I only have Siemens fieldmap (phase difference and two magnitude images) in a dataset and the fieldmaps are 4 mm isotopic.
I would like to combine PRELUDE/FUGUE with eddy tool using --field option in order to minimise the number of interpolations. I have a few questions regarding how to prepare the fieldmap for eddy.
I used to run the following operations from the fsl_prepare_fieldmap script on a masked fieldmap in order to prepare the fieldmap:1) Convert the fieldmap into radians2) Unwrap the fieldmap with PRELUDE3) Convert the fieldmap to rad/s (division by the echo time difference)4) Call FUGUE to extrapolate from mask (fill holes, etc)5) Demean to avoid gross shifting6) Clean up edge voxelsThen, I smoothed a little bit the fieldmap (2mm 3D Gaussian) prior to registering the fieldmap onto the b0 for the preprocessing with fugue.
I have two main questions:1) In the documentation of FSL eddy, the --field flag requires the prepared fieldmap in Hz, however I am not sure when to do that. Can I simply replace the step 3 by the conversion into Hz?
2) Regarding the regularisation step of the fieldmap, I was advised to do a 3D smoothing of 2mm but I did not find any documentation about it. Does the fieldmap still need to be smoothed for eddy? In a former thread, I read that we may need to smooth the warpfield in order to be invertible. Should I first try with no smoothing then iteratively increase the smoothing of the fieldmap if eddy does not work?
Thanks in advance for your answers.
Best,Alexandre
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