Dear Mike,
Two additional notes:
For Siemens scanners you probably want to adjust fieldmap.m according to notes.txt included in this file http://www.mccauslandcenter.sc.edu/CRNL/wp-content/tools/fieldmap/fieldmap.zip from Rorden Lab to better reflect the scaling of the data.
> because the phase-encoding direction of my fieldmap is from right to left
If this is really then case then you probably have to adjust some of the fieldmap m files (or reorient the data), see http://www.fil.ion.ucl.ac.uk/spm/toolbox/fieldmap/ :
"f) All versions of FieldMap and Unwarp are only designed to work with images collected with the phase-encode direction in y.
a) The convention used to describe the direction of the k-space traversal is now based on the coordinate system used by SPM. In this coordinate system, the phase encode direction corresponds with the y-direction and is defined as positive from the posterior to the anterior of the head. The x-direction is defined as positive from left to right and the z-direction is defined as positive from foot to head. The polarity of the phase-encode blips describes in which direction k-space is traversed along the y-axis with respect to the coordinate system described here."
Best
Helmut
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