio of oxygenated blood to deoxygenated blood and indirectly measures brain activity. They need more oxygen when neurons are active. Oxyhemoglobin is diamagnetic and deoxyhemoglobin is paramagnetic. When in a rest state, deoxyhemoglobin is on the venous side. The venous side of the circulation is a low-pressure system compared with the arterial side. In an active state, there is increased blood flow, a decrease in deoxyhemoglobin, and a BOLD signal decrease. FMRI uses a magnetic field to create images. It is used in surgical planning, training programs, and treatment outcomes. The benefits of FMRI are that it is non-invasive, has a good spatial resolution, and it is easily available. The disadvantages of FMRI are that it has a low temporal resolution, correlation does not cause something, and many ways to analyze FMRI data.


Diffusion Tensor Imaging

iffusion Tensor Imaging, DTI, is an advanced magnetic resonance imaging(MRI) technique. DTI is a promising method for characterizing microstructural, which are very small scales of structure, material changes or differences with neuropathology and treatment. Neuropathology is the study of diseases of the eyes and of the nervous system, which includes the brain and spinal cord. DTI measures the diffusion of water molecules. More specifically, DTI measures the rate of water diffusion between cells to understand and create maps of the body’s internal structures. Most of the time, it is used to provide imaging of the brain. DTI shows connections of fibers and reveals patterns of neural networks in the brain with the random movement of water molecules. It maps fiber orientation and can be used to detect disease in white matter.  

Freesurfer Installation Tutorials for MacOS & Windows Machines

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