1. Intro to FreeSurfer Jargon voxel surface volume vertex surface-based recon cortical, subcortical parcellation/segmentation registration, morph, deform, transforms (computing vs. resampling)

2. What FreeSurfer Does… FreeSurfer creates computerized models of the brain from MRI data. Input: T1-weighted (MPRAGE,SPGR) 1mm 3 resolution (.dcm) Output: Segmented & parcellated conformed volume (.mgz)

3. Intro to FreeSurfer Jargon voxel

4. Intro to FreeSurfer Jargon surface

5. Intro to FreeSurfer Jargon surface

6. Intro to FreeSurfer Jargon vertex

7. Intro to FreeSurfer Jargon vertex Volume = Surface Area x Thickness

8. Recon “ recon your data” …short for reconstruction …cortical surface reconstruction … shows up in command recon-all

9. Recon

10. Volumes orig.mgzT1.mgzbrainmask.mgzwm.mgz filled.mgz (Subcortical Mass)

11. Cortical vs. Subcortical GM coronal sagittal subcortical gmcortical gm

12. Cortical vs. Subcortical GM coronal sagittal subcortical gm

13. Parcellation vs. Segmentation (subcortical) segmentation(cortical) parcellation