FUGUE: FMRIB's Utility for Geometrically Unwarping EPIs - User Guide

FUGUE Version 2.2 (in c# minor)

INTRODUCTION

This document gives a brief description of the various command line programs available in the FUGUE component of FSL - used for unwarping geometric distortion in EPI images. At present no GUI interface exists.

For each of the programs described here, a full list of available options can be obtained by running the command with the -h option.

Note that for all programs the options follow the normal convention that "single minus" options are separated by a space from their arguments (if any) whilst "double minus" options are separated by an equals sign and no space. For example,
prelude -c data --unwrap=result
or
prelude --complex=data -u result

PRELUDE

prelude (Phase Region Expanding Labeller for Unwrapping Discrete Estimates) performs 3D phase unwrapping of images. The input can either be a single complex analyse file, or a pair of real analyse files giving the phase and absolute values separately. If the files are 4D files, then each 3D volume is unwrapped separately, and the result saved as a 4D file of unwrapped phase images. The output in either case is a real, unwrapped phase image (in radians).

The two main forms of usage are:

prelude -c data -u result
uses a single complex input file
prelude -a data_abs -p data_phase -u result
uses separate phase and absolute input files

Additional options that are useful are:

-m mask
uses the user defined mask
-n num
specifies the number of phase partitions the algorithm uses for labelling - a larger value is likely to be more robust but slower
-s
unwrap in 2D, then stick slices together with appropriate offsets - this is less robust but fast - mainly used for very high-resolution images where speed is an issue
--labelslices
does labelling in 2D, but unwrapping in 3D - the default for high-res images

FUGUE

fugue (FMRIB's Utility for Geometrically Unwarping EPIs) performs unwarping of an EPI image based on fieldmap data. The input required consists of the EPI image, the fieldmap (as an unwrapped phase map or a scaled fieldmap in rad/s) and appropriate image sequence parameters (dwell time for EPI and asymmetric spin echo time for unwrapped phase fieldmap pairs).

The main forms of usage are:

fugue -i epi -p unwrappedphase -d dwelltoasymratio -s 0.5 -u result
fieldmap specified by a 4D file unwrappedphase containing two unwrapped phase images - a symmetric and an asymmetric spin echo - plus the ratio of dwell time to asymmetric spin echo time
fugue -i epi --dwell=dwelltime --loadfmap=fieldmap -u result
uses a previously calculated fieldmap

Note the option -s 0.5 is an example of how to specify the regularisation to apply to the fieldmap (2D Gaussian smoothing of sigma=0.5 in this case which is a reasonable default). There are many different forms of regularisation available which can be applied separately or together. These are:

-s sigma
2D Gaussian smoothing
--smooth3=sigma
3D Gaussian smoothing
-m
2D median filtering
--poly=n
3D Polynomial fitting of degree n
--fourier=n
3D Sinusoidal fitting of degree n

Some other uses are:

fugue -p unwrappedphase --asym=asymtime --savefmap=fieldmap -s 0.5
computes the fieldmap, applying some regularisation - useful for seeing the fieldmap and the effect of regularisation
fugue -i undistortedimage -p unwrappedphase -d dwelltoasymratio -s 0.5 -w warpedimage
applies the fieldmap as a forward warp, turning an undistorted image into a distorted one - useful for creating a registration target for the EPI from the undistorted absolute fieldmap image

Additional options that are useful are:

--unwarpdir=dir
specifies the direction of the unwarping/warping - i.e. phase-encode direction - with dir being one of x,y,z,x-,y-,z- (default is y)
--phaseconj
uses the phase conjugate correction method, rather than pixel shifts
--icorr
applies an intensity correction term when using the pixel shift method - often poorly conditioned for standard fieldmap acquisitions

Mark Jenkinson

Copyright © 2001, University of Oxford