fsl.utils.parse_data

This module contains support for neuroimaging data in argparse

Argparse is the built-in python library for resolving command line arguments.

The functions in this module can be passed on to the type argument in the ArgumentParser.add_command method to interpret command line arguments as neuroimaging objects (.e.g, NIFTI image files)

Image Reads in an image from a NIFTI or Analyze file.
ImageOut Uses the FSL convention to create a complete image output filename
Mesh Reads in a mesh from either a GIFTI (.surf.gii) or a VTK (.vtk) file
Atlas Reads in the atlas from the FSL standard atlases
fsl.utils.parse_data.Image(filename, *args, **kwargs)[source]

Reads in an image from a NIFTI or Analyze file.

Parameters:filename – filename provided by the user
Returns:fsl.data.image.Image object

All other arguments are passed through to the Image upon creation.

fsl.utils.parse_data.ImageOut(basename)[source]

Uses the FSL convention to create a complete image output filename

Parameters:basename – filename provided by the user
Returns:filename with extension
fsl.utils.parse_data.Mesh(filename)[source]

Reads in a mesh from either a GIFTI (.surf.gii) or a VTK (.vtk) file

Parameters:filename – filename provided by the user
Returns:GIFTI or VTK sub-class of fsl.data.mesh.Mesh
fsl.utils.parse_data.Atlas(name)[source]

Reads in the atlas from the FSL standard atlases

Parameters:name – name of the atlas
Returns:fsl.data.atlases.Atlas representation of an FSL atlas