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

This is an abridged version of the more detailed list provided elsewhere in the wiki.

Structural

1. Slicer
   • In terminal, Slicer &
   • Load data brainmask.nii
   • Save data as brainmask.mgz
   • Results: creates brainmask.mgz file
2. Autorecon 1
   • In terminal, autorecon1_SC.sh FS_0184
   • Don't bother editing after this step; skip to autorecon 2
   • Result: populates mri folder (includes "T1.mgz")
3. 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.
   • Results: creates lh.cortex.label and rh.cortex.label in label folder
4. Autorecon 3
   • In terminal, autorecon3_SC.sh FS_0184
   • Editing
     • In terminal, tksurfer -annot aparc FS_0184 lh pial
     • If needed, reference tksurfer -annot aparc fsaverage lh pial
     • Repeat with right hemi
     • Make sure to EXPORT ANNOTATION! Do not "save overlay!"
     • Again, be sure to see the autorecon3 page
   • Result: populates label folder (includes "lh.aparc.annot" and "rh.aparc.annot")

Functional

1. Bold file preparation
   • Semcat processing
     • Step a: In terminal, matlab &
     • Step b: In matlab, startup_smp8
     • Step c:
   • LDT processing

1. Analysis
2. Contrasts
3. Pre-processing
4. Selxavg
5. (Optional) Clut and Subparcellation
6. Blobs