Phase Unwrapping

Having set the input images, you are now ready for the first stage of QSM: phase unwrapping. Phase values are only stored in images within the range ±π. As the phase evolves in gradient-echo sequences, the true phase value can stray outside this range. In order to recover the true phase value, phase unwrapping is needed: by detecting the sharp transitions in phase from +π to −π (or −π to +π) the phase is restored to its true value.

The settings for this stage are:

• If present, the B₀ field strength can be found from the input image header. If it is not present, then de-select this option and enter the field strength (in Tesla) in the box.
• If present, the echo times can be found from the input image header. If not present, then de-select this option and enter the TE values (in milliseconds) in the box as a comma-separated list of numbers.
• Normally, the phase evolution with increasing echo time is estimated just by fitting to the input image data. However, if you have very few echoes (e.g., two) and you know that the phase value at zero echo time should be zero, then try this option: it may make the frequency estimation more robust.
• Phase unwrapping may be unreliable at the edges of your interior region mask, where the phase evolves rapidly and may be corrupted by noise. To remove these less-reliable phase estimates, select this option. The residuals of the phase fitting will be examined, and where the error estimate is greater than the value you set in the spinner below, these pixels will be removed from the mask.

Now click the to button start the phase unwrapping.

The output from this phase-unwrapping stage is a set of images with names taken from the input image (or first input image, if you multiple input images), but with a suffix appended to the name. These suffices are:

• _Unwrapped - a 4-D image showing the unwrapped (true) phase value for all the echoes. The phase values are in radians.
• _Magnitude - a magnitude image that is synthesised from all the echoes.
• _InteriorMask - a (possibly eroded) version of the interior mask.
• _R2Star - an image of R₂^* - the exponential decay constant derived from the gradient-echo decay rate. This will only be produced if there is more than one echo in the input images.
• _TFS - an image of the Total Field Shift - the B₀ field strength and echo times are used to derive the field deviation from the unwrapped phase values. The field shift units are parts-per-million (PPM).
• _Weights - an weights image derived from the magnitude data, which is used in a later stage of processing.

One slice of the total field shift (TFS) image produced as part of phase unwrapping and frequency fitting

You can now go on to the next stage, which is background removal.