@e0046902 are you sure that these fieldmaps belong to this BOLD EPI sequence. I would suggest acquiring the field map with identical properties (voxel spacing, resolution, angulation, etc). I notice your images have different voxel spacing and different resolution, resulting in a different field of view (FoV). I have never tried to use FSL’s FUGUE in with these variations. I do wonder if the change in the FOV leads the scanner to re-shim in order to provide the optimal homogeneity for the selected volume. This would change the physical values that the field map measures.
fslhd /Users/chrisrorden/Desktop/sub-ID01/fmap/sub-ID01_magnitude1.nii.gz
...
pixdim1 4.125000
pixdim2 4.125000
pixdim3 2.000000
...
sto_xyz:1 0.000000 0.000000 2.000000 -79.000000
sto_xyz:2 -4.125000 -0.000000 0.000000 123.369247
sto_xyz:3 0.000000 4.125000 0.000000 -144.218826
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
fslhd sub-ID01_task-meditation_bold.nii.gz
...
pixdim1 1.100917
pixdim2 1.100917
pixdim3 1.100000
...
sto_xyz:1 0.000000 0.000000 -1.100000 68.750000
sto_xyz:2 -1.100917 0.000000 0.000000 97.043587
sto_xyz:3 0.000000 1.100917 0.000000 -135.242950
sto_xyz:4 0.000000 0.000000 0.000000 1.000000