I figured out that the input I needed to have for the magnitude file needed to include a .gz at the end. Thanks for your help! I am running inot another issue now though.

When I run fsl_prepare_fieldmap I get the error message

Loading volumes
Phase loaded
Magnitude loaded
Mask loaded
ERROR: input phase image exceeds allowable phase range.
Allowable range is 6.283 radians.  Image range is: 12.5541 radians.
Aborting.
Cannot open volume /tmp/fsl_cvXneJ_tmp_ph_radians_unwrapped for reading!
Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_cvXneJ_tmp_ph_rps
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
Cannot open volume fmap_rads for reading!
Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_cvXneJ_tmp_fmapmasked
Cannot open volume fmap_rads for reading!
Image Exception : #22 :: ERROR: Could not open image fmap_rads
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
Cannot open volume /tmp/fsl_cvXneJ_tmp_fmapfilt for reading!
Cannot open volume fmap_rads for reading!
Done. Created fmap_rads for use with FEAT.

My magnitude image is the average of two magnitude field maps. could this be causing the problem (12.5 rads instead of allowable 6.2 rads)?

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