Freesurfer
Freesurfer is an open source software suite for processing and analyzing human brain MRI images: https://surfer.nmr.mgh.harvard.edu/
For a structural MRI scan, Freesurfer can:
- perform skull stripping
- segment gray matter from white matter
- label cortical and subcortical structures
This functionality is a gear on Flywheel.
Follow instructions on the [Freesurfer wiki] (https://surfer.nmr.mgh.harvard.edu/fswiki)
To check if Freesurfer was downloaded successfully, open Matlab and type the following in the command window:
getenv('FREESURFER_HOME')
getenv('SUBJECTS_DIR')
These Matlab calls should return paths, not empty vectors:
/Applications/freesurfer
Your/Freesurfer_subjects/directory/Freesurfer_subjects
Tip: If you use Freesurfer frequently, it might be tedious to add it to your path every time you open Matlab. Follow the instruction [HERE] (https://github.com/vistalab/vistasoft/wiki/Mac-vistasoft-software-configuration) or watch the first 2 tutorials [HERE] (http://psych.nyu.edu/winawerlab/Vistasoft%20Code%20Review/index.htm) if you want to have Freesurfer path available every time you launch Matlab.
- Vistasoft
- Getting Started
- mrVista Overview
- Anatomy
- Functional MRI
- mrVista
- Retinotopy tutorial
- Population RF methods also prf Model, prf_tutorial, prf tutorial
- Diffusion weighted MRI
- Visualization
- Tractography
- Tutorials
- Software overview