Data Processing of RestingState f MRI Part 3

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Data Processing of Resting-State f. MRI (Part 3): DPARSF Advanced Edition YAN Chao-Gan 严超赣

Data Processing of Resting-State f. MRI (Part 3): DPARSF Advanced Edition YAN Chao-Gan 严超赣 Ph. D. ycg. yan@gmail. com State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, China 1

Outline • Overview • New Functions • Template Parameters 2

Outline • Overview • New Functions • Template Parameters 2

DPARSF (Yan and Zang, 2010)

DPARSF (Yan and Zang, 2010)

Based on Matlab, SPM, REST, MRIcro. N’s dcm 2 nii 4

Based on Matlab, SPM, REST, MRIcro. N’s dcm 2 nii 4

DPARSF Basic Edition • Type in “DPARSF” to start • Simple but not flexible

DPARSF Basic Edition • Type in “DPARSF” to start • Simple but not flexible • Strong parameters checking and wrong processing prevention 5

DPARSF Advanced Edition • Type in “DPARSFA” to start • The processing steps can

DPARSF Advanced Edition • Type in “DPARSFA” to start • The processing steps can be freely skipped or combined • The processing can be start with any Starting Directory Name • Support Re. Ho, ALFF/f. ALFF and Functional Connectivity calculation in individual space • The masks or ROI files would be resampled automatically if the dimension mismatched the functional images. 6

DPARSF Advanced Edition • The masks or ROI files in standard space can be

DPARSF Advanced Edition • The masks or ROI files in standard space can be warped into individual space by using the parameters estimated in unified segmentaion • Support VBM analysis by checking "Segment" only • Support reorientation interactively if the images in a bad orientation • Support define regions of interest interactively based on the participant's T 1 image in individual space 7

Outline • Overview • New Functions • Template Parameters 8

Outline • Overview • New Functions • Template Parameters 8

Same as DPARSF Basic Edition: Please refer to Data Processing Multimedia Course (Part 1)

Same as DPARSF Basic Edition: Please refer to Data Processing Multimedia Course (Part 1) Working Dir where stored Starting Number time Directoryof(e. g. , Detected participants points Fun. Raw) TR 9

Template Parameters Standard Steps Calculate in Original Space (Warp) Intraoperative Processing VBM 10

Template Parameters Standard Steps Calculate in Original Space (Warp) Intraoperative Processing VBM 10

Same as DPARSF Basic Edition: Please refer to Data Processing Multimedia Course (Part 1)

Same as DPARSF Basic Edition: Please refer to Data Processing Multimedia Course (Part 1) DICOM to NIf. TI, based on MRIcro. N’s Removedcm 2 nii several first time points Slice Timing 11

Same as DPARSF Basic Edition: Please refer to Data Processing Multimedia Course (Part 1)

Same as DPARSF Basic Edition: Please refer to Data Processing Multimedia Course (Part 1) Total slice number Slice order: 1: 2: 33, 2: 2: 32 Reference slice: (interleaved scanning) slice acquired in the middle time offiles eachto. TR T 1 DICOM Realign NIf. TI 12

Coregister T 1 image to functional space A hidden step in normalization by using

Coregister T 1 image to functional space A hidden step in normalization by using T 1 image segmentation in DPARSF Basic Edition 13

Normalize Methods: • Normalize by using EPI templates • Structural image was coregistered to

Normalize Methods: • Normalize by using EPI templates • Structural image was coregistered to the mean image after the motion • functional Normalize by using T 1 correction image • The transformed structural image was then segmented unified segmentation 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)

Coregister T 1 image to functional space • Source Image: T 1 image •

Coregister T 1 image to functional space • Source Image: T 1 image • Reference Image: mean*. img generated in realign step. • If there is no mean*. img generated in realign step DPARSFA will generate a mean functional image automatically. 15

Reorient Interactively Reorientat interactively if the images in a bad orientation 16

Reorient Interactively Reorientat interactively if the images in a bad orientation 16

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Reorient Interactively The reorientation effects on coregisted T 1 image and realigned (if realign

Reorient Interactively The reorientation effects on coregisted T 1 image and realigned (if realign is performed) functional images. 19

Segment A hidden step in normalization by using T 1 image segmentation in DPARSF

Segment A hidden step in normalization by using T 1 image segmentation in DPARSF Basic Edition Now it can be used in VBM alone. 20

By-Product: VBM GM in original WM in space CSF in original Matrix to original

By-Product: VBM GM in original WM in space CSF in original Matrix to original Matrix space to warp image space warp image Modulated from MNI GM in individual GM in space to normalized space to MNI normalized individual space

Same as DPARSF Basic Edition: Please refer to Data Processing Multimedia Course (Part 1)

Same as DPARSF Basic Edition: Please refer to Data Processing Multimedia Course (Part 1) Bounding box Normalize Voxel size Normalize by using EPI templates 22

Normalize by using T 1 image unified segmentation • Parameter File: *_seg_sn. mat generated

Normalize by using T 1 image unified segmentation • Parameter File: *_seg_sn. mat generated in unified segmentation • Images to Write: Functional images (e. g. , r*. img if realign is performed) 23

Same as DPARSF Basic Edition: Please refer to Data Processing Multimedia Course (Part 1)

Same as DPARSF Basic Edition: Please refer to Data Processing Multimedia Course (Part 1) Delete files before normalization to save disk space. The raw data (Fun. Raw and T 1 Raw) will be reserved. 24

Smooth FWHM Checked: Thekernel following processing steps are based Unchecked: The on Data with

Smooth FWHM Checked: Thekernel following processing steps are based Unchecked: The on Data with smooth (e. g. , following processing ALFF, f. ALFF, Funtional steps are based on Data Connectivity) without smooth (e. g. , Re. Ho) 25

Same as DPARSF Basic Edition: Please refer to Data Processing Multimedia Course (Part 1)

Same as DPARSF Basic Edition: Please refer to Data Processing Multimedia Course (Part 1) Delete detrented files Remove linear trend to save diskpass space. Do Ideal band filter not select this option if f. ALFF is wanted. 26

Mask Default mask: SPM 5 apriori mask If the resolution of default mask or

Mask Default mask: SPM 5 apriori mask If the resolution of default mask or (brainmask. nii) user-defined mask is different thresholded atmask 50%. User-defined from the functional data: • (1) In DPARSF (Basic Edition): Error • (2) In DPARSF (Advanced Edition): resample the masks automatically 27

Mask Resample Default mask (Brain. Mask_05_91 x 109 x 91. img, voxel The first

Mask Resample Default mask (Brain. Mask_05_91 x 109 x 91. img, voxel The first time point size: or user of 2 x 2 x 2) functional -defined mask images 0 – Nearest Neighbor {Work Dir}Masks 28

Same as DPARSF Basic Edition: Please refer to Data Processing Multimedia Course (Part 1)

Same as DPARSF Basic Edition: Please refer to Data Processing Multimedia Course (Part 1) Re. Ho Calculation ALFF/f. ALFF Calculation 29

Regress out nuisance Covariates rp*. txt Brain. Mask_05_61 x 73 x 61. img White.

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 30

Regress out nuisance Covariates If the resolution of masks is different from the functional

Regress out nuisance Covariates If the resolution of masks is different from the functional data: • (1) In DPARSF (Basic Edition): Error • (2) In DPARSF (Advanced Edition): resample the masks automatically (based on *_91 x 109 x 91. img, voxel size: 2 x 2 x 2) 31

Same as DPARSF Basic Edition: Please refer to Data Processing Multimedia Course (Part 1)

Same as DPARSF Basic Edition: Please refer to Data Processing Multimedia Course (Part 1) Define ROI Functional Extract. Connectivity ROI time courses (also(voxel-wise) for ROI-wise Functional Connectivity) 32

Define ROI Interactively 33

Define ROI Interactively 33

0 means define ROI Radius for each ROI seperately 34

0 means define ROI Radius for each ROI seperately 34

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Extract AAL time courses If the resolution of AAL mask is different from the

Extract AAL time courses If the resolution of AAL mask is different from the functional data: • (1) In DPARSF (Basic Edition): Error • (2) In DPARSF (Advanced Edition): resample the masks automatically (based on aal. nii, voxel size: 1 x 1 x 1) 36

Warp Masks into Individual Space • Parameter File: *_seg_inv_sn. mat stored in "T 1

Warp Masks into Individual Space • Parameter File: *_seg_inv_sn. mat stored in "T 1 Img. Segment" directory which is estimated in the T 1 image unified segmentation 37

Warp Masks into Individual Space • Images to Write: • 1. The calculation mask

Warp Masks into Individual Space • Images to Write: • 1. The calculation mask (also regarded as the whole-barin mask, e. g. the "Default mask") • 2. The covariates masks in regressing out covariates • 3. The ROI masks used in Functional Connectivity or Extracting ROI Time courses • 4. The AAL mask used in Extracting AAL time courses (90 regions) 38

Warp Masks into Individual Space Stored in {Work Dir}Masks The ROIs defined Interactively will

Warp Masks into Individual Space Stored in {Work Dir}Masks The ROIs defined Interactively will NOT be warped since they are defined in the INDIVIDUAL SPACE 39

Starting Directory Name If you do not start with raw DICOM images, you need

Starting Directory Name If you do not start with raw DICOM images, you need to specify the Starting Directory Name. E. g. "Fun. Img. ARW" means you start with images which have been slice timed, realigned and normalized. Abbreviations: A - Slice Timing R - Realign W - Normalize S - Smooth D - Detrend F - Filter C - Covariates Removed 40

Outline • Overview • New Functions • Template Parameters 41

Outline • Overview • New Functions • Template Parameters 41

Template Parameters • Standard Steps • Calculate in Original Space (Warp) • Intraoperative Processing

Template Parameters • Standard Steps • Calculate in Original Space (Warp) • Intraoperative Processing • VBM 42

Standard Steps 43

Standard Steps 43

DPARSF's standard procedure l Convert DICOM files to NIFTI images. l Remove First 10

DPARSF's standard procedure l Convert DICOM files to NIFTI images. l Remove First 10 Time Points. l Slice Timing. l Realign. l Normalize. l Smooth (optional). l Detrend. l Filter. l Calculate Re. Ho, ALFF, f. ALFF (optional). l Regress out the Covariables (optional). l Calculate Functional Connectivity (optional). l Extract AAL or ROI time courses for further analysis (optional). Please refer to Data Processing Multimedia Course (Part 1)

Calculate in Original Space (Warp) Segment to produce *_seg_inv_sn. mat stored in "T 1

Calculate in Original Space (Warp) Segment to produce *_seg_inv_sn. mat stored in "T 1 Img. Segment" directory Warp masks into Individual space The calculation is performed in individual space 45

Intraoperative Processing No realign since there is no head motion. DPARSFA will generate the

Intraoperative Processing No realign since there is no head motion. DPARSFA will generate the mean functional images automatically. Reorient interactively since T 1 images are in a bad Define ROI Interactively orientation. Reorientation since is not effectsnormalization on coregistered T 1 performed image and functional images after slice timing correction 46

VBM Only Segment checkbox is checked Define the Starting Directory Name as T 1

VBM Only Segment checkbox is checked Define the Starting Directory Name as T 1 Raw 47

Further Help Further questions: www. restfmri. net 48

Further Help Further questions: www. restfmri. net 48

Thanks to DONG Zhang-Ye GUO Xiao-Juan HE Yong LONG Xiang-Yu SONG Xiao-Wei YAO Li

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! 50

Thanks for your attention! 50