Dear Aldana,
>
> Dear FSL experts,
>
> I have a set of DWI images acquired with a Siemens PET/MR Biograph mMR. Due to a mistake in the acquisitions parameters, only the phase image was reconstructed from the double-echo GRE field map sequence. I would like to know if it´s possible to perform the correction of susceptibility-induced distortions even without the magnitude images. Since the most important information is on the phase image, I've tried to solve the problem in different ways but none worked so far. Have you seen a problem like this before?
I haven’t come across this problem before, so I am not sure, but I think there might be a solution to your problem. The magnitude image is really only used to mask the phase image to ensure that we only consider the phase in voxels where it is meaningful. In voxels where the signal is zero (or close to zero) the phase is essentially random, and we want to mask those voxels out. It should be possible to see by just looking at your phase images where the phase is “meaningful” and where it is just noise. So it should be possible for you to use fsleyes or fslview to manually draw regions of interest, delineating the “meaningful” area in each transversal image. You can then save that out as a binary 3D file that you can pass into PRELUDE as your magnitude image.
As I said, I haven’t tried it myself, but I can’t see why it wouldn’t work. Just make sure you try it on one subject to make sure it works before you start drawing ROIs in all subjects. I’m afraid it will involve a lot of work.
Jesper
>
> Thanks in advance!
>
> Aldana
>
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