using Statistical Parametric Mapping (SPM8)

Preprocessing of fMRI data

Sunghyon Kyeongsunghyon.kyeong@gmail.com

Institute of Behavioural Science in Medicine, Yonsei University College of Medicine

Steps in the spatial preprocessing of event related and resting state fMRI data

are the same.

Sunghyon Kyeong (Yonsei Univ) | Preprocessing and Analysis of fMRI data | p

Summary of Preprocess

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Input Output

EPI1.niiEPI2.nii

…

aEPI1.niiaEPI2.nii

…

aEPI1.niiaEPI2.nii

…

meanaEPI.nii aEPI1.nii (realigned)aEPI2.nii (realigned)

rp_EPI.txt …

meanaEPI.nii anat.nii

meanaEPI.nii anat.nii (coregistered)

anat.nii aEPI1.niiaEPI2.nii

…

wanat.nii waEPI1.nii waEPI1.nii

…

waEPI1.niiwaEPI2.nii

…

Slice Timing

Realignment

CoregistrationT1 → 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 SPMGroup-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.niiswaEPI1.nii

…

실습

Spatial preprocessing

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Sunghyon Kyeong (Yonsei Univ) | Preprocessing and Analysis of fMRI data | p

DICOM Import

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(1)

(2)

(3)

select .dcm files

select output directory

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 slicesTR repetition time in secondTA 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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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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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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Sunghyon Kyeong (Yonsei Univ) | Preprocessing and Analysis of fMRI data | p

Check Registration!

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(1)restanat.niimeanrest.nii Select T1 and meanEPI images

※ T1과 meanEPI 영상이 잘 정합 되었는지 반드시 확인!!

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 SPM8\template

Sunghyon Kyeong (Yonsei Univ) | Preprocessing and Analysis of fMRI data | p

Smoothing

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(1)

(2)

(3)

^wa.*

Sunghyon Kyeong (Yonsei Univ) | Preprocessing and Analysis of fMRI data | p

Now, we have

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swaEPI1.niiswaEPI1.nii

…

Event Related fMRI analysis- Task-related brain activation - PPI analysis (connectivity)

Resting State fMRI analysis- functional connectivity - graph theoretical analysis

preprocessed fMRI data