Intro to Free Surfer Jargon voxel surface volume

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

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

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 subcortical gm sagittal coronal

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

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

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

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 Flirt 6 dof 9 dof target subject Flirt

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

Intra-subject, multi-modal example before spatial alignment 12/13/2011 after spatial alignment

before spatial alignment after spatial alignment 12/13/2011

before spatial alignment 12/13/2011 after spatial alignment

Inter-subject non-linear example target 12/13/2011 CVS reg

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

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

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)

Intro to Free. Surfer Jargon voxel

Intro to Free. Surfer Jargon surface

Intro to Free. Surfer Jargon vertex

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

Recon

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 subcortical gm sagittal coronal

Parcellation vs. Segmentation (cortical) parcellation (subcortical) 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 Glossary, FAQ, or Free. Surfer Mailing List Archives

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 12/13/2011

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 12/13/2011

Linear registration: 6, 9, 12 DOF Flirt 6 dof 9 dof target subject Flirt 12 DOF 12/13/2011

Linear registration: 6, 9, 12 DOF Flirt 6 DOF 9 target subject Flirt 12 DOF 12/13/2011

Intra-subject, multi-modal example before spatial alignment 12/13/2011 after spatial alignment

before spatial alignment after spatial alignment 12/13/2011

before spatial alignment 12/13/2011 after spatial alignment

Inter-subject non-linear example target 12/13/2011 CVS reg

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 12/13/2011