Data Processing of Resting-State fMRI (Part 1)
-
Upload
harding-banks -
Category
Documents
-
view
44 -
download
2
description
Transcript of Data Processing of Resting-State fMRI (Part 1)
![Page 1: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/1.jpg)
1
YAN Chao-Gan严超赣Ph. D
State Key Laboratory of Cognitive Neuroscience and Learning,
Beijing Normal University, China
Data Processing of Resting-State fMRI
(Part 1)
![Page 2: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/2.jpg)
2
Outline
• Overview
• Data Preparation
• Preprocess
• ReHo, ALFF, fALFF Calculation
• Functional Connectivity
• Utilities
![Page 3: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/3.jpg)
3
Overview
Based on Matlab, SPM, REST, MRIcroN’s dcm2nii
![Page 4: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/4.jpg)
4
Setup
E:\ITraWork\100402Trainning\Softs\DPARSF_V1.0_100201
NO Chinese character or space in the path.
![Page 5: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/5.jpg)
5
DPARSF's standard procedure
Convert DICOM files to NIFTI images. Remove First 10 Time Points. Slice Timing. Realign. Normalize. Smooth (optional). Detrend. Filter. Calculate ReHo, ALFF, fALFF (optional). Regress out the Covariables (optional). Calculate Functional Connectivity (optional). Extract AAL or ROI time courses for further analysis (optional).
![Page 6: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/6.jpg)
6
Outline
• Overview
• Data Preparation
• Preprocess
• ReHo, ALFF, fALFF Calculation
• Functional Connectivity
• Utilities
![Page 7: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/7.jpg)
7
Data preparation
Arrange the information of the subjects
![Page 8: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/8.jpg)
8
Data preparation
Information of subjects
![Page 9: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/9.jpg)
9
Data preparation
Arrange the information of the subjects
Arrange the MRI data of the subjects
Functional MRI data
Structural MRI data
DTI data
![Page 10: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/10.jpg)
10
被试信息整理
原始数据整理
![Page 11: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/11.jpg)
11
Sort DICOM data
![Page 12: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/12.jpg)
12
IMAdcmnone
![Page 13: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/13.jpg)
13
Data preparation
Arrange each subject's fMRI DICOM images in one directory, and th
en put them in "FunRaw" directory under the working directory.
Subject 1’s DICOM filesFunRaw directory, please name as thisSubject 1’s directoryWorking directory
![Page 14: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/14.jpg)
14
Data preparation
Arrange each subject's T1 DICOM images in one directory, and then
put them in “T1Raw" directory under the working directory.
Subject 1’s DICOM filesT1Raw directory, please name as thisSubject 1’s directoryWorking directory
![Page 15: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/15.jpg)
15
Data preparation
Set the parameters in DPARSF
Set the working directorySet the time points (volumes)The detected subjects’ IDSet the TR
![Page 16: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/16.jpg)
16
Outline
• Overview
• Data Preparation
• Preprocess
• ReHo, ALFF, fALFF Calculation
• Functional Connectivity
• Utilities
![Page 17: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/17.jpg)
17
Preprocess
• DICOM -> NIFTI
• Remove First 10 Time Points
• Slice Timing
• Realign
• Normalize
• Smooth
• Detrend
• Filter: 0.01-0.08
![Page 18: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/18.jpg)
18
DICOM->NIFTI
MRIcroN’s dcm2niigui
SPM5’s DICOM Import
![Page 19: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/19.jpg)
19
DICOM->NIFTI
DPARSF
![Page 20: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/20.jpg)
20
Preprocess
• DICOM -> NIFTI
• Remove First 10 Time Points
• Slice Timing
• Realign
• Normalize
• Smooth
• Detrend
• Filter: 0.01-0.08
![Page 21: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/21.jpg)
21
Remove First 10 Time Points
DPARSF
![Page 22: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/22.jpg)
22
Preprocess
• DICOM -> NIFTI
• Remove First 10 Time Points
• Slice Timing
• Realign
• Normalize
• Smooth
• Detrend
• Filter: 0.01-0.08
![Page 23: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/23.jpg)
23
Slice Timing
Why?
![Page 24: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/24.jpg)
24
Slice Timing
Why?
Huettel et al., 2004
![Page 25: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/25.jpg)
25
Slice Timing
1:2:25,2:2:24252 2-(2/25)25
![Page 26: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/26.jpg)
26
Slice Timing
![Page 27: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/27.jpg)
27
Slice Timing
DPARSF
1:2:25,2:2:24
![Page 28: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/28.jpg)
28
Slice TimingIf you start with NIFTI images (.hdr/.img pairs) before slice timing,
you need to arrange each subject's fMRI NIFTI images in one
directory, and then put them in "FunImg" directory under the
working directory.
FunImg directory, please name as this
![Page 29: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/29.jpg)
29
Preprocess
• DICOM -> NIFTI
• Remove First 10 Time Points
• Slice Timing
• Realign
• Normalize
• Smooth
• Detrend
• Filter: 0.01-0.08
![Page 30: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/30.jpg)
30
Realign
Why?
![Page 31: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/31.jpg)
31
Realign
![Page 32: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/32.jpg)
32
Realign
DPARSF
![Page 33: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/33.jpg)
33
Realign
Check head motion:
Excluding Criteria: 2.5mm and 2.5 degreeNone
Excluding Criteria: 2.0mm and 2.0 degreeSub_013
Excluding Criteria: 1.5mm and 1.5 degreeSub_013
Excluding Criteria: 1.0mm and 1.0 degreeSub_007Sub_012Sub_013Sub_017Sub_018
![Page 34: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/34.jpg)
34
Preprocess
• DICOM -> NIFTI
• Remove First 10 Time Points
• Slice Timing
• Realign
• Normalize
• Smooth
• Detrend
• Filter: 0.01-0.08
![Page 35: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/35.jpg)
35
Normalize
Why?
Huettel et al., 2004
![Page 36: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/36.jpg)
36
Normalize
Methods:
I. Normalize by using EPI templates
II. Normalize by using T1 image unif
ied segmentation
![Page 37: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/37.jpg)
37
mean_name.img
r*.img
EPI.nii
-90 -126 -72; 90 90 1083 3 3
![Page 38: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/38.jpg)
38
Normalize I
![Page 39: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/39.jpg)
39
Normalize
Methods:
• Normalize by using EPI templates• Normalize by using T1 image unifi
ed segmentation
Structural image was coregistered to the mean functional image after the motion correction
The transformed structural image was then segmented into gray matter, white matter, cerebrospinal fluid by using a unified segmentation algorithm
Normalize: the motion corrected functional volumes were spatially normalized to the MNI space using the normalization parameters estimated during unified segmentation (*_seg_sn.mat)
![Page 40: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/40.jpg)
40
Normalize II: Coregister
mean_name.img T1.img
![Page 41: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/41.jpg)
41
Normalize II:
T1_Coregisted.img
Light Clean
ICBM space template
– East Asian brains
– European brains
![Page 42: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/42.jpg)
42
Normalize II:Segment
New “Segment”
![Page 43: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/43.jpg)
43
New “Normalize: Write”
New “Subject”
name_seg_sn.mat
-90 -126 -72; 90 90 1083 3 3
r*.img
Normalize II:
![Page 44: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/44.jpg)
44
Normalize
DPARSF
T1 Data should be a
rranged in T1Raw
or T1Img (co*.img)
directory!
Delete files before n
ormalization:
raw NIfTI files, slic
e timing files, realig
n files.
![Page 45: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/45.jpg)
45
Normalize
Check Normalization with DPARSF{WROKDIR}\PicturesForChkNormalization
![Page 46: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/46.jpg)
46
GM in
original
spaceWM in
original
space
GM in
normalized
space
Modulated
GM in
normalized
space
CSF in
original
space
By-Product: VBM
![Page 47: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/47.jpg)
47
Preprocess
• DICOM -> NIFTI
• Remove First 10 Time Points
• Slice Timing
• Realign
• Normalize
• Smooth
• Detrend
• Filter: 0.01-0.08
![Page 48: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/48.jpg)
48
Smooth
Why?
• Reduce the effects of the bad n
ormalization
• …
![Page 49: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/49.jpg)
49
w*.imgFWHM kernel
Smooth
![Page 50: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/50.jpg)
50
Smooth
DPARSF
ALFF, fALFF, Funt
ional Connectivity:
Data with smooth
ReHo:
Data without smoot
h
Without former steps:
Data arranged in Fu
nImgNormalized dir
ectory.
![Page 51: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/51.jpg)
51
Preprocess
• DICOM -> NIFTI
• Remove First 10 Time Points
• Slice Timing
• Realign
• Normalize
• Smooth
• Detrend
• Filter: 0.01-0.08
![Page 52: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/52.jpg)
52
Detrend
![Page 53: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/53.jpg)
53
Preprocess
• DICOM -> NIFTI
• Remove First 10 Time Points
• Slice Timing
• Realign
• Normalize
• Smooth
• Detrend
• Filter: 0.01-0.08
![Page 54: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/54.jpg)
54
滤波
Why? • Low frequency (0.01–0.08 Hz) fluctuations (LF
Fs) of the resting-state fMRI signal were of physi
ological importance. (Biswal et al., 2005)
• LFFs of resting-state fMRI signal were suggeste
d to reflect spontaneous neuronal activity (Logot
hetis et al., 2001; Lu et al., 2007).
Biswal B, Yetkin FZ, Haughton VM, Hyde JS (1995) Functional connectivity in the motor cortex of resting human brain using echo-planar MRI. Magn Reson Med 34: 537–541. Logothetis NK, Pauls J, Augath M, Trinath T, Oeltermann A (2001) Neurophysiological investigation of the basis of the fMRI signal. Nature 412: 150–157. Lu H, Zuo Y, Gu H, Waltz JA, Zhan W, et al. (2007) Synchronized delta oscillations correlate with the resting-state functional MRI signal. Proc Natl Acad Sci U S A 104: 18265–18269.
![Page 55: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/55.jpg)
55
Filter
![Page 56: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/56.jpg)
56
Detrend and Filter
DPARSF
If you want to calcu
late fALFF, please
do not delete the det
rended files
Without former steps:
Data arranged in Fu
nImgNormalized or
FunImgNormalizedS
moothed directory.
![Page 57: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/57.jpg)
57
Outline
• Overview
• Data Preparation
• Preprocess
• ReHo, ALFF, fALFF Calculation
• Functional Connectivity
• Utilities
![Page 58: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/58.jpg)
58
ReHo (Regional Homogeneity)
Note: Please do not smooth your data in preprocessing, just smooth your data after ReHo calculation.
Zang et al., 2004
Zang YF, Jiang TZ, Lu YL, He Y, Tian LX (2004) Regional homogeneity approach to fMRI data analysis. Neuroimage 22: 394–400.
![Page 59: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/59.jpg)
59
ReHo
If the resolution of your data is not 61*61*73, please resample your mask file at first.
![Page 60: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/60.jpg)
60
Choose one of your functional image. e.g. your normalized functional image or image after Detrend and Filter.
Choose the mask file or ROI
definition file. e.g.
BrainMask_05_61x73x61.img Resample Mask
Resample other kind of data
Data Resample
![Page 61: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/61.jpg)
61
Data Resample
![Page 62: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/62.jpg)
62
Data Resample
0 – Nearest Neighbor
1 – Trilinear
2- 2nd degree b-spline
![Page 63: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/63.jpg)
63
Please ensure the
resolution of your
own mask is the
same as your
functional data.
Without former steps:
Data arranged in Fu
nImgNormalizedDet
rendedFiltered
directory.
ReHo
DPARSF
Get the smReHo -1
or mReHo - 1 data f
or one sample T test.
Smooth the mReHo
results. The FWHM
kernel is the same a
s set in the smooth s
tep.
![Page 64: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/64.jpg)
64
Zang et al., 2007
Zang YF, He Y, Zhu CZ, Cao QJ, Sui MQ, et al. (2007) Altered baseline brain activity in children with ADHD revealed by resting-state functional MRI. Brain Dev 29: 83–91.
ALFF(Amplitude of Low
Frequency Fluctuation )
![Page 65: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/65.jpg)
65
fALFF(fractional ALFF )
Zou et al., 2008
Zou QH, Zhu CZ, Yang Y, Zuo XN, Long XY, et al. (2008) An improved approach to detection of amplitude of low-frequency fluctuation (ALFF) for resting-state fMRI: fractional ALFF. J Neurosci Methods 172: 137-141.
PCC: posterior cingulate cortexSC: suprasellar cistern
![Page 66: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/66.jpg)
66
ALFF
fALFF: DO NOT filter!
![Page 67: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/67.jpg)
67
Without former steps:
Data arranged in Fu
nImgNormalizedSmo
othedDetrendedFilte
red
or FunImgNormalize
dSmoothedDetrende
d directory.
Please ensure the
resolution of your
own mask is the
same as your
functional data.
ALFF and fALFF
DPARSF
Get the mALFF - 1
or (mfALFF - 1) da
ta for one sample T
test.
Please DO NOT del
ete the detrended fil
es before filter. DP
ARSF will calculate
d the fALFF based
on data before filter.
![Page 68: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/68.jpg)
68
Outline
• Overview
• Data Preparation
• Preprocess
• ReHo, ALFF, fALFF Calculation
• Functional Connectivity
• Utilities
![Page 69: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/69.jpg)
69
Regress out nuisance covariates
• Head motion parameters: rp_name.txt
• Global mean signal
• White matter signal
• Cerebrospinal fluid signal
![Page 70: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/70.jpg)
70
Extract
Covariates
![Page 71: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/71.jpg)
71
Extract
Covariates
![Page 72: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/72.jpg)
72
Extract
Covariates
![Page 73: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/73.jpg)
73
Extract
Covariates
![Page 74: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/74.jpg)
74
Extract
Covariates
![Page 75: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/75.jpg)
75
Extract
Covariates
Extract one subject’s
Covariates
![Page 76: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/76.jpg)
76
Extract
Covariates
Extract multi subjects’
Covariates
![Page 77: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/77.jpg)
77
Extract
Covariates
![Page 78: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/78.jpg)
78
Extract
Covariates
![Page 79: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/79.jpg)
79
Regress out nuisance Covariates
Extract Covariates• Head motion parameters: rp_name.txt• Global mean signal• White matter signal• Cerebrospinal fluid signal
• Combine the covariates for future using in REST
RPCov=load('rp_name.txt'); BCWCov=load('ROI_FCMap_name.txt'); Cov=[RPCov,BCWCov]; save('Cov.txt', 'Cov', '-ASCII', '-DOUBLE','-TABS');
![Page 80: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/80.jpg)
80
Regress out
Covariates
![Page 81: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/81.jpg)
81
Extract
Covariates CovList.txt:
Covariables_List:X:\Process\Sub3Cov.txtX:\Process\Sub2Cov.txtX:\Process\Sub1Cov.txt
CovList.txt:
![Page 82: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/82.jpg)
82
Without former steps:
Data arranged in Fu
nImgNormalizedDet
rendedFiltered
or FunImgNormalize
dSmoothedDetrende
dFiltered
directory.
rp*.txt
DPARSF
CsfMask_07_61x73
x61.img
BrainMask_05_61x
73x61.img
Regress out nuisance Covariates
WhiteMask_09_61x
73x61.img
![Page 83: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/83.jpg)
83
Without former steps:
Data arranged in Fu
nImgNormalizedDet
rendedFiltered
or FunImgNormalize
dSmoothedDetrende
dFiltered
directory.
DPARSF
Regress out Covariates
![Page 84: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/84.jpg)
84
Regress out
Covariates
![Page 85: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/85.jpg)
85
Please ensure
the resolution
of your ROI
file is the same
as your
functional data.
Regress out
Covariates
![Page 86: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/86.jpg)
86
Functional Conncetivity
Voxel-wise
ROI-wise
r=0.36
![Page 87: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/87.jpg)
87
Voxel-w
ise
![Page 88: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/88.jpg)
88
Voxel-w
ise
Please ensure
the resolution
of your ROI
file is the same
as your
functional data.
SeedList.txt:
Seed_Time_Course_List:X:\Process\Sub3Seed.txtX:\Process\Sub2Seed.txtX:\Process\Sub1Seed.txt
![Page 89: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/89.jpg)
89
Voxel-w
ise
![Page 90: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/90.jpg)
90
Voxel-w
ise
![Page 91: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/91.jpg)
91
Voxel-w
ise
![Page 92: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/92.jpg)
92
Voxel-w
ise
![Page 93: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/93.jpg)
93
Voxel-w
ise
CovList.txt
CovList.txt:
Covariables_List:X:\Process\Sub6Cov.txtX:\Process\Sub5Cov.txtX:\Process\Sub4Cov.txtX:\Process\Sub3Cov.txtX:\Process\Sub2Cov.txtX:\Process\Sub1Cov.txt
![Page 94: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/94.jpg)
94
RO
I-wise
![Page 95: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/95.jpg)
95
RO
I-wise
![Page 96: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/96.jpg)
96
RO
I-wise
CovList.txt
CovList.txt:
Covariables_List:X:\Process\Sub6Cov.txtX:\Process\Sub5Cov.txtX:\Process\Sub4Cov.txtX:\Process\Sub3Cov.txtX:\Process\Sub2Cov.txtX:\Process\Sub1Cov.txt
![Page 97: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/97.jpg)
97
RO
I-wise
![Page 98: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/98.jpg)
98
Without former steps:
Data arranged in Fu
nImgNormalizedDet
rendedFilteredCovre
moved
or FunImgNormalize
dSmoothedDetrende
dFilteredCovremove
d directory.
Please ensure the
resolution of your
own mask is the
same as your
functional data.
Functional Connectivity
DPARSF
![Page 99: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/99.jpg)
99
Fu
nction
al C
onn
ectivity
![Page 100: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/100.jpg)
100
You will get the Voxel-wise
functional connectivity results
of each ROI in {working
directory}\Results\FC:
zROI1FCMap_Sub_001.img
zROI2FCMap_Sub_001.img
For ROI-wise results,
please see Part Utilities:
Extract ROI time courses.
Functional Connectivity
DPARSF
![Page 101: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/101.jpg)
101
Outline
• Overview
• Data Preparation
• Preprocess
• ReHo, ALFF, fALFF Calculation
• Functional Connectivity
• Utilities
![Page 102: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/102.jpg)
102
Without former steps:
Data arranged in Fu
nImgNormalizedDet
rendedFilteredCovre
moved
or FunImgNormalize
dSmoothedDetrende
dFilteredCovremove
d directory.
Extract ROI time courses
DPARSF
![Page 103: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/103.jpg)
103
Extract R
OI tim
e courses
![Page 104: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/104.jpg)
104
Results in {working direcotry}\FunI
mgNormalizedDetrendedFilteredCo
vremoved_RESTdefinedROITC:
Extract ROI time courses
DPARSF
Sub_001_ROITimeCourses.txt: Time courses, each column represent a time
course of one ROI.
Sub_001_ResultCorr.txt: ROI-wise Functional Connectivity
![Page 105: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/105.jpg)
105
Without former steps:
Data arranged in Fu
nImgNormalizedDet
rendedFilteredCovre
moved
or FunImgNormalize
dSmoothedDetrende
dFilteredCovremove
d directory.
Extract AAL time courses
DPARSF
![Page 106: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/106.jpg)
106
Results in {working direcotry}\FunI
mgNormalizedDetrendedFilteredCo
vremoved_AALTC:
Extract AAL time courses
DPARSF
Sub_001_AALTC.mat: Time courses of each AAL region.
![Page 107: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/107.jpg)
107
Normalization by usin
g T1 image segmentati
on: co*.img
Realign without Slice
Timeing: a*.img
Change prefix of Images
DPARSF
![Page 108: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/108.jpg)
108
Normalization by usin
g T1 image segmentati
on: co*.img
Change prefix of Images
DPARSF
aa*.img -> ra*.img
ra
![Page 109: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/109.jpg)
109
Save parameters to
*.mat
Save and Load Parameters
DPARSF
Load parameters
from *.mat
![Page 110: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/110.jpg)
110
www.restfmri.net
Further Help
Further questions:
![Page 111: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/111.jpg)
111
Thanks to
DONG Zhang-YeGUO Xiao-JuanHE YongLONG Xiang-YuSONG Xiao-WeiYAO LiZANG Yu-FengZHANG HanZHU Chao-ZheZOU Qi-HongZUO Xi-Nian……
All the group members!
SPM Team: Wellcome Department of Imaging Neuroscience, UCL
MRIcroN Team: Chris Rorden
……
![Page 112: Data Processing of Resting-State fMRI (Part 1)](https://reader036.fdocuments.net/reader036/viewer/2022062301/56812d16550346895d91ff47/html5/thumbnails/112.jpg)
112
Thanks for your attention!