T1 bias correction using N4

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This pipeline uses the N4 algorithm, implemented in the Insight ToolKit, in order to correct for magnetic field bias.

The only required input is the structural T1 image, e.g. -i T1.nii.gz You can simply use the following line to use the pipeline:


The following paragraph describes some other optional arguments:

usage: perform_bias_field_correction.py [-h] -i input_img [input_img ...]
                                        [-m input_mask [input_mask ...]]
                                        [-o directory] [--output_pre prefix]
                                        [--output_suf suffix] [-g]

Pipeline to perform a bias field correction on an input image
or a list of input images.

optional arguments:
  -h, --help            show this help message and exit
  -i input_img [input_img ...], --img input_img [input_img ...]
                        Image file or list of input images
  -m input_mask [input_mask ...], --mask input_mask [input_mask ...]
                        Mask image or list of mask images (optional)
  -o directory, --output_dir directory
                        Output directory containing the registration result
                        Default is the current directory
  --output_pre prefix   Output result prefix
  --output_suf suffix   Output result suffix
  -g, --graph           Print a graph describing the node connections

Further information can be found here: