Freesurfer Abridged: Difference between revisions

Revision as of 12:22, 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
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

@@ Line 3: / Line 3: @@
 == Structural ==
-# Slicer
+*Slicer
-:*In terminal, <code>Slicer &</code>
+** In terminal, <code>Slicer &</code>
-:*Load data brainmask.nii
+** Load data brainmask.nii
-:*Save data as brainmask.mgz
+** Save data as brainmask.mgz
-# Autorecon 1
+* Autorecon 1
-:*In terminal, <code>autorecon1_SC.sh FS_0184</code>
+** In terminal, <code>autorecon1_SC.sh FS_0184</code>
-:*Don't bother editing after this step; skip to autorecon 2
+** Don't bother editing after this step; skip to autorecon 2
-# Autorecon 2
+* Autorecon 2
-:*In terminal, <code>autorecon2_SC.sh FS_0184</code>
+** In terminal, <code>autorecon2_SC.sh FS_0184</code>
-:*Editing
+** Editing
-:**One terminal, <code>tksurfer FS_0184 lh inflated</code>
+*** One terminal, <code>tksurfer FS_0184 lh inflated</code>
-:**In another terminal, <code>tkmedit FS_0184 brainmask.mgz -aux T1.mgz -surfs</code>
+*** In another terminal, <code>tkmedit FS_0184 brainmask.mgz -aux T1.mgz -surfs</code>
-:**Look for any noticable spikes in the tksurfer brain
+*** 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.
-:**Click on that point
+* Autorecon 3
-# Autorecon 3
+** In terminal, <code>autorecon3_SC.sh FS_0184</code>
+** Editing
+***
 == Functional ==