fsl.wrappers.flirt

This module provides wrapper functions for the FSL FLIRT tool, and other related tools.

flirt

Wrapper for the flirt command.

applyxfm

Convenience function which runs flirt -applyxfm ....

applyxfm4D

Wrapper for the applyxfm4D command.

invxfm

Use convert_xfm to invert an affine.

concatxfm

Use convert_xfm to concatenate two affines.

mcflirt

Wrapper for the mcflirt command.

fsl.wrappers.flirt.flirt(src, ref, **kwargs)[source]

Wrapper for the flirt command.

The twod argument may be used in place of the 2D command line option.

fsl.wrappers.flirt.applyxfm(src, ref, mat, out, interp='spline', **kwargs)[source]

Convenience function which runs flirt -applyxfm ....

fsl.wrappers.flirt.applyxfm4D(src, ref, out, mat, **kwargs)[source]

Wrapper for the applyxfm4D command.

fsl.wrappers.flirt.invxfm(inmat, omat)[source]

Use convert_xfm to invert an affine.

fsl.wrappers.flirt.concatxfm(atob, btoc, atoc)[source]

Use convert_xfm to concatenate two affines. Note that the order of the input matrices is the opposite of the order expected by convert_xfm.

Parameters
  • atob – Input matrix, transforming from “A” to “B”.

  • btoc – Input matrix, transforming from “B” to “C”.

  • atoc – Output matrix, transforming from “A” to “C”.

fsl.wrappers.flirt.mcflirt(infile, **kwargs)[source]

Wrapper for the mcflirt command.