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hcp-surface-format's Introduction

Modified HCP pipeline

This project project freesurfer/MNI volume space data to HCP CIFTI files and downsample to resolutions < 32k.

Data input

Structural - Freesurfer recon-all results (white matter boarder visually inspected)
Functional - Basic preprocessed resting state timeseries and average volumes in MNI space.

fMRI preprocessing:

  • Motion correction
  • Noise regression
  • Band-pass filtered
  • No smoothing

Optional:

  • Global signal regression

Environment setup

HCP pipeline (minimum: files under HCPpipeline/global/)
BALSA_database
Freesurfer
FSL
Connectome workbench

Order

common space template

Only need to run these files once

  1. CreateNewResTemplate.sh
  2. DownsampleGroupTemplate.sh

subject preprocessing

  1. GiftiReady.sh
  2. GoodvoxelsRibbon.sh
  3. NeocorticalResampler.sh
  4. SubcorticalResampler.sh

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