Free Surfer Introduction Outline What is Free Surfer

Free. Surfer Introduction

Outline • What is Free. Surfer? • What are Surfaces Good For Anyway? • Inferring Microstructural Features • Longitudinal Analysis • DWI/Tractography • f. MRI

What is Free. Surfer? • Neuroimaging analysis software package • Fully Characterizes anatomy • Cortex – thickness, folding patterns, ROIs • Longitudinal • Surface-based Inter-subject Registration • Multi-modal integration • DWI/Tractography & f. MRI (task, rest, retinotopy)

What is Free. Surfer? Total # licenses distributed as of Halloween, 2017 (over 39, 000 by Feb, 2019)

Outline • What is Free. Surfer? • What are Surfaces Good For Anyway? • Inferring Microstructural Features • Longitudinal Analysis • DWI/Tractography • f. MRI

Surfaces: White and Pial

Cortical Thickness • Distance between white and pial surfaces • One value per vertex white/gray surface lh. thickness, rh. thickness pial surface

Surface Flattening – Whole Hemisphere central anterior sylvian Inflated surface with cuts posterior superior temporal Metrically optimal flat map calcarine

Retinotopy Field Sign Maps • Changes in orientation between V 1, V 2, etc • Function follows the surface • Pattern is lost in the volume but clear on the surface From (Sereno et al, 1995, Science).

A Surface-Based Registration Common space for group analysis (like Talairach) “fsaverage”

Outline • A Brief History of Free. Surfer • What are Surfaces Good For Anyway? • Inferring Microstructural Locations • Longitudinal Analysis • DWI/Tractography • f. MRI

Surface-based Registration Performance Brodmann, 1909

Motivation To a large degree, function follows the folding patterns. So if you align the folding patterns between two subjects you will align the function. 56

Predicting Brodmann Areas: Talairach Coordinates 10 subjects overlap 1 subject overlap BA 17 (V 1) (Amunts et al, 2000, 2004) BA 18 (V 2) BA 44 (Broca’s) BA 45 (Broca’s)

Predicting Brodmann Areas from Folding Patterns BA 17 (V 1) 0% BA 44 BA 18 (V 2) 100% Overlap BA 45 Fischl, et al, 2007. Thanks to Katrin Amunts, Karl Zilles and Hartmut Mohlberg for the data, and to Niranjini Rajendran and Evelina Busa for the analysis.

Automatic Gyral Segmentation Precentral Gyrus Postcentral Gyrus Based on individual’s folding patterns Superior Temporal Gyrus

Volume Analysis: Automatic Individualized Segmentation Surface-based coordinate system/registration appropriate for cortex but not for thalamus, ventricular system, basal ganglia, etc… Anatomy is extremely variable – measuring the variance and accounting for it is critical (more in the individual subject talk)!

Volumetric Segmentation (aseg) Cortex White Matter Lateral Ventricle Thalamus Caudate Pallidum Hippocampus Not Shown: Nucleus Accumbens Putamen Amygdala

Volume Differences Predictive of AD Lateral Ventricular Volume (Percent of Brain) Healthy Did NOT convert Did convert Probable AD Data courtesy of Drs Marilyn Albert and Ron Killiany

Combined Segmentation aseg aparc wmparc Nearest Cortical Label to point in white matter

Ex vivo MRI of hippocampal subfields Resolution as high as 0. 1 mm isotropic Allows precise manual tracing of hippocampal subfields. The delineation only relies on geometry for subdividing the CA. Joint work with J. Eugenio Iglesias, Koen van Leemput and Jean Augustinack

Outline • A Brief History of Free. Surfer • What are Surfaces Good For Anyway? • Inferring Microstructural Locations • Longitudinal Analysis • DWI/Tractography • f. MRI

Robust Registration Target Reuter et al, 2010 Neuro. Image Target

Robust Registration Registered Src correlation ratio Reuter et al, 2010 Neuro. Image Registered Src Robust

Outline • A Brief History of Free. Surfer • What are Surfaces Good For Anyway? • Inferring Microstructural Locations • Longitudinal Analysis • DWI/Tractography • f. MRI

Tractography with TRACULA (TRActs Constrained by the Underlying Anatomy) • Completely automated modeling of 18 major fascicles • Uses prior probabilistic information on the anatomical structures that each fascicle goes through or next to Collaboration with Anastasia Yendiki, Lilla Zöllei, Saad Jbabdi, Tim Behrens and Jean Augustinack

Outline • A Brief History of Free. Surfer • What are Surfaces Good For Anyway? • Inferring Microstructural Locations • Longitudinal Analysis • DWI/Tractography • f. MRI

Visual/Auditory/Motor Activation Paradigm 15 sec ‘ON’, 15 sec ‘OFF’ • Flickering Checkerboard • Auditory Tone • Finger Tapping 33

On-vs-Off SPMs +3% 0% -3% Contrast Amplitude CON, COPE, CES Contrast Amplitude Variance Significance t-Map (p, z, F) (Error Bars) (Thresholded p<. 01) VARCOPE, CESVAR 34

Sampling on the Surface 15 sec ‘ON’, 15 sec ‘OFF’ • Flickering Checkerboard • Auditory Tone • Finger Tapping

Group f. MRI Analysis: Volume vs Surface Affine registration to MNI 305 5 mm volume smoothing vs. 10 mm surface smoothing

What Is Free. Surfer? Inflation Surface Mesh E D Group Template Surface ROI J Curvature C Sphere F Individual T 1 I Spatial Normalization A A Surface Extraction Thickness B G Deformation Field H 2 mm 4 mm Apply Deformation Volume ROI O Statistical Map N M p<. 01 Group Analysis L K Smooth p<. 01 Other Subjects Thickness (Group Space)

What is Free. Surfer? • • • Cortical extraction and labeling Subcortical Segmentation Surface-based Inter-subject Registration Fully automated Multi-modal integration Use Free. Surfer Be Happy

Search for Answers

The Free. Surfer Course will resume shortly… We’ll begin the next scheduled talk on the hour. In the meantime, if you have any questions for the presenter that weren’t answered you can find a list of talks presenters and their contact information at this website: https: //surfer. nmr. mgh. harvard. edu/fswiki/Teach. Yo urself. Free. Surfer