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Data Processing of Resting-State fMRI (Part 1)

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Data Processing of Resting-State fMRI (Part 1) YAN Chao-Gan Ph. D ycg.yan_at_gmail.com State Key Laboratory of Cognitive Neuroscience and Learning, – PowerPoint PPT presentation

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Title: Data Processing of Resting-State fMRI (Part 1)


1
Data Processing of Resting-State fMRI (Part 1)
YAN Chao-Gan ??? Ph. D ycg.yan_at_gmail.com State
Key Laboratory of Cognitive Neuroscience and
Learning, Beijing Normal University, China
2
Outline
  • Overview
  • Data Preparation
  • Preprocess
  • ReHo, ALFF, fALFF Calculation
  • Functional Connectivity
  • Utilities

3
Overview
Based on Matlab, SPM, REST, MRIcroNs dcm2nii
4
Setup
E\ITraWork\100402Trainning\Softs\DPARSF_V1.0_1002
01 NO Chinese character or space in the path.
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).

6
Outline
  • Overview
  • Data Preparation
  • Preprocess
  • ReHo, ALFF, fALFF Calculation
  • Functional Connectivity
  • Utilities

7
Data preparation
Arrange the information of the subjects
8
Data preparation
Information of subjects
9
Data preparation
Arrange the information of the subjects Arrange
the MRI data of the subjects
Functional MRI data Structural MRI data DTI data
10
?????? ??????
11
Sort DICOM data
12
IMA dcm none
13
Data preparation
Arrange each subject's fMRI DICOM images in one
directory, and then put them in "FunRaw"
directory under the working directory.
Subject 1s DICOM files
FunRaw directory, please name as this
Subject 1s directory
Working directory
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 1s DICOM files
T1Raw directory, please name as this
Subject 1s directory
Working directory
15
Data preparation
Set the parameters in DPARSF
Set the working directory
Set the time points (volumes)
The detected subjects ID
Set the TR
16
Outline
  • Overview
  • Data Preparation
  • Preprocess
  • ReHo, ALFF, fALFF Calculation
  • Functional Connectivity
  • Utilities

17
Preprocess
  • DICOM -gt NIFTI
  • Remove First 10 Time Points
  • Slice Timing
  • Realign
  • Normalize
  • Smooth
  • Detrend
  • Filter 0.01-0.08

18
DICOM-gtNIFTI
  • MRIcroNs dcm2niigui
  • SPM5s DICOM Import

19
DICOM-gtNIFTI
  • DPARSF

20
Preprocess
  • DICOM -gt NIFTI
  • Remove First 10 Time Points
  • Slice Timing
  • Realign
  • Normalize
  • Smooth
  • Detrend
  • Filter 0.01-0.08

21
Remove First 10 Time Points
  • DPARSF

22
Preprocess
  • DICOM -gt NIFTI
  • Remove First 10 Time Points
  • Slice Timing
  • Realign
  • Normalize
  • Smooth
  • Detrend
  • Filter 0.01-0.08

23
Slice Timing
Why?
24
Slice Timing
Why?
Huettel et al., 2004
25
Slice Timing
1225,2224
25
2
2-(2/25)
25
26
Slice Timing
27
Slice Timing
  • DPARSF

1225,2224
28
Slice Timing
If 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
29
Preprocess
  • DICOM -gt NIFTI
  • Remove First 10 Time Points
  • Slice Timing
  • Realign
  • Normalize
  • Smooth
  • Detrend
  • Filter 0.01-0.08

30
Realign
Why?
31
Realign
32
Realign
  • DPARSF

33
Realign
Excluding Criteria 2.5mm and 2.5
degree None Excluding Criteria 2.0mm and 2.0
degree Sub_013 Excluding Criteria 1.5mm and
1.5 degree Sub_013 Excluding Criteria 1.0mm
and 1.0 degree Sub_007 Sub_012 Sub_013 Sub_017 Sub
_018
Check head motion
34
Preprocess
  • DICOM -gt NIFTI
  • Remove First 10 Time Points
  • Slice Timing
  • Realign
  • Normalize
  • Smooth
  • Detrend
  • Filter 0.01-0.08

35
Normalize
Why?
Huettel et al., 2004
36
Normalize
Methods
  • I. Normalize by using EPI templates
  • II. Normalize by using T1 image unified
    segmentation

37
mean_name.img
r.img
EPI.nii
-90 -126 -72 90 90 108
3 3 3
38
Normalize I
39
Normalize
Methods
  • Normalize by using EPI templates
  • Normalize by using T1 image unified 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)

40
Normalize II Coregister
mean_name.img
T1.img
41
Normalize II
T1_Coregisted.img
Light Clean
ICBM space template East Asian brains
European brains
42
Normalize IISegment
New Segment
43
Normalize II
New Normalize Write
New Subject
name_seg_sn.mat
r.img
-90 -126 -72 90 90 108
3 3 3
44
Normalize
  • DPARSF

Delete files before normalization raw NIfTI
files, slice timing files, realign files.
T1 Data should be arranged in T1Raw or T1Img
(co.img) directory!
45
Normalize
  • Check Normalization with DPARSF

WROKDIR\PicturesForChkNormalization
46
By-Product VBM
GM in original space
WM in original space
CSF in original space
Modulated GM in normalized space
GM in normalized space
47
Preprocess
  • DICOM -gt NIFTI
  • Remove First 10 Time Points
  • Slice Timing
  • Realign
  • Normalize
  • Smooth
  • Detrend
  • Filter 0.01-0.08

48
Smooth
Why?
  • Reduce the effects of the bad normalization

49
Smooth
w.img
FWHM kernel
50
Smooth
  • DPARSF

Without former steps Data arranged in
FunImgNormalized directory.
ReHo Data without smooth
ALFF, fALFF, Funtional Connectivity Data with
smooth
51
Preprocess
  • DICOM -gt NIFTI
  • Remove First 10 Time Points
  • Slice Timing
  • Realign
  • Normalize
  • Smooth
  • Detrend
  • Filter 0.01-0.08

52
Detrend
53
Preprocess
  • DICOM -gt NIFTI
  • Remove First 10 Time Points
  • Slice Timing
  • Realign
  • Normalize
  • Smooth
  • Detrend
  • Filter 0.01-0.08

54
??
Why?
  • Low frequency (0.010.08 Hz) fluctuations (LFFs)
    of the resting-state fMRI signal were of
    physiological importance. (Biswal et al., 2005)
  • LFFs of resting-state fMRI signal were suggested
    to reflect spontaneous neuronal activity
    (Logothetis 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 537541.
  • Logothetis NK, Pauls J, Augath M, Trinath T,
    Oeltermann A (2001) Neurophysiological
    investigation of the basis of the fMRI signal.
    Nature 412 150157.
  • 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 1826518269.

55
Filter
56
Detrend and Filter
  • DPARSF

Without former steps Data arranged in
FunImgNormalized or FunImgNormalizedSmoothed
directory.
If you want to calculate fALFF, please do not
delete the detrended files
57
Outline
  • Overview
  • Data Preparation
  • Preprocess
  • ReHo, ALFF, fALFF Calculation
  • Functional Connectivity
  • Utilities

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 394400.
59
ReHo
If the resolution of your data is not 616173,
please resample your mask file at first.
60
Data Resample
Choose the mask file or ROI definition file. e.g.
BrainMask_05_61x73x61.img
Choose one of your functional image. e.g. your
normalized functional image or image after
Detrend and Filter.
Resample Mask
Resample other kind of data
61
Data Resample
62
Data Resample
0 Nearest Neighbor 1 Trilinear 2- 2nd degree
b-spline
63
ReHo
  • DPARSF

Without former steps Data arranged in
FunImgNormalizedDetrendedFiltered directory.
Please ensure the resolution of your own mask is
the same as your functional data.
Smooth the mReHo results. The FWHM kernel is the
same as set in the smooth step.
Get the smReHo -1 or mReHo - 1 data for one
sample T test.
64
ALFF(Amplitude of Low Frequency Fluctuation )
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 8391.
65
fALFF(fractional ALFF )
PCC posterior cingulate cortex SC suprasellar
cistern
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.
66
ALFF
fALFF DO NOT filter!
67
ALFF and fALFF
  • DPARSF

Without former steps Data arranged in
FunImgNormalizedSmoothedDetrendedFiltered or
FunImgNormalizedSmoothedDetrended directory.
Please ensure the resolution of your own mask is
the same as your functional data.
Please DO NOT delete the detrended files before
filter. DPARSF will calculated the fALFF based on
data before filter.
Get the mALFF - 1 or (mfALFF - 1) data for one
sample T test.
68
Outline
  • Overview
  • Data Preparation
  • Preprocess
  • ReHo, ALFF, fALFF Calculation
  • Functional Connectivity
  • Utilities

69
Regress out nuisance covariates
  • Head motion parameters rp_name.txt
  • Global mean signal
  • White matter signal
  • Cerebrospinal fluid signal

70
Extract Covariates
71
Extract Covariates
72
Extract Covariates
73
Extract Covariates
74
Extract Covariates
75
Extract Covariates
Extract one subjects Covariates
76
Extract Covariates
Extract multi subjects Covariates
77
Extract Covariates
78
Extract Covariates
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
  • RPCovload('rp_name.txt')
  • BCWCovload('ROI_FCMap_name.txt')
  • CovRPCov,BCWCov
  • save('Cov.txt', 'Cov', '-ASCII',
    '-DOUBLE','-TABS')

80
Regress out Covariates
81
Extract Covariates
CovList.txt Covariables_List X\Process\Sub3Cov
.txt X\Process\Sub2Cov.txt X\Process\Sub1Cov.txt
CovList.txt
82
Regress out nuisance Covariates
  • DPARSF

Without former steps Data arranged in
FunImgNormalizedDetrendedFiltered or
FunImgNormalizedSmoothedDetrendedFiltered
directory.
rp.txt
BrainMask_05_61x73x61.img
WhiteMask_09_61x73x61.img
CsfMask_07_61x73x61.img
83
Regress out Covariates
  • DPARSF

Without former steps Data arranged in
FunImgNormalizedDetrendedFiltered or
FunImgNormalizedSmoothedDetrendedFiltered
directory.
84
Regress out Covariates
85
Regress out Covariates
Please ensure the resolution of your ROI file is
the same as your functional data.
86
Functional Conncetivity
Voxel-wise ROI-wise
r0.36
87
Voxel-wise
88
Voxel-wise
SeedList.txt Seed_Time_Course_List X\Process\S
ub3Seed.txt X\Process\Sub2Seed.txt X\Process\Sub
1Seed.txt
Please ensure the resolution of your ROI file is
the same as your functional data.
89
Voxel-wise
90
Voxel-wise
91
Voxel-wise
92
Voxel-wise
93
Voxel-wise
CovList.txt Covariables_List X\Process\Sub6Cov
.txt X\Process\Sub5Cov.txt X\Process\Sub4Cov.txt
X\Process\Sub3Cov.txt X\Process\Sub2Cov.txt X\
Process\Sub1Cov.txt
CovList.txt
94
ROI-wise
95
ROI-wise
96
ROI-wise
CovList.txt Covariables_List X\Process\Sub6Cov
.txt X\Process\Sub5Cov.txt X\Process\Sub4Cov.txt
X\Process\Sub3Cov.txt X\Process\Sub2Cov.txt X\
Process\Sub1Cov.txt
CovList.txt
97
ROI-wise
98
Functional Connectivity
DPARSF
Without former steps Data arranged in
FunImgNormalizedDetrendedFilteredCovremoved or
FunImgNormalizedSmoothedDetrendedFilteredCovremove
d directory.
Please ensure the resolution of your own mask is
the same as your functional data.
99
Functional Connectivity
100
Functional Connectivity
DPARSF
You will get the Voxel-wise functional
connectivity results of each ROI in working
directory\Results\FC zROI1FCMap_Sub_001.img zROI
2FCMap_Sub_001.img
For ROI-wise results, please see Part Utilities
Extract ROI time courses.
101
Outline
  • Overview
  • Data Preparation
  • Preprocess
  • ReHo, ALFF, fALFF Calculation
  • Functional Connectivity
  • Utilities

102
Extract ROI time courses
DPARSF
Without former steps Data arranged in
FunImgNormalizedDetrendedFilteredCovremoved or
FunImgNormalizedSmoothedDetrendedFilteredCovremove
d directory.
103
Extract ROI time courses
104
Extract ROI time courses
DPARSF
Results in working direcotry\FunImgNormalizedDet
rendedFilteredCovremoved_RESTdefinedROITC
Sub_001_ROITimeCourses.txt Time courses, each
column represent a time course of one
ROI. Sub_001_ResultCorr.txt ROI-wise Functional
Connectivity
105
Extract AAL time courses
DPARSF
Without former steps Data arranged in
FunImgNormalizedDetrendedFilteredCovremoved or
FunImgNormalizedSmoothedDetrendedFilteredCovremove
d directory.
106
Extract AAL time courses
DPARSF
Results in working direcotry\FunImgNormalizedDet
rendedFilteredCovremoved_AALTC
Sub_001_AALTC.mat Time courses of each AAL
region.
107
Change prefix of Images
DPARSF
Normalization by using T1 image segmentation
co.img Realign without Slice Timeing a.img
108
Change prefix of Images
DPARSF
Normalization by using T1 image segmentation
co.img
a.img -gt ra.img
a
ra
109
Save and Load Parameters
DPARSF
Save parameters to .mat
Load parameters from .mat
110
Further Help
Further questions
www.restfmri.net
111
Thanks to
SPM Team Wellcome Department of Imaging
Neuroscience, UCL MRIcroN Team Chris Rorden
  • DONG Zhang-Ye
  • GUO Xiao-Juan
  • HE Yong
  • LONG Xiang-Yu
  • SONG Xiao-Wei
  • YAO Li
  • ZANG Yu-Feng
  • ZHANG Han
  • ZHU Chao-Zhe
  • ZOU Qi-Hong
  • ZUO Xi-Nian

All the group members!
112
  • Thanks for your attention!
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