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Scripts for resting-state fMRI functional connectivity processing
This project forked from jpluta26/ants-rs-fmri
Scripts for resting-state fMRI functional connectivity processing
# Processing steps # # see help in individual scripts for more detail # # # 0) Preprocess data (using SPM, pipedream, etc) # generate binary brainmask, 3 tissue segmentations, and ROIs in T1 space # generate a 4D-nifti file of functional data # # 1) ANTs_fmriToT1.sh # motion correction of fmri data, coregistration between T1 and fmri # put everythign into fmri space # # # $>~/scripts/ANTs_fmriToT1.sh -i fmri_series.nii.gz -o sub01 -t sub01_T1.nii.gz -r sub01_ROI.nii.gz -c sub01_csf.nii.gz -w sub01_wm.nii.gz -g sub01_gm.nii.gz -b sub01_brainmask.nii.gz # # # 2) ANTs_rsfmri_pre.sh # extract the time series under each ROI # # $>~/scripts/ANTs_rsfmri_pre.sh -i fmri_series_MOCO.nii.gz -o sub01 -r sub01_ROI_fmri.nii.gz -c sub01_csf_fmri.nii.gz -g sub01_gm_fmri.nii.gz -w sub01_wm_fmri.nii.gz -b sub01_brainmask_fmri.nii.gz -a sub01avg.nii.gz # # # # 3) ANTs_rsfmri_filter.sh # filter each time series for motion, nuisance variables (csf, wm, global signal), and filter by a specified frequency. create a correlation matrix (or matrices) using correlation or wavelet decomposition. generate SPM-style plot of motion correction parameters # # $>~/scripts/ANTs_rsfmri_filter.sh -f sub01.csv -d 0 -m sub01MOCOparams.csv -n sub01compcorr_compcorr.csv -tr 3 -w -o sub01
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