FUGUE DOCS

# FUGUE EPI Unwarping FMRIB's Utility for Geometrically Unwarping EPIs - v2.5 (in d minor) |

## INTRODUCTION

Standard functional images, using the EPI sequence, are distorted due to magnetic field inhomogeneities. These inhomogeneities are caused by magnetic susceptibility differences in neighbouring tissues within the head - particularly for air/bone or air/tissue interfaces in the sinuses. Consequently, the functional (EPI) images suffer from geometrical distortion and signal loss, particularly in the inferior frontal and temporal regions.

It is possible to measure the field inhomogeneities with a fieldmap sequence, use the measured field values to calculate the geometric distortion and signal loss, and then use the calculated information to compensate for these artefacts. Compensating for these artefacts is done by geometrically unwarping the EPI images and by applying cost-function masking in registrations to ignore areas of signal loss. Note that areas where signal loss has occurred cannot be restored with any form of post-processing, as the signal has been lost - only different acquisition techniques can restore signal in these areas.

Furthermore, there are two situations where dealing with these distortions: (1) for correcting motion-dependent changes; and (2) for registration with non-distorted images (e.g. structurals). With FUGUE, only the second case is dealt with. The issue of motion-dependent signal changes (due to motion-dependent changes in field inhomogeneity and distortion directions) is not dealt with in the current version.

### Fieldmap Acquisition

Unfortunately, there is no standard sequence for fieldmap acquisitions and different scanners return different images. Normally these images require processing before they represent images with field values in the desired units (of radians/second) in each voxel.

The most common sequence acquires two images with different echo times. The change in MR phase from one image to the other is proportional to both the field inhomogeneity in that voxel and the echo time difference. The field value is therefore given by the difference in phase between these two images divided by the echo time difference. This is true for Spin Echo, Gradient Echo or EPI sequences. However, EPI-based fieldmaps suffer from the same distortions (more or less) as the functional images, while Spin Echo or Gradient Echo based fieldmap images do not. Within FSL you cannot use EPI-based fieldmaps with the standard processing, and their use in general is very problematic. We strongly recommend that Spin Echo or Gradient Echo fieldmap sequences are used to acquire the images.

MR phase is the most important quantity in a fieldmap sequence, whereas in normal imaging this phase is not of interest and is normally not saved when reconstructing the images. As a consequence, raw fieldmap scans are somewhat different from most scans, and may contain images of complex values, or separate phase and magnitude images. Furthermore, some scanners/sites may do the full reconstruction of acquired scans to yield a real-valued map of field inhomogeneities (in units of Hz, radians per second, Tesla or ppm). Alternatively no reconstruction may be done, and the raw phase and magnitude (or complex) images may be saved instead. It is important for each different scanner/site/sequence to know what form your data is in. If they have been converted to NIFTI or ANALYZE format, then you can use the FSL tools (particularly `fslinfo`) to determine the types of images present. To obtain fieldmaps that can be used within FSL using the FSL tools (in particular, PRELUDE and FUGUE), please refer to the page on preparing fieldmaps for FEAT.

### GUI and command line software

A GUI interface exists for applying FUGUE to unwarp images as part of the FEAT preprocessing options. We strongly recommend using the pre-stats part of FEAT to do all such processing (note that it is not necessary to have fMRI data for this - even single volumes can be processed in FEAT by selecting pre-stats only). See the detailed documentation on FEAT and documentation on using PRELUDE/FUGUE for preparing fieldmaps for FEAT.

The rest of this document gives a brief description of the individual command line programs available in the FUGUE component of FSL - used for unwarping geometric distortion in EPI images. 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

See separate page on PRELUDE for phase unwrapping. Note that if you need to run phase unwrapping for fieldmap unwarping, then PRELUDE is run before FUGUE.

## 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 for the EPI and fieldmap acquisitions: the dwell time for EPI (also known as the echo spacing); and the echo time difference (called asym time herein).

The main forms of usage are:

fugue -i epi -p unwrappedphase --dwell=dwelltime --asym=asymtime -s 0.5 -u result
  fieldmap specified by a 4D file unwrappedphase containing two unwrapped phase images - from different echo times - plus the dwell time and echo time difference (asym 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 -i undistortedimage -p unwrappedphase --dwell=dwelltime --asym=asymtime --nokspace -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:

--mask=maskname
  uses a user-defined mask (called maskname) instead of deriving it from the phasemaps or fieldmaps
--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
--nokspace
  for forward warping (only) - uses an image-space method for forward warping
--icorr
  applies an intensity correction term when using the pixel shift method - often poorly conditioned for standard fieldmap acquisitions

#### Mark Jenkinson
Copyright © 2001-2010, University of Oxford