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


From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Anna Schmidt <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Monday, 23 May 2016 at 10:15
To: "[log in to unmask]" <[log in to unmask]>
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.

https://drive.google.com/open?id=0BwbKkBtmWbwkYU92S2ExU1hmRmc

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:

https://drive.google.com/open?id=0BwbKkBtmWbwkVERwbmhyYXBwM3c

https://drive.google.com/open?id=0BwbKkBtmWbwkck5TVzI3OUQxUm8

https://drive.google.com/open?id=0BwbKkBtmWbwkNVdDc0FUX3dNQ2s

Does anyone know how to fix this?

Thank you so much for your help in advance!


Best,

Anna