Function-Structure Integration in FreeSurfer
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1 Function-Structure Integration in FreeSurfer
2 Outline Function-Structure Integration Function-Structure Registration in FreeSurfer fmri Analysis Preprocessing First-Level Analysis Higher-Level (Group) Analysis Correction for Multiple Comparisons Data Hierarchies FreeSurfer Functional Analysis STream (FSFAST) Tutorial Demos
3 Function-Structure Integration Viewing Functional Maps on Structural Volume, Surface Inter-Subject Registration Region of Interest (ROI) Analysis Retinotopy Structural-Functional Covariates Eg, use thickness at a voxels as covariate Voxel-wise design matrices
4 FreeSurfer Registration FreeSurfer Subject-Specific Volumes Surfaces Thickness ROIs Registration Your Data/Software fmri (FSL, SPM, ) DTI PET EEG/MEG Registration Matrix Affine 4x4 As many as 12 DOF (usually 6) Text file
5 Registration FreeSurfer Anatomical (orig) Template Functional Note: Registering the template functional volume to the anatomical volume is sufficient to register the template to the surface.
6 Manual Registration tkregister2 Visually inspect registration Manually edit registration (6 DOF) Cf Manual Talairach registration tkregister2 --help
7 Tips Rigid = 6 DOF = No stretching Use CSF to get a sense of where the folds are Avoid using B0 distortion regions Avoid using ventricles Warning about edge of the brain Same Subject, Left-Right Flips
8 Command-line Tools Automatic Registration: fslregister help spmregister help reg-feat2anat help } Manual Registration: tkregister2 --help Transformations: mri_vol2surf --help mri_vol2vol --help mri_label2vol --help mri_surf2vol --help FreeSurfer Scripts
9 Sampling on the Surface Pial White/Gray Pial Half Way Average White/Gray Projection Fraction --projfrac 0.5
10 Sampling on the Surface
11 fmri Analysis Pipeline Overview Subject 1 First Level Design HRF, Nuisance, Contrasts Registration Higher Level Design Group Model Group Contrasts Subject 2 Convert/Import (Hierarchy) Convert/Import (Hierarchy) Preprocess MC, STC, Smth Preprocess MC, STC, Smth Fit First Level GLM, Compute Contrasts Fit First Level GLM, Compute Contrasts Resample to Common Space Resample to Common Space HRF Amp HRF Var Fit Higher Level GLM RFx,WRFx,FFx Compute Contrasts Correct for Multiple Comparisons SPM AFNI FSL Brain Voy FSFAST Registration
12 fmri Preprocessing Stages Motion Correction Slice-timing Correction (Interleaved vs Seq) B0 Distortion Correction Intensity Normalization: 4D or 3D? Masking zeroing non-brain Resampling to Common Space Spatial Smoothing 3D or 2D? Temporal Filtering is NOT Preprocessing!
13 Reasons for Smoothing Improve CNR/SNR Reduce interpolation effects Make statistics more valid (GRF) Improve inter-subject registration Improve function-surface registration
14 Effects of Smoothing No Smoothing FWHM = 5mm
15 Effects of Smoothing
16 First Level Design and Analysis First-Level = First Standard Deviation First-Level Design Event Definition and HRF Specification Nuisance Regressors Temporal Filtering Temporal Whitening First-Level Contrasts Univariate (t) Pass up to next level Multivariate (F) Analysis (Voxel-wise = Massively Univariate ) Contrasts of HRF Amplitudes Variances of the Contrasts
17 First Level Design: HRF Shapes Block 0s Block 10s SPM FSL FSFAST Block 20s Block 30s
18 Stimulus Schedule/FSFAST Paradigm File Codes Stimulus Schedule (and Weight) Four Columns Onset Time (Since Acq of 1st Saved Volume) Stimulus Code (0, 1, 2,3 ) Stumulus Duration Stimulus Weight (default is 1) Any other columns ignored Simple Text File Code 0 Always Fixation/NULL
19 First-Level Design Matrix Task convolved with HRF Polynomial (0-2) Nuisance Regressors MC Parameters reduced from 6 to 3 FIR
20 Higher-Level (Group) Analysis Higher-Level Design Groups and covriates Contrasts Analysis Method Random Effects (RFx, OLS = ordinary least squares) Weighted Random Effects (WRFx, WLS=weighted least squares) Mixed Effects Fixed Effects (FFx) Correction for Multiple Comparisons Clustering (GRF, Monte Carlo, Permutation)
21 Group Effect Models Random Effects (RFx, OLS; WRFx, WLS) Does effect exist in the general population that my subjects were drawn from? Weighted weight each subject by 1/First Level Noise Fixed Effects (FFx) Does effect exist within the group of subjects that I am studying? Like having one subject scanned multiple times. Mixed Effects use First Level (within-subject) Noise AND between-subject noise to do better weighting.
22 One-Sample Group Mean (OSGM) No groups, No Covariates Does average = 0? One-sample t-test Group Design Matrix: Vector of All 1s
23 FS-FAST Directory Hierarchy Study/Project analysis1 Session 1 Session 2 Session 3 Configuration bold subjectname Functional Subdirectory (FSD) masks brain.nii paradigm file f.nii (raw data) fmc.nii (motion corrected) register.dat beta.nii X.mat meanfunc.nii rvar.nii analysis1 contrast1 analysis2 contrast2 sig.nii ces.nii cesvar.nii Use unpacksdcmdir to import Session in Siemens dicom to FS-FAST.
24 FS-FAST Tutorial Data - fbirn 5 Subjects 4 Runs Each (TR=3, 85TP) Sensory Motor Task 15 sec Blocks 9 OFF 8 ON Code Odd and Even Separately Test Odd vs Even surfer.nmr.mgh.harvard.edu/fswiki/fsfasttutorial
25 FS-FAST Tutorial Exercises Data setup Import in to hierarchy Create paradigm files Link to FreeSurfer Anatomical Analysis Viewing Functional Results in TkMedit/TkSurfer Preprocessing MC and Smoothing Registration automated and manual First Level Design and Contrasts: Gamma, Finite Impulse Response (FIR) First Level Analysis Visualization volume and surface Group Level Analysis One-Sample Group Mean (OSGM) QA RFx, WRFx, FFx Volume (Talairach) and Surface
26 FS-FAST Tutorial Exercises Four main directories at various levels of processing in $FSFTUTDIR: 1. fb1-raw raw data, nifti format, unorganized 2. fb1-raw-study raw data organized in FSFAST hierarchy 3. fb1-preproc-study preprocessed data 4. fb1-analysis-study fully analyzed 1. First-level Analyses 2. Group Analyses in Tal and Surf You don t necessarily need to run any processing can just run visualization. Start Terminal firefox& surfer.nmr.mgh.harvard.edu/fswiki/fsfasttutorial
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