data processing & analysis of resting-state fmri chao-gan yan, ph.d. 严超赣 [email protected]...
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Data Processing & Analysis of Resting-State fMRI
Chao-Gan YAN, Ph.D.严超赣
[email protected]://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 [email protected]: 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!