Tags » Freesurfer

How do we measure thickness, area, and volume of the cerebral cortex?

There are various ways one could estimate morphometric parameters of the cortex, such as its thickness, area, and volume. For example, it is possible to use voxelwise partial volume effects using volume-based representations of the brain, such as in voxel-based morphometry (VBM), in which estimates per voxel become available. 1,253 more words

Surface Models

Freesurfer Resources




FreeSurfer Lecture #1: Overview of FreeSurfer and recon-all by Andrew Jahn (this video covers pretty much all of his introductory freesurfer videos into one long video) 19 more words


Doing Freesurfer in Steps with Recon-all Flags

Create Data Folder

  1. Connect to PC and pull over subjects T1 co file into: /usr/local/freesurfer/subjects
  2. Open terminal and go into subjects folder
    1. cd $SUBJECTS_DIR

Run Recon1… 907 more words


Anatomical Analysis- Recon 1

Recon 1

  1. Create folder in freesurfer subjects directory (usr/local/freesurfer/subjects) titled _DICOMS
    1. Can be done in the files program or using terminal (instructions bellow)
      1. cd $SUBJECTS_DIR…
  2. 346 more words

Open science is better science!

Repeat after me, open science is better science! 

I believe that, and in that spirit, I am starting to do my best to move the peer review process to open forums when possible (authors permitting of course). 182 more words

Freesurfer: Version

  • cat /usr/local/freesurfer/build-stamp.txt