1. Data Processing & Analysis of Resting-State fMRI
Chao-Gan YAN, Ph.D.
严超赣
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, Front Syst Neurosci. 4

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

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

7. Data Organization ProcessingDemoData.zip FunRaw T1Raw
Sub_001
Sub_002
Sub_003
T1Raw
Functional DICOM data
Structural DICOM data 7

8. Data Organization ProcessingDemoData.zip FunImg T1Img
Sub_001
Sub_002
Sub_003
T1Img
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

12. 12

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

14. Detected participants
Preprocessing
Detected participants 14

15. (if 0, detect automatically) (if 0, detect from NIfTI header)
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 control18

19. 19

20. For checking EPI coverage and generating group mask
Automask generation
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 Segment bet Apply Coregister T1ImgCoreg/Sub_001
T1Img/Sub_001
RealignParameter/Sub_001/mean*.nii
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 Calculation26

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. This mask is very important for group statistical analysis!!!
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 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
Yan et al., 2013, Neuroimage 45

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

47. 47

48. Statistical Analysis 48

49. {DPABI_Dir}/StatisticalAnalysis/y_GroupAnalysis_Image.m49

50. Attention!!! 50

51. {DPABI_Dir}/StatisticalAnalysis/y_GroupAnalysis_Image.m
Smoothness estimation based on the 4D residual is built in this function!!! 51

52. {Download}/ProcessingDemoData/StatisticalDemo/AD_MCI_NC/
Statistical Analysis
{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: [ ]
Smooth kernel estimated on statistical image (T to Z, as in easythresh): [ ]
ReHo: AD – NC Two Sample T Test:
Smooth kernel estimated on 4D residual: [ ]
Smooth kernel estimated on statistical image (T to Z, as in easythresh): [ ]
Thus, only using smooth kernel applied in preprocessing is NOT sufficient!!! 52

53. Outline Overview Data Preparation Preprocessing
R-fMRI measures Calculation
Quality Control
Statistical Analysis
Results Viewing 53

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61. Voxel Z > 2.3, Cluster P < 0.05, Two One-Tailed Corrections:
equivalent to
Voxel P < , Cluster P < 0.1, Two Tailed. 61

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68. Further Help Further questions: http://rfmri.org/dpabi
The R-fMRI Network 68 68

69. Further Help 69 69

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72. Send emails only to rfmri. org@gmail
Send s only to 1) sending new means you are posting your personal blogs, 2) replying means you are posting comments to that topic/blog, 3) then all the other R-fMRI nodes will receive updates of your posts. 72 72

73. Xin-Di Wang Programmer Yu-Feng Zang Consultant

74. Acknowledgments Nathan Kline Institute Charles Schroeder
Stan Colcombe
Gary Linn
Mark Klinger
Hangzhou Normal University Yu-Feng Zang
Beijing Normal University
Yong He
NYU Child Study Center
F. Xavier Castellanos
Adriana Di Martino
Clare Kelly
Fudan University
Tian-Ming Qiu
Chinese Academy of Sciences Xi-Nian Zuo
Different Axis!!!
Child Mind Institute
Michael P. Milham
R. Cameron Craddock
Zhen Yang
Princeton University
Han Liu

75. Advertisement Charles E. Schroeder F. Xavier Castellanos NKI/Columbia
NKI/NYU
Charles E. Schroeder
NKI/Columbia
David A. Leopold
NIMH 75

76. Thanks for your attention!76