FUGUE EPI UnwarpingFMRIB's Utility for Geometrically Unwarping EPIs - v2.5 (in d minor) | ![]() |
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.
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.
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
The main forms of usage are:
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:
Some other uses are:
Additional options that are useful are: