Freesurfer Abridged

Setting Up

• Note: I am using FS_0184 (semcat) as an example; fill in the parts specific to FS_0184 with the parts specific to your subject

Structural

1. Slicer

• In terminal, Slicer &
• Load data brainmask.nii
• Save data as brainmask.mgz

1. Autorecon 1

• In terminal, autorecon1_SC.sh FS_0184
• Don't bother editing after this step; skip to autorecon 2

1. Autorecon 2

• In terminal, autorecon2_SC.sh FS_0184
• Editing
  • One terminal, tksurfer FS_0184 lh inflated
  • In another terminal, tkmedit FS_0184 brainmask.mgz -aux T1.mgz -surfs
  • Look for any noticable spikes in the tksurfer brain
  • Click on that point

1. Autorecon 3

Functional

1. Matlab
2. Analysis
3. Contrasts
4. Pre-processing
5. Selxavg
6. Sub-parcellation
7. Clut
8. Blobs