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, Beijing Normal University, China
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Outline

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

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

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Outline

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

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Data preparation
Arrange the information of the subjects
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Data preparation
Information of subjects
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Data preparation
Arrange the information of the subjects Arrange
the MRI data of the subjects
Functional MRI data Structural MRI data DTI data
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?????? ??????
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Sort DICOM data
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IMA dcm none
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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
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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
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Data preparation
Set the parameters in DPARSF
Set the working directory
Set the time points (volumes)
The detected subjects ID
Set the TR
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Outline

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

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Preprocess

• DICOM -gt NIFTI
• Remove First 10 Time Points
• Slice Timing
• Realign
• Normalize
• Smooth

• Detrend
• Filter 0.01-0.08

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DICOM-gtNIFTI

• MRIcroNs dcm2niigui
• SPM5s DICOM Import

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DICOM-gtNIFTI

• DPARSF

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Preprocess

• DICOM -gt NIFTI
• Remove First 10 Time Points
• Slice Timing
• Realign
• Normalize
• Smooth

• Detrend
• Filter 0.01-0.08

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Remove First 10 Time Points

• DPARSF

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Preprocess

• DICOM -gt NIFTI
• Remove First 10 Time Points
• Slice Timing
• Realign
• Normalize
• Smooth

• Detrend
• Filter 0.01-0.08

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Slice Timing
Why?
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Slice Timing
Why?
Huettel et al., 2004
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Slice Timing
1225,2224
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2
2-(2/25)
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Slice Timing
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Slice Timing

• DPARSF

1225,2224
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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
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Preprocess

• DICOM -gt NIFTI
• Remove First 10 Time Points
• Slice Timing
• Realign
• Normalize
• Smooth

• Detrend
• Filter 0.01-0.08

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Realign
Why?
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Realign
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Realign

• DPARSF

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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
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Preprocess

• DICOM -gt NIFTI
• Remove First 10 Time Points
• Slice Timing
• Realign
• Normalize
• Smooth

• Detrend
• Filter 0.01-0.08

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Normalize
Why?
Huettel et al., 2004
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Normalize
Methods

• I. Normalize by using EPI templates
• II. Normalize by using T1 image unified
  segmentation

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mean_name.img
r.img
EPI.nii
-90 -126 -72 90 90 108
3 3 3
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Normalize I
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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)

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Normalize II Coregister
mean_name.img
T1.img
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Normalize II
T1_Coregisted.img
Light Clean
ICBM space template East Asian brains
European brains
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Normalize IISegment
New Segment
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Normalize II
New Normalize Write
New Subject
name_seg_sn.mat
r.img
-90 -126 -72 90 90 108
3 3 3
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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!
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Normalize

• Check Normalization with DPARSF

WROKDIR\PicturesForChkNormalization
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By-Product VBM
GM in original space
WM in original space
CSF in original space
Modulated GM in normalized space
GM in normalized space
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Preprocess

• DICOM -gt NIFTI
• Remove First 10 Time Points
• Slice Timing
• Realign
• Normalize
• Smooth

• Detrend
• Filter 0.01-0.08

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Smooth
Why?

• Reduce the effects of the bad normalization

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Smooth
w.img
FWHM kernel
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Smooth

• DPARSF

Without former steps Data arranged in
FunImgNormalized directory.
ReHo Data without smooth
ALFF, fALFF, Funtional Connectivity Data with
smooth
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Preprocess

• DICOM -gt NIFTI
• Remove First 10 Time Points
• Slice Timing
• Realign
• Normalize
• Smooth

• Detrend
• Filter 0.01-0.08

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Detrend
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Preprocess

• DICOM -gt NIFTI
• Remove First 10 Time Points
• Slice Timing
• Realign
• Normalize
• Smooth

• Detrend
• Filter 0.01-0.08

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??
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.

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Filter
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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
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Outline

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

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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.
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ReHo
If the resolution of your data is not 616173,
please resample your mask file at first.
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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
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Data Resample
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Data Resample
0 Nearest Neighbor 1 Trilinear 2- 2nd degree
b-spline
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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.
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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.
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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.
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ALFF
fALFF DO NOT filter!
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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.
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Outline

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

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Regress out nuisance covariates

• Head motion parameters rp_name.txt
• Global mean signal
• White matter signal
• Cerebrospinal fluid signal

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Extract Covariates
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Extract Covariates
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Extract Covariates
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Extract Covariates
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Extract Covariates
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Extract Covariates
Extract one subjects Covariates
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Extract Covariates
Extract multi subjects Covariates
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Extract Covariates
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Extract Covariates
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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')

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Regress out Covariates
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Extract Covariates
CovList.txt Covariables_List X\Process\Sub3Cov
.txt X\Process\Sub2Cov.txt X\Process\Sub1Cov.txt
CovList.txt
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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
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Regress out Covariates

• DPARSF

Without former steps Data arranged in
FunImgNormalizedDetrendedFiltered or
FunImgNormalizedSmoothedDetrendedFiltered
directory.
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Regress out Covariates
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Regress out Covariates
Please ensure the resolution of your ROI file is
the same as your functional data.
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Functional Conncetivity
Voxel-wise ROI-wise
r0.36
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Voxel-wise
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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.
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Voxel-wise
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Voxel-wise
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Voxel-wise
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Voxel-wise
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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
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ROI-wise
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ROI-wise
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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
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ROI-wise
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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.
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Functional Connectivity
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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.
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Outline

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

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Extract ROI time courses
DPARSF
Without former steps Data arranged in
FunImgNormalizedDetrendedFilteredCovremoved or
FunImgNormalizedSmoothedDetrendedFilteredCovremove
d directory.
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Extract ROI time courses
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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
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Extract AAL time courses
DPARSF
Without former steps Data arranged in
FunImgNormalizedDetrendedFilteredCovremoved or
FunImgNormalizedSmoothedDetrendedFilteredCovremove
d directory.
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Extract AAL time courses
DPARSF
Results in working direcotry\FunImgNormalizedDet
rendedFilteredCovremoved_AALTC
Sub_001_AALTC.mat Time courses of each AAL
region.
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Change prefix of Images
DPARSF
Normalization by using T1 image segmentation
co.img Realign without Slice Timeing a.img
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Change prefix of Images
DPARSF
Normalization by using T1 image segmentation
co.img
a.img -gt ra.img
a
ra
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Save and Load Parameters
DPARSF
Save parameters to .mat
Load parameters from .mat
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Further Help
Further questions
www.restfmri.net
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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!
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• Thanks for your attention!