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1_generate_example_func

This script performs data processing steps on functional MRI (fMRI) data.

The steps are as follows
  1. Set up directory structure for the experiment.
  2. Identify and prepare the raw functional volume for processing.
  3. Convert the raw DICOM file to a NIFTI format using dcm2niix.
  4. Deoblique correct the NIFTI file using AFNI's 3dWarp tool.
  5. Extract the brain from the image using AFNI's Automask tool with specific parameters.
The script assumes that
  • The raw DICOM files are available in a directory named 'raw' under '2.data'.
  • The processed data should be stored in a structure under 'preprocessed' directory, with example

functions stored in a subdirectory called 'example_func'.

The code is written to run on a Unix-based system. It uses AFNI and dcm2niix tools for processing.