Is there a way to use FAST from FSL only for bias field correction?

1

I am running the following command. I only need the _resore.nii.gz, but this command applies segmentation too, which I think makes it so slow. Is there another command that just does bias field correction?

        # Set the full path to the input file
        input_file = os.path.join(input_dir1, file)
        # Construct the FAST command
        fast_cmd = [os.path.join(fsl_dir, "fast"), "-t", "1", "-B", input_file]
        # -t : for T1W
        # -b output estimated bias field 
        # -B output restored image (bias corrected image)
        # Run the FAST command using subprocess
        completed_process = subprocess.run(fast_cmd)
2

Hi @Yasmine,

You can use this ANTs command: N4BiasFieldCorrection · ANTsX/ANTs Wiki · GitHub

Best,
Steven

3

The FSL fast tool simultaneously models the bias field and tissue probabilities, so the latter cannot be disabled.

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