pandas_fslcc.py

import subprocess
import io
import pandas as pd

# The fslcc binary to use
FSLCC = '/opt/fsl/5.0.11/bin/fslcc'

# Parameters for the command line. No thresholding, report 4 digits.
FSLCC_PARAMS = ['-t', '0', '-p', '4']


def call_fslcc(file1, file2):
    """
    Compute cross-correlation by calling fslcc and parsing the output
    into a pd DataFrame.
    """
    cc = subprocess.check_output([FSLCC, *FSLCC_PARAMS, file1, file2])
    return pd.read_csv(io.StringIO(cc.decode()), delimiter='\s+',
                       header=None, names=['file1', 'file2', 'CC'])
  
  
  # Example:
  df = call_fslcc('sub-01.ica/melodic_IC.nii.gz', 'sub-02.ica/melodic_IC.nii.gz')