PRELUDE - Phase Unwrapping
Phase Region Expanding Labeller for Unwrapping Discrete Estimates
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PRELUDE
prelude performs 3D phase unwrapping of images. This is useful
for fieldmap acquisitions, susceptibility weighted imaging (SWI), or
other applications involving phase in MR (or non-MR) images. The input
can either be a single complex image (NIfTI or Analyze), or a pair of
real images giving the phase and absolute values separately. Also see
fslcomplex for
more ways to manipulate complex image formats.
If the images are 4D images, then each 3D volume is unwrapped
separately, and the result saved as a 4D image of unwrapped phase
images. The output in either case is a real, unwrapped phase image
(in radians).
For higher resolution images (e.g. for Susceptibility Weighted
Imaging) a mask should be used in order to reduce run-times since any
areas that include noisy voxels will significantly increase the
required run-time. The best way to generate a mask for a whole brain
image is to run BET to perform brain extraction on the absolute image.
The three 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
- prelude -a data_abs -p data_phase -u result -m mask
- uses separate phase and absolute input files with a mask
Additional options that are useful are:
- -m mask
- uses the user-defined mask (e.g. a BET mask - especially for high resolution images)
- -n num
- specifies the number of phase partitions
the algorithm uses for initial 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 optimising speed is an issue
- --labelslices
- does labelling in 2D, but
unwrapping in 3D - the default for high-res images
Mark Jenkinson
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