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Intro to FreeSurfer Jargon

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.

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Intro to FreeSurfer Jargon

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  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) 1mm3 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.mgz T1.mgz brainmask.mgz wm.mgz filled.mgz (Subcortical Mass)

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

  12. Cortical vs. Subcortical GM subcortical gm sagittal coronal

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

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