Intro to FreeSurfer Jargon voxel surface volume vertex surface-based recon cortical, subcortical parcellation/segmentation registration, morph, deform,

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Presentation transcript:

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

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)

Intro to FreeSurfer Jargon voxel

Intro to FreeSurfer Jargon surface

Intro to FreeSurfer Jargon surface

Intro to FreeSurfer Jargon vertex

Intro to FreeSurfer Jargon vertex Volume = Surface Area x Thickness

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

Recon

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

Cortical vs. Subcortical GM coronal sagittal subcortical gmcortical gm

Cortical vs. Subcortical GM coronal sagittal subcortical gm

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