data processing & analysis of resting-state fmri chao-gan yan, ph.d. 严超赣 ycg.yan@gmail.com...

Data Processing & Analysis of Resting-State fMRI

Chao-Gan YAN, Ph.D.严超赣

ycg.yan@gmail.comhttp://rfmri.org

Research Scientist The Nathan Kline Institute for Psychiatric Research

Research Assistant Professor Department of Child and Adolescent Psychiatry /

NYU Langone Medical Center Child Study Center, New York University

Outline• Overview

• Data Preparation

• Preprocessing

• R-fMRI measures Calculation

• Quality Control

• Statistical Analysis

• Results Viewing2

DPARSF

(Yan and Zang, 2010) 3

Data Processing Assistant for Resting-

State fMRI (DPARSF)

Yan and Zang, 2010. Front Syst Neurosci.

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http://rfmri.org/DPARSF

DPABI: a toolbox for Data Processing & Analysis of Brain

Imaging

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http://rfmri.org/dpabi

http://dpabi.org

License: GNU GPL

Chao-Gan Yan Programmer

Initiator

Xin-Di Wang Programmer

Outline• Overview

• Data Preparation

• Preprocessing

• R-fMRI measures Calculation

• Quality Control

• Statistical Analysis

• Results Viewing6

Data Organization

ProcessingDemoData.zip

FunRawSub_001

Sub_002

Sub_003

T1RawSub_001

Sub_002

Sub_003

Functional DICOM data

Structural DICOM data

http://rfmri.org/DemoData7

Data Organization

ProcessingDemoData.zip

FunImgSub_001

Sub_002

Sub_003

T1ImgSub_001

Sub_002

Sub_003

Functional NIfTI data (.nii.gz., .nii or .img)

Structural NIfTI data (.nii.gz., .nii or .img)

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Outline• Overview

• Data Preparation

• Preprocessing

• R-fMRI measures Calculation

• Quality Control

• Statistical Analysis

• Results Viewing11

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Preprocessing

Working Dir where stored Starting Directory (e.g.,

FunRaw)Detected participants

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Detected participants

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Preprocessing

Number of time points(if 0, detect

automatically)TR(if 0, detect from

NIfTI header)

Template Parameters

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Preprocessing

Resting State fMRI Data Processing

Template Parameters

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What’s new?

Reorient and Quality control

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Automask generation

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For checking EPI coverage and generating group mask

FunImgAR/Sub_001

Masks/AutoMasks/

Brain extraction(Skullstrip)

For Linux and Mac: Need to install FSL.

For Windows:Thanks to Chris Rorden's compiled version of bet in MRIcroN, our modified version can work on NIfTI images directly.

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For better coregistration

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T1Img/Sub_001

T1ImgBet/Sub_001

RealignParameter/Sub_001/mean*.nii

RealignParameter/Sub_001/Bet_mean*.nii

bet

Coregister

Apply

T1ImgCoreg/Sub_001

Segment

Bet & Coregistration

Nuisance regression

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Nuisance Regression

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Mask based on segmentation or SPM apriori CompCor or mean [note: for CompCor, detrend (demean) and variance

normalization will be applied before PCA, according to Behzadi et al., 2007] Global Signal based on Automask

Outline• Overview

• Data Preparation

• Preprocessing

• R-fMRI measures Calculation

• Quality Control

• Statistical Analysis

• Results Viewing25

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R-fMRI measures

Calculation

Outline• Overview

• Data Preparation

• Preprocessing

• R-fMRI measures Calculation

• Quality Control

• Statistical Analysis

• Results Viewing27

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Quality Control

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Quality Control

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Quality Control

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Quality Control

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Quality Control

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Quality Control

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Quality Control

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Quality Control

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Quality Control

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Quality Control

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Quality Control

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Quality Control

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Quality Control

This mask is very important for group statistical analysis!!!

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Quality Control

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Quality Control

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Quality Control

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Quality Control

Yan et al., 2013, Neuroimage

Using the visual inspection step within DPARSF, subjects showing severe head motion in the T1 image and subjects showing extremely poor coverage in the functional images, as well as subjects showing bad registration were excluded

Subjects with overlap with the group mask (voxels present at least 90% of the participants) less than 2*SD under the group mean overlap (threshold: 92.2%) were excluded

Subjects with motion (Mean FD Jenkinson greater than 2*SD above the group mean motion (threshold: 0.192) were excluded

Outline• Overview

• Data Preparation

• Preprocessing

• R-fMRI measures Calculation

• Quality Control

• Statistical Analysis

• Results Viewing46

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Statistical Analysis

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Statistical Analysis

{DPABI_Dir}/StatisticalAnalysis/y_GroupAnalysis_Image.m

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Attention!!!

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Statistical Analysis

{DPABI_Dir}/StatisticalAnalysis/y_GroupAnalysis_Image.m

Smoothness estimation based on the 4D residual is built in this function!!!

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Statistical Analysishttp://rfmri.org/DemoData

{Download}/ProcessingDemoData/StatisticalDemo/AD_MCI_NC/

ALFF: AD – NC Two Sample T Test:

• Applied smooth kernel in preprocessing: [4 4 4]

• Smooth kernel estimated on 4D residual: [6.77 6.88 6.71]

• Smooth kernel estimated on statistical image (T to Z, as in easythresh): [6.90 7.33 6.94]

ReHo: AD – NC Two Sample T Test:

• Applied smooth kernel in preprocessing: [4 4 4]

• Smooth kernel estimated on 4D residual: [8.10 8.50 7.93]

• Smooth kernel estimated on statistical image (T to Z, as in easythresh): [8.33 8.94 8.24]

Thus, only using smooth kernel applied in preprocessing is NOT sufficient!!!

Outline• Overview

• Data Preparation

• Preprocessing

• R-fMRI measures Calculation

• Quality Control

• Statistical Analysis

• Results Viewing53

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Voxel Z > 2.3, Cluster P < 0.05, Two One-Tailed Corrections:

equivalent to

Voxel P < 0.0214, Cluster P < 0.1, Two Tailed.

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Further Help

Further questions:

http://rfmri.org/dpabi

http://dpabi.orgThe R-fMRI Network

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Further Help

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Send emails only to rfmri.org@gmail.com: 1) sending new email means you are posting your personal blogs, 2) replying email means you are posting comments to that topic/blog, 3) then all the other R-fMRI nodes will receive email updates of your posts.

Xin-Di Wang Programmer

Yu-Feng Zang Consultant

Acknowledgments

Nathan Kline Institute

Charles Schroeder

Stan Colcombe

Gary Linn

Mark Klinger

Child Mind Institute

Michael P. Milham

R. Cameron Craddock

Zhen Yang

NYU Child Study Center

F. Xavier Castellanos

Adriana Di Martino

Clare Kelly Chinese Academy of Sciences

Xi-Nian Zuo

Hangzhou Normal University

Yu-Feng Zang

Princeton University

Han Liu

Fudan University

Tian-Ming Qiu

Beijing Normal University

Yong He

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F. Xavier CastellanosNKI/NYU

Charles E. SchroederNKI/Columbia

David A. LeopoldNIMH

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Thanks for your attention!