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2_preprocessing_raw

This script converts DICOM files to NIFTI format and performs
  • Deoblique correction
  • Brain extraction using AFNI Automask
  • Spatial registration against a reference volume (AFNI 3dvolreg)

All processing is done in the provided directory structure. The script uses AFNI's dcm2niix, 3dWarp, Automask, and 3dvolreg commands. After processing each volume, it organizes files into run-specific directories and removes unnecessary intermediate files to save space.