Data Processing Demo of RestingState f MRI YAN

Data Processing Demo of Resting-State f. MRI YAN Chao-Gan 严超赣 Ph. D. Candidate ycg. yan@gmail. com State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, China 1

Demo Data Processing. Demo. Data. zip Fun. Raw Sub_001 Functional DICOM data Sub_002 Sub_003 T 1 Raw Sub_001 Structural DICOM data Sub_002 Sub_003 http: //www. restfmri. net/forum/Demo. Data

Processing Demo Based on Matlab, SPM, REST, MRIcro. N’s dcm 2 nii

Processing Demo

Preprocessing and ALFF/f. ALFF/FC Calculation Processing. Demo. Data. zipDPARS F_Preprocess_ALFF_FC. mat Working Dir where Number of time stored Fun. Raw Detected participants points DICOMTR to NIf. TI, based on MRIcro. N’s Removedcm 2 nii several first time points

Slice Timing Why? Huettel et al. , 2004

Preprocessing and ALFF/f. ALFF/FC Calculation Total slice number Slice order: 1: 2: 33, 2: 2: 32 Reference slice: (interleaved scanning) slice acquired in the middle time of each TR

Realign Why?

Excluding Criteria: 2. 5 mm and 2. 5 degree None Realign Excluding Criteria: 2. 0 mm and 2. 0 degree Check head motion: Sub_013 Excluding Criteria: 1. 5 mm and 1. 5 degree Sub_013 Excluding Criteria: 1. 0 mm and 1. 0 degree Sub_007 Sub_012 Sub_013 Sub_017 Sub_018

Preprocessing and ALFF/f. ALFF/FC Calculation

Normalize Why? Huettel et al. , 2004

Preprocessing and ALFF/f. ALFF/FC Calculation Bounding box Voxel size Normalizeby byusing. EPI T 1 templates image unified segmentation

Normalize Methods: • Normalize by using EPI templates v Structural image was coregistered to the mean image after the motion • functional Normalize by using T 1 correction image v The transformed structural image was then segmented unified segmentation into gray matter, white matter, cerebrospinal fluid by using a unified segmentation algorithm v Normalize: the motion corrected functional volumes were spatially normalized to the MNI space using the normalization parameters estimated during unified segmentation (*_seg_sn. mat)

Preprocessing and ALFF/f. ALFF/FC Calculation DICOM to NIf. TI, A prior probability based on MRIcro. N’s distribution for affine Affine registration Regularisation dcm 2 nii of in ADelete priorfiles probability Segmentation beforeto East-Asian brains distribution fortoaffine normalization MNI space: save registration ofraw disk space. The This was derived from European brains to data (Fun. Raw and 65 seg_inv_sn. mat files MNI space. T 1 Raw) will be from Singapore. reserved.

Normalize Check Normalization with DPARSF {WROKDIR}Pictures. For. Chk. Normalization

By-Product: VBM GM in original WM in space CSF in original space Modulated GM in normalized space

Preprocessing and ALFF/f. ALFF/FC Calculation

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

Preprocessing and ALFF/f. ALFF/FC Calculation FWHM kernel ALFF, f. ALFF, Funtional Connectivity: Data with For Re. Ho, Smooth should be performed after Re. Ho calculation

Preprocessing and ALFF/f. ALFF/FC Calculation Remove linear trend Ideal band pass filter

Filter Why? • Low frequency (0. 01– 0. 08 Hz) fluctuations (LFFs) of the resting-state f. MRI signal were of physiological importance. (Biswal et al. , 2005) • LFFs of resting-state f. MRI signal were suggested to reflect spontaneous neuronal activity (Logothetis et al. , 2001; Lu et al. , 2007). l 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. l Logothetis NK, Pauls J, Augath M, Trinath T, Oeltermann A (2001) Neurophysiological investigation of the basis of the f. MRI signal. Nature 412: 150– 157. l 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.

Preprocessing and ALFF/f. ALFF/FC Calculation Delete detrented files to save disk space. Do not selectmask: this option Default SPM 5 if f. ALFF wanted. aprioriis mask (brainmask. nii) thresholded at 50%.

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: 83– 91.

f. ALFF (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 f. MRI: fractional ALFF. J Neurosci Methods 172: 137 -141.

Preprocessing and ALFF/f. ALFF/FC Calculation Frequency band Minus one to perform One-Sample T-Test in SPM

Preprocessing and ALFF/f. ALFF/FC Calculation Regress out nuisance Covariates rp*. txt Brain. Mask_05_61 x 73 x 61. img White. Mask_09_61 x 73 x 61. img Csf. Mask_07_61 x 73 x 61. img

Preprocessing and ALFF/f. ALFF/FC Calculation Functional Connectivity Define ROI

Please ensure the resolution of your ROI file is the same as your functional data.

Seed Region Posterior Cingulate Cortex (PCC): − 5, − 49, 40 (Talairach coordinates) (Raichle et al. , 2001; Fox et al. , 2005)

Re. Ho Calculation Processing. Demo. Data. zip DPARSF_Re. Ho. mat Data is preprocessed and stored in Fun. Img. Normalized Data without Remove linearsmooth trend Smooth be Ideal band should pass filter performed after Re. Ho calculation Default mask: SPM 5 apriori mask (brainmask. nii) thresholded at 50%.

Re. Ho Calculation Re. Ho calculation Cluster: 27 m. Re. Ho voxels Smooth the results. The FWHM kernel is the same as set in the smooth step. Get the sm. Re. Ho -1 or m. Re. Ho - 1 data for one sample T test in SPM.

Demo Results Processing. Demo. Data. zip Demo. Results ALFF f. ALFF FC Re. Ho Processed with: Windows XP, MATAB 7. 3, SPM 5 with updates 3381, REST_V 1. 4_100426 and DPARSF_V 1. 0_100510

Statistical Analysis Demo Processing. Demo. Data. zip Statistical. Demo AD_MCI_NC Re. Ho/ALFF/f. ALFF for three groups: Alzheimer’s disease patients, Mild cognitive impairment patients and normal controls EO_EC Re. Ho/ALFF/f. ALFF for one group of participants in eyesclosed and eyes-open conditions

Statistical Analysis in REST

One-Sample T-Test 1 for m* images a group of m* images Brain Mask or keep empty T Statistic Image

Two-Sample T-Test T Statistic Image: positive corresponds to the mean of Group 1 is greater than the mean of Group 2

Two-Sample T-Test with covariates: e. g. gray matter proportion images (Oakes et al. , 2007, Neuroimage) Other covariate can be also specified as text files. (E. g. age, brain size, IQ etc. )

ANOVA or ANCOVA F Statistic Image

Paired T-Test Condition 1 – Condition 2 Please make sure the correspondence T Statistic Image

Further Help Detailed course: http: //www. restfmri. net/forum/Course Further questions: http: //www. restfmri. net

Thanks to 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 …… SPM Team: Wellcome Department of Imaging Neuroscience, UCL MRIcro. N Team: Chris RORDEN Xjview Team: CUI Xu …… All the group members!

Thanks for your attention! 42