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)

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)

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)

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)

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