Dear Dr. Mark Jenkinson and/or other FUGUE Developers,
I am having trouble figuring out how to properly use FUGUE to get useful output. The exact command I am running is as follows:
fugue -i $datadir/EPI.nii --dwell=0.524 --asym=1 --loadfmap=$datadir/BFieldMasked.nii.gz --unwarpdir=y- --poly=4 -u $datadir/epi_Bcorrected_poly
The B-field image was originally collected with a 128*128 matrix, and I downsampled it to 64*64. When I tried this command prior to resampling, it ran VERY quickly and produced output that was identical to the input. After resampling, it took longer to run but the output was really garbled. It had sweeping gray lines through an image that was otherwise dark except around the edges of the brain. I've also tried various unwarp directions, with no success. If it would help, I would be happy to upload any relevant data files, or provide any additional info.
I did try searching through the discussion group archive, but I was unable to find anything clearly relevant to this issue.
I would greatly appreciate any help with this.
Thanks in advance,
Will
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