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Data Processing & Analysis of Resting-State fMRI

Data Processing & Analysis of Resting-State fMRI. Chao-Gan YAN, Ph.D. 严超赣 y cg.yan@gmail.com http:// rfmri.org Research Scientist The Nathan Kline Institute for Psychiatric Research Research Assistant Professor Department of Child and Adolescent Psychiatry /

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Data Processing & Analysis of Resting-State fMRI

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  1. Data Processing & Analysis of Resting-State fMRI Chao-Gan YAN, Ph.D. 严超赣 ycg.yan@gmail.com http://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

  2. Outline • Overview • Data Preparation • Preprocessing • R-fMRI measures Calculation • Quality Control • Statistical Analysis • Results Viewing 2

  3. DPARSF (Yan and Zang, 2010) 3

  4. Data Processing Assistant for Resting-State fMRI (DPARSF) Yan and Zang, 2010. Front SystNeurosci. http://rfmri.org/DPARSF 4

  5. DPABI: a toolbox for Data Processing & Analysis of Brain Imaging License: GNU GPL Chao-Gan Yan Programmer Initiator Xin-Di Wang Programmer http://rfmri.org/dpabi http://dpabi.org 5

  6. Outline • Overview • Data Preparation • Preprocessing • R-fMRI measures Calculation • Quality Control • Statistical Analysis • Results Viewing 6

  7. Data Organization • ProcessingDemoData.zip • FunRaw • Sub_001 • Sub_002 • Sub_003 • T1Raw • Sub_001 • Sub_002 • Sub_003 Functional DICOM data Structural DICOM data http://rfmri.org/DemoData 7

  8. Data Organization • ProcessingDemoData.zip • FunImg • Sub_001 • Sub_002 • Sub_003 • T1Img • Sub_001 • Sub_002 • Sub_003 Functional NIfTI data (.nii.gz., .nii or .img) Structural NIfTI data (.nii.gz., .nii or .img) 8

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  11. Outline • Overview • Data Preparation • Preprocessing • R-fMRI measures Calculation • Quality Control • Statistical Analysis • Results Viewing 11

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  13. Preprocessing Working Dir where stored Starting Directory (e.g., FunRaw) Detected participants 13

  14. Preprocessing Detected participants 14

  15. Preprocessing Number of time points (if 0, detect automatically) TR (if 0, detect from NIfTI header) Template Parameters 15

  16. Resting State fMRI Data Processing Template Parameters 16

  17. What’s new? 17

  18. Reorient and Quality control 18

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  20. Automaskgeneration For checking EPI coverage and generating group mask FunImgAR/Sub_001 Masks/AutoMasks/ 20

  21. Brain extraction(Skullstrip) For better coregistration 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. 21

  22. Bet & Coregistration T1ImgCoreg/Sub_001 Segment bet RealignParameter/Sub_001/mean*.nii T1Img/Sub_001 Apply Coregister RealignParameter/Sub_001/Bet_mean*.nii T1ImgBet/Sub_001 22

  23. Nuisance regression 23

  24. Nuisance Regression • 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 24

  25. Outline • Overview • Data Preparation • Preprocessing • R-fMRI measures Calculation • Quality Control • Statistical Analysis • Results Viewing 25

  26. R-fMRI measures Calculation 26

  27. Outline • Overview • Data Preparation • Preprocessing • R-fMRI measures Calculation • Quality Control • Statistical Analysis • Results Viewing 27

  28. 28

  29. Quality Control 29

  30. Quality Control 30

  31. Quality Control 31

  32. Quality Control 32

  33. Quality Control 33

  34. Quality Control 34

  35. Quality Control 35

  36. Quality Control 36

  37. Quality Control 37

  38. Quality Control 38

  39. Quality Control 39

  40. Quality Control 40

  41. Quality Control This mask is very important for group statistical analysis!!! 41

  42. Quality Control 42

  43. Quality Control 43

  44. Quality Control 44

  45. Quality Control • 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 registrationwere 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 Jenkinsongreater than 2*SD above the group mean motion (threshold: 0.192) were excluded Yan et al., 2013, Neuroimage 45

  46. Outline • Overview • Data Preparation • Preprocessing • R-fMRI measures Calculation • Quality Control • Statistical Analysis • Results Viewing 46

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  48. Statistical Analysis 48

  49. Statistical Analysis {DPABI_Dir}/StatisticalAnalysis/y_GroupAnalysis_Image.m 49

  50. Attention!!! 50

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