The document outlines the preprocessing of fMRI data using statistical parametric mapping (SPM8), emphasizing various steps such as slice timing correction, realignment, coregistration, normalization, and smoothing for both event-related and resting state fMRI analysis. It details the input and output files at each stage and the application of regression for nuisance parameters and functional connectivity analysis. Additionally, the document includes guidelines for performing group-wise analyses and specific GLM specifications in SPM.

1. using Statistical Parametric Mapping (SPM8)
Preprocessing of fMRI data
Sunghyon Kyeong
sunghyon.kyeong@gmail.com
Institute of Behavioural Science in Medicine,
Yonsei University College of Medicine

2. Steps in the spatial preprocessing of
event related and resting state fMRI data
are the same.

3. Sunghyon Kyeong (Yonsei Univ) | Preprocessing and Analysis of fMRI data | p
Summary of Preprocess
3
Input Output
EPI1.nii
EPI2.nii
…
aEPI1.nii
aEPI2.nii
…
aEPI1.nii
aEPI2.nii
…
meanaEPI.nii
aEPI1.nii (realigned)
aEPI2.nii (realigned)
rp_EPI.txt
…
meanaEPI.nii
anat.nii
meanaEPI.nii
anat.nii (coregistered)
anat.nii
aEPI1.nii
aEPI2.nii
…
wanat.nii
waEPI1.nii
waEPI1.nii
…
waEPI1.nii
waEPI2.nii
…
Slice Timing
Realignment
Coregistration
T1 → meanEPI
Normalisation
Smoothing
Event related fMRI analysis
Resting state fMRI analysis
Preprocessing
• Specify 1st-level in SPM
Individual GLM with Stimulus onset
and rp_EPI.txt as regressors
• Specify 2nd-level in SPM
Group-wise analysis
one sample, two sample, factorial
design, flexible design
• Linear detrending of EPI time series
at each voxel.
• bandpass filtering (0.009~0.08Hz) to
capture Low-frequency fluctuation
• regression nuisance parameters
such as head motion, white matter,
ventricle, and global signal
• Functional connectivity analysis and
Complex network analysis
swaEPI1.nii
swaEPI1.nii
…

4. 실습
Spatial preprocessing
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5. Sunghyon Kyeong (Yonsei Univ) | Preprocessing and Analysis of fMRI data | p
DICOM Import
5
(1)
(2)
(3)
select .dcm files
select output directory

6. Sunghyon Kyeong (Yonsei Univ) | Preprocessing and Analysis of fMRI data | p
Slice timing correction
(1) Data
select image files (*.nii or *.img)
Number of Slices
specify number of slices
TR
repetition time in second
TA
TA=TR-(TR/nslices)
Slice order
ex) 1:nslices (ascending)
ex) 1:2:nslices 2:2:nslices (interleaved)
Reference Slice
usually a middle slice in space
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7. Sunghyon Kyeong (Yonsei Univ) | Preprocessing and Analysis of fMRI data | p
Realignment
(1) Realign (Estimate & Reslice)
Data
slice timing corrected images (a*.nii)
Num Passes
Register to first
Resliced images
Mean Image Only
^a.*
(2)
(3)
select directory
(4)(5)
첫번째 volume에 모든 EPI
영상을 정합
meana~~.nii 가 생성되고,
coregistration에 사용됨.
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8. Sunghyon Kyeong (Yonsei Univ) | Preprocessing and Analysis of fMRI data | p
Co-registration
(1) Coregistration (Estimate)
Reference Image
select a mean EPI image which was
created after realignment process
Source Image
select an anatomical (T1) image
※ fMRI 과제가 여러개인 경우에 T1 영상을 각 fMRI 과에별로 복사해서 사용할 것을 권장함.
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9. Sunghyon Kyeong (Yonsei Univ) | Preprocessing and Analysis of fMRI data | p
Check Registration!
9
(1) restanat.nii
meanrest.nii
Select T1 and meanEPI images
※ T1과 meanEPI 영상이 잘 정합 되었는지 반드시 확인!!

10. Sunghyon Kyeong (Yonsei Univ) | Preprocessing and Analysis of fMRI data | p
Normalisation
(1)
Normalise (Estimate&Write)
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Source Image
select the coregistered T1 image
Images to Write
select the coregistered T1 & realigned
EPI images
Template Image
select T1 template file (T1.nii)
which is located at SPM8template

11. Sunghyon Kyeong (Yonsei Univ) | Preprocessing and Analysis of fMRI data | p
Smoothing
11
(1)
(2)
(3)
^wa.*

12. Sunghyon Kyeong (Yonsei Univ) | Preprocessing and Analysis of fMRI data | p
Now, we have
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swaEPI1.nii
swaEPI1.nii
…
Event Related fMRI analysis
- Task-related brain activation
- PPI analysis (connectivity)
Resting State fMRI analysis
- functional connectivity
- graph theoretical analysis
preprocessed fMRI data