FreeSurfer Overview

Date: January 16, 2024 1:15 PM

Table of Contents

  1. FreeSurfer Overview

**Freesurfer is a neuroimaging software package. More information at https://surfer.nmr.mgh.harvard.edu/

Function of FreeSurfer

  • Takes your T1 weighted image from fMRI or MRI → Labelled brain and stats
  • will completely label the anatomy of the brain
    • output an array of measures of anatomy (5-10hrs of analysis)
    • automated— go check for artifacts if it’s relevant to your results
    • cortex flattened out
    • subcortical organs
  • does cortex-surface-based analysis & volumetric analysis
  • multi-modal integration
    • fMRI (task, rest, retinopy)
    • diffusion data

Download and Install FreeSurfer

FreeSurfer 7 Download ← Installation Walk Through

Installation Demo Video for MacOS:

https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall?action=AttachFile&do=get&target=installFS_demo.mp4

Source: FreeSurfer Download and Install

FreeSurfer Tutorials

All Tutorials Tutorials by Version

Overview

Basics

Specialized topics:

Other:

Running Full Anatomical Analysis on FreeSurfer

Running

Open terminal →

recon-all \
  -i  <one slice in the anatomical dicom series> \
  -s  <subject id that you make up> \
  -sd <directory to put the subject folder in> \
  -all
  • will take 5-20 hours

“-i file.dcm”

  • only need to say 1 file in the set of ~180, it will find automatically the rest
  • you can also use .nii files
  • add “-i file2.dcm” if you have two series of diff scans you want to run

“bert”

  • use whatever name you want it to be, maybe subject ID

Screen Shot 2024-01-17 at 10.32.19 AM.png

Upon completion…

Will create folder with subfolders:

~400 MB

mri=volume analysis

surf, label =surface analysis

stats = txt files with stats for all the other files in other folders

Screen Shot 2024-01-17 at 10.42.15 AM.png

To check for errors/ debug:

scripts/recon-all.log ← shows all the terminal commands that ran, log

What happens inside this full processing?

All commands: Recon-All Dev Table

  • This shows you the command, function and output for each step

Terms

  • anatomically derived defect

    A topological defect in the cortical surface that arises from a feature of normal neuroanatomy to be distinguished from defects arising entirely from segmentation errors. See topological defect

  • artifact

    A feature that appears in an image but is not actually present in the imaged object.

  • average convexity

    The signed distance that a vertex moves during the inflation process.

  • brain volume

    The T1 volume after the skull and other non-brain structures have been removed. This volume can be viewed using tkmedit.

  • canonical surface

    Surface-based atlas constructed from the cortical surfaces of 40 normal individuals (used for inter-subject averaging).

  • conversion/averaging

    Process of converting and averaging multiple structural acquisitions from the native magnet format into the native FreeSurfer format (see COR files).

  • COR files

    The native file format used by FreeSurfer to store 3D structural image data.

  • Euler number

    After Leonhard Euler (1707-83). A topological invariant of a surface that can be computed from the number of edges, vertices and faces in a polygonal tessellation (command mris_euler_number ). The Euler number of a sphere will equal 2; the Euler number of a surface with n handles is 2 – 2n.

  • filled volume

    The wm volume after separation of the left and right hemispheres and filling of each hemisphere. This volume can be viewed using tkmedit.

  • flattening

    Producing a planar (flat) representation of a patch of the cortical surface that has minimal metric distortion.

  • gyrus

    A fold or convolution of brain tissue (an outward folded region).

  • hypointensities (wm)

    Dark white matter on a T1-weighted image.

  • hypointensities (non-wm)

    Dark gray matter on a T1-weighted image.

  • inflated surface

    The smoothwm surface after inflation. This surface can be viewed using surfer.

  • inflation

    The process of smoothing the cortex while minimizing metric distortion, so that all sulci are fully visible and surface distances are apparent to visual inspection.

  • intensity

    Measured amount of magnetic field at a given spatial location, represented by a voxel (higher SNR signal to noise ratio means voxels will have a higher intensity relative to the background noise, and appear brighter).

  • label

    A particular region of interest. e.g. in tksurfer the label would be a region of interest in the surface. In tkmedit a label is a region of interest in the volume.

  • morphing

    Computer graphics technique whereby a mapping is computed that smoothly transforms one image or surface into another.

  • morphometrics

    The study of geometric properties of the human brain.

  • motion correction

    Processing multiple structural volumes so that the effects of subject movement are minimized. This is typically done by aligning multiple images/volume to an initial image/volume (see conversion/averaging).

  • MRI volume

    The three dimensional volumetric data set collected from a MRI scanner.

  • orig volume

    The original MRI volume. This volume can be viewed using tkmedit.

  • orig surface

    The first surface constructed by covering the labeled voxels in the filled volume. This surface can be viewed using surfer.

  • pial

    Pertaining to the delicate pia mater which envelops the brain (gray matter). Also, the model of the pial surface (?h.pial).

  • pial surface

    The refined estimate of the gray/CSF boundary (pial surface). This surface can be viewed using surfer.

  • region growing process

    An algorithm that groups voxels or sub-regions into larger regions.

  • RF-field inhomogeneities

    Spatial variations in the Radio Frequency (RF) excitation pulse. These variations result in changes in the measured intensity for a given tissue class that are related to the spatial location of the voxel.

  • segmentation

    Labeling of tissue classes from MRI data (e.g. white matter).

  • smoothing

    Process of producing a relatively even and regular cortical surface.

  • smoothwm surface

    The orig surface after smoothing. This surface can be viewed using surfer.

  • sulcus

    A groove or furrow in brain tissue (an inward folded region).

  • supertessellated icosahedron

    Polygonal approximation to a sphere.

  • T1

    Longitudinal relaxation constant.

  • T1 volume

    The MRI volume after intensity normalization. This volume can be viewed using tkmedit.

  • T1 Weighted Image

    A magnetic resonance image where the contrast is predominantly dependent on T1.

  • T2 Weighted Image

    A magnetic resonance image where the contrast is predominantly dependent on T2.

  • T2

    Transverse relaxation constant.

  • Talairach coordinate

    The corresponding location in the Talairach atlas for a given point in a brain that has been coregistered with the atlas (Talairach et al, 1967).

  • tessellation

    Covering of a surface by repeated use of a single shape.

  • topology

    The properties of a surface related to its connectivity that are unaffected by geometric (i.e. rubber sheet) transformations.

  • topological defect

    A portion of a surface that results in the surface topology differing from that of a sphere.

  • volume

    A 3-D data set that typically contains either intensity information derived from the original MRI, or the results of segmenting this data into tissue classes.

  • voxel

    The basic element of an MRI volume (analogous to a pixel in a 2-D image). The volume of a structural voxel is approximately 1 mm3.

  • white surface

    The refined estimate of the gray/white boundary. This surface can be viewed using surfer.

  • wm volume

    The brain volume after white matter segmentation. This is also the volume that is manually edited. This volume can be viewed using tkmedit.