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

• Slicer
  • In terminal, Slicer &
  • Load data brainmask.nii
  • Save data as brainmask.mgz
• Autorecon 1
  • In terminal, autorecon1_SC.sh FS_0184
  • Don't bother editing after this step; skip to autorecon 2
• 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 and edit the brainmask (tkmedit). See wiki page for details; this is the most labor intensive part of anatomical so make sure you're doing it right.
• Autorecon 3
  • In terminal, autorecon3_SC.sh FS_0184
  • Editing

Functional

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