Freesurfer Abridged: Difference between revisions
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(Created page with "== 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 :*...") |
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== Structural == | == Structural == | ||
*Slicer | |||
** In terminal, <code>Slicer &</code> | |||
** Load data brainmask.nii | |||
** Save data as brainmask.mgz | |||
* Autorecon 1 | |||
** In terminal, <code>autorecon1_SC.sh FS_0184</code> | |||
** Don't bother editing after this step; skip to autorecon 2 | |||
* Autorecon 2 | |||
** In terminal, <code>autorecon2_SC.sh FS_0184</code> | |||
** Editing | |||
*** One terminal, <code>tksurfer FS_0184 lh inflated</code> | |||
*** 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. | |||
* Autorecon 3 | |||
** In terminal, <code>autorecon3_SC.sh FS_0184</code> | |||
** Editing | |||
*** | |||
== Functional == | == Functional == |
Revision as of 12:22, 17 November 2017
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
- In terminal,
- Autorecon 1
- In terminal,
autorecon1_SC.sh FS_0184
- Don't bother editing after this step; skip to autorecon 2
- In terminal,
- 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.
- One terminal,
- In terminal,
- Autorecon 3
- In terminal,
autorecon3_SC.sh FS_0184
- Editing
- In terminal,
Functional
- Matlab
- Analysis
- Contrasts
- Pre-processing
- Selxavg
- Sub-parcellation
- Clut
- Blobs