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Intro to FreeSurfer Jargon

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). Intro to FreeSurfer Jargon. voxel. Intro to FreeSurfer Jargon.

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Intro to FreeSurfer Jargon

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  1. Intro to FreeSurfer Jargon

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

  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. What FreeSurfer Does… FreeSurfer creates computerized models of the brain from MRI data. Input: T1-weighted (MPRAGE) 1mm3 resolution (.dcm) Output: Segmented & parcellated conformed volume (.mgz)

  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

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

  15. Registration • Goal: • to find a common coordinate system for the input data sets • Examples: • comparing different MRI images of the same individual (longitudinal scans, diffusion vs functional scans) • comparing MRI images of different individuals

  16. Inter-subject, uni-modal example target subject flirt 6 DOF flirt 9 DOF flirt 12 DOF

  17. target subject Flirt 9 DOF Flirt 12 DOF Flirt 6 DOF Linear registration: 6, 9, 12 DOF

  18. Linear registration: 6, 9, 12 DOF Flirt 12 DOF Flirt 6 DOF target Flirt 9 DOF subject

  19. Flirt 6 DOF Flirt 9 DOF target subject Linear registration: 6, 9, 12 DOF Flirt 12 DOF

  20. Intra-subject, multi-modal example before spatial alignment after spatial alignment

  21. before spatial alignment after spatial alignment

  22. before spatial alignment after spatial alignment

  23. Inter-subject non-linear example target CVS reg

  24. Some registration vocabulary • Input datasets: • Fixed / template / target • Moving / subject • Transformation models • rigid • affine • nonlinear • Objective / similarity functions • Applying the results • deform, morph, resample, transform • Interpolation types • (tri)linear • nearest neighbor

  25. FreeSurfer Questions Search for terms and answers to all your questions in the Glossary, FAQ, or FreeSurfer Mailing List Archives

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