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Further Processing following Fmriprep

Full steps:

  • run recon-all first: job_recon_all.sh
  • skip 4 frames (done in CBIG_preproc)
  • run fmriprep (--output-space fsaverage6): fmriprep_singleSub.sh and run_fmriprep_GSP.sh
  • run all post-processing steps: run_postproc_GSP.sh
    • regression (GLM using motion, wm, csf, whole-brain regressors) with censoring: fmriprep_regress.sh
    • interpolation and bandpass: fmriprep_censor_bp.sh
    • smooth and downsample to fsaverage5: fmriprep_sm_ds.sh
  • run QC (single subject for now): fmriprep_QC.sh
  • compute clusters: fmriprep_clustering.sh

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