Hi Mark!
Thank you so much for your quick response!
Here are the two original phase images:
If what you are saying is the problem, could you
please specify what you mean by "more sophisticated
methods of reconstructing phase from multiple coils"
Thank you so much!!
Best,
Anna
----- Original Message -----
Sent: Tuesday, May 24, 2016 8:04:05 AM
Subject: Re: [FSL] Prelude Unwrapping Problem
Hi,
It's hard to say exactly what is happening without
seeing the original, wrapped phase images, but I suspect
that the problem lies in phase reconstruction
errors. We have seen this before when phase is
reconstructed from multiple coils that are not combined
correctly. It can be identified as a phase wrapping
line (discontinuity) that just stops at some
point. This does not represent a true phase signal that
can be unwrapped, and is a consequence of switching from
one coil's phase measurement to another, normally where
the signal is very low. Unfortunately, PRELUDE is only
capable of dealing with phase images that derive from a
single, continuous, phase image that is wrapped. A
piecewise phase image, with other discontinuities at the
borders, cannot be unwrapped like this and needs
attention in the acquisition/reconstruction. We have
found that acquiring the phase using a single coil
produces correct phase, as can more sophisticated
methods of reconstructing phase from multiple
coils. Either way, it needs to be dealt with prior to
running the FSL tools.
If you want to check if this is really the problem
then send us an image of the original, wrapped phase
image and we can confirm if this is the case.
Sorry I don't have better news.
All the best,
Mark
Date: Monday, 23 May 2016 at 10:15
Subject: [FSL] Prelude Unwrapping Problem
Dear FSL Experts,
I am trying to prepare fieldmaps for FUGUE and have a
problem with the prelude command where the fieldmaps
dont fully unwrap.
I am using Siemens 7T data with two pahse and two
magnitude images which
I can not feed into fsl_prepare_fieldmap (due to
having seperate phase images), so I followed the
steps of non-siemens data.
The phase images are in radians as prescribed.
After using the proposed prelude commands:
prelude -a fieldmap_mag -p phase0_rad -o
phase0_unwrapped_rad
prelude -a fieldmap_mag -p phase1_rad -o
phase1_unwrapped_rad
I found, that the images are not fully unwrapped with
sharp edges.
So I changed it to the following:
prelude -a fieldmap_mag -p phase0_rad -o
phase0_unwrapped_rad -n 30 -m
prelude -a fieldmap_mag -p phase1_rad -o
phase1_unwrapped_rad -n 30 -m
(with m being the mask from the magnitude image)
The unwrapping was still not good so I changed the n
value several times,
but everytime one area that was unwrapped previously
got fixed, another
showed up in a different area:
Does anyone know how to fix this?
Thank you so much for your help in advance!
Best,
Anna