Freesurfer Abridged: Difference between revisions

Revision as of 12:59, 17 November 2017

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

Slicer
- In terminal, Slicer &
- Load data brainmask.nii
- Save data as brainmask.mgz
- Creates brainmask.mgz file
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")
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
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")

@@ Line 7: / Line 7: @@
 ** Load data brainmask.nii
 ** Save data as brainmask.mgz
+** Creates brainmask.mgz file
 * Autorecon 1
 ** In terminal, <code>autorecon1_SC.sh FS_0184</code>
 ** Don't bother editing after this step; skip to autorecon 2
+** Result: populates mri folder (includes "T1.mgz")
 * Autorecon 2
 ** In terminal, <code>autorecon2_SC.sh FS_0184</code>
@@ Line 16: / Line 18: @@
 *** In another terminal, <code>tkmedit FS_0184 brainmask.mgz -aux T1.mgz -surfs</code>
 *** 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
 * Autorecon 3
 ** In terminal, <code>autorecon3_SC.sh FS_0184</code>
 ** Editing
-***
+*** In terminal, <code>tksurfer -annot aparc FS_0184 lh pial</code>
+*** If needed, reference <code>tksurfer -annot aparc fsaverage lh pial</code>
+*** 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 ==