What is a FreeSurfer?

What is a FreeSurfer?

FreeSurfer is an open source package for the analysis and visualization of structural, functional, and diffusion neuroimaging data from cross-sectional and longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging.

Who created FreeSurfer?

FreeSurfer is a brain imaging software package originally developed by Bruce Fischl, Anders Dale, Martin Sereno, and Doug Greve. Development and maintenance of FreeSurfer is now the primary responsibility of the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging.

Why use FreeSurfer?

FreeSurfer provides a full processing stream for structural MRI data, including: Labeling of regions on the cortical surface, as well as subcortical brain structures. Nonlinear registration of the cortical surface of an individual with a stereotaxic atlas. Statistical analysis of group morphometry differences.

How can I use FreeSurfer on Windows?

Steps for Setting Up WSL to run freesurfer:

  1. Enable WSL on the windows machine +
  2. Install WSL on the windows machine +
  3. Download/install a linux distribution into WSL ++
  4. Download/install an X-server on the windows machine +++
  5. From a terminal window running inside the linux distribution, download and install freesurfer ++++

What is Freeview FreeSurfer?

Introduction. Freeview is a visualization tool similar in functionality to tkmedit, tksurfer, and scuba. It differs from tkmedit in that it can load multiple volumes at once and can be used to visualize high resolution (100um) data as well as tractography splines.

How do I install Freeview on my TV?

Setting up a Freeview recorder

  1. Plug your aerial lead into the aerial socket on your box (1).
  2. Using an HDMI cable, connect to the equivalent socket on your TV to the port marked HDMI 1 on the box.
  3. Put your TV on standby, then switch the TV on using your TV remote control.

How long does FreeSurfer recon-all take?

How long does it take for recon-all to finish processing one subject? 20-24 hours.

How long does it take to run FreeSurfer?

around sixteen to twenty-four hours
As you will soon find out, FreeSurfer takes a long time to process an individual subject – around sixteen to twenty-four hours on a typical iMac, with some variation due to factors such as the quality of the input data.

What is TkMedit?

TkMedit is the main volume viewer and editor for FreeSurfer. Use it to view volumes, overlay surfaces onto them in 2D, edit reconstruction defects, view functional overlays and time courses, view segmentations, and draw or edit labels.

Where is FreeSurfer developed?

It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. FreeSurfer is the structural MRI analysis software of choice for the Human Connectome Project.

What can I do with Freesurfer?

FreeSurfer contains a range of packages allowing a broad spectrum of uses, including: FreeView, a tool to visualize FreeSurfer output, can also display common MRI image formats. LGI, to calculate the degree of folding or local GI.

Where is subject data stored in FreeSurfer?

SUBJECTS_DIR (location of subject data) FreeSurfer requires an environment variable called SUBJECTS_DIR. This is the directory where subject data is stored. By default, the FreeSurfer setup script will create the SUBJECTS_DIR environment variable and set it to the FREESURFER_HOME/subjects directory – if it is not yet defined.

How do I obtain a license for FreeSurfer?

Obtaining a license is free and comes in the form of a license.txt file. Once you obtain the license.txt key file, copy it to your FreeSurfer installation directory. This is also the location defined by the FREESURFER_HOME environment variable. Follow this link to obtain a license key. A free and open platform that can be used to run FreeSurfer.

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