Intro to Free Surfer Jargon Intro to Free

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Intro to Free. Surfer Jargon

Intro to Free. Surfer Jargon

Intro to Free. Surfer Jargon voxel surface volume vertex surface-based recon cortical, subcortical parcellation/segmentation

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

Intro to Free. Surfer Jargon voxel

Intro to Free. Surfer Jargon voxel

Intro to Free. Surfer Jargon surface

Intro to Free. Surfer Jargon surface

Intro to Free. Surfer Jargon surface

Intro to Free. Surfer Jargon surface

Intro to Free. Surfer Jargon vertex

Intro to Free. Surfer Jargon vertex

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

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

Recon

Recon

Volumes orig. mgz T 1. mgz brainmask. mgz wm. mgz filled. mgz (Subcortical Mass)

Volumes orig. mgz T 1. mgz brainmask. mgz wm. mgz filled. mgz (Subcortical Mass)

Cortical vs. Subcortical GM cortical gm subcortical gm sagittal coronal

Cortical vs. Subcortical GM cortical gm subcortical gm sagittal coronal

Cortical vs. Subcortical GM subcortical gm sagittal coronal

Cortical vs. Subcortical GM subcortical gm sagittal coronal

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

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

Intro to Free. Surfer Jargon voxel surface volume vertex surface-based recon cortical, subcortical parcellation/segmentation

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

Free. Surfer Questions Search for terms and answers to all your questions in the

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

What Free. Surfer Does… Free. Surfer creates computerized models of the brain from MRI

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

Registration Goal: to find a common coordinate system for the input data sets Examples:

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

Inter-subject, uni-modal example target Flirt 612/13/2011 DOF subject Flirt 9 DOF Flirt 12 DOF

Inter-subject, uni-modal example target Flirt 612/13/2011 DOF subject Flirt 9 DOF Flirt 12 DOF

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

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

Linear registration: 6, 9, 12 DOF Flirt 6 dof 9 dof target subject Flirt

Linear registration: 6, 9, 12 DOF Flirt 6 dof 9 dof target subject Flirt 12 DOF

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

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

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

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

before spatial alignment after spatial alignment

before spatial alignment after spatial alignment

before spatial alignment after spatial alignment

before spatial alignment after spatial alignment

Inter-subject non-linear example target CVS reg

Inter-subject non-linear example target CVS reg

Some registration vocabulary • Input datasets: – Fixed / template / target – Moving

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