Dear FSL Experts and Developers,
I am currently working on performing distortion correction on DWI data using field mapping (no reverse phase images acquired). The artefacts I see within the diffusion images include "stretching" of the frontal lobe (a horn like effect) and very large intensities in the temporal lobes. I am trying (unsuccessfully at this point) to utilize fugue to fix this.
I have what appears to be a fairly standard SIEMENS fieldmap sequence consisting of a magnitude image (2 volumes) and a phase image (intensity min 0 max 4094), deltaTE = 2.46ms.
However, the output of...
fsl_prepare_fieldmap SIEMENS <phase.nii> <magnitude.nii> <fieldout.nii> 2.46
gives me a "fieldout.nii" with an intensity range (for this one example) of min -524.421387 max 831.840830. My understanding is this output should be in Rad/S (i.e. 0 - 6.28). I have made sure that my single volume magnitude.nii image is aggressively skull stripped to not include non brain voxels.
Accordingly, when I use this output of fsl_prepare_fieldmap to perform the distortion correction...
fugue -i <dwi.nii> --dwell=.00069 --loadfmap=<fieldout.nii> -u <dwi_corrected.nii>
I see no effect on the dwi images.
After reading through the archives and stepping through fsl_prepare_fieldmap I suspect this is due to a scaling issue (i.e. the phase image does not appear to be properly scaled into radians, prior to unwrapping using prelude, and then radians/sec). However, I don't understand why this would be the case given my seemingly standard phase-map acquisition.
Any assistance you would be able to provide would be greatly appreciated. I see others have had issues with this pipeline but their solutions seem rather case specific. I would be more than happy to provide some example data if it is useful.
Thank you for all of your hard work!
Best, Derek
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