What is FreeSurfer segmentation?

What is FreeSurfer segmentation?

FreeSurfer is a widely used software suite that enables fully-automated surface-based cortical segmentation as well as subcortical volume-based segmentation2,3,4,5,6.

What Atlas does FreeSurfer use?

This atlas is also known as the ‘Desikan-Killiany’ cortical atlas. It is a gyral based atlas: ie, a gyrus was defined as running between the bottoms of two adjacent sulci. That is, a gyrus includes the part visible on the pial view + adjacent banks of the sulci limiting this gyrus.

How do I source FreeSurfer?

If you want FreeSurfer to be automatically sourced every time you open a terminal. Alternately, the configuration file for the shell can be set up to source the FreeSurfer script automatically each time the shell is started. In the home directory of the user who will be running FreeSurfer binaries, edit the file .

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.

What does recon all do?

recon-all : Performs all, or any part of, the FreeSurfer cortical reconstruction process.

How long does FreeSurfer recon all take?

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

How is the claustrum segmentation done in FreeSurfer?

After transformation takes place in diffusion space these ROIs are then used to seed for fiber tracking. Since Freesurfer does not provide automatic claustrum segmentation, the claustrum is manually traced on MP-RAGE space.

What is totalbrainseg in APARC+ASEG?

BrainSeg – volume of all voxels in the aparc+aseg.mgz that are neither background nor brain stem. This is the same as pre-5.2 versions except that brain stem is not included. This will also include the “vessel”, “optic-chiasm”, and “CSF” segmentations.

What algorithm do you use to segment the brain?

We use a Bayesian segmentation algorithm that relies on a probabilistic atlas of the brainstem (and neighboring brain structures) built upon manual delineations of the structures on interest in 49 scans (10 for the brainstem structures, 39 for the surrounding structures).

What are the functionalities of freefreesurfer?

FreeSurfer includes a variety of functionalities, including volumetric segmentation of macroscopically-visible brain features (Fischl et al., 2002, 2004), hippocampal subfield segmentation (Van Leemput et al., 2009), architectonic boundaries estimation (Fischl et al., 2008, 2009;


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