I get this error when trying to use fsl_prepare_fieldmap for several of my subjects.
fsl_prepare_fieldmap SIEMENS /Volumes/DANIEL/AES119/AES119.Ex/field_map/phase_map_gre_field_mapping_20170323131718_5_ph.nii /Volumes/DANIEL/AES119/AES119.Ex/field_map/skull_strip_avg_mag_eroded.nii.gz /Volumes/DANIEL/AES119/AES119.Ex/field_map/fmap_rads.nii 2.46
Phase and Magnitude images must have the same number of voxels and voxel dimensions
Current dimensions are:
Phase image: 96 x 96 x 53 with dims of 2.000000 x 2.000000 x 2.500000 mm
Magnitude image: 96 x 96 x 53 with dims of 2.000000 x 2.000000 x 2.499999 mm
Fix this (probably in reconstruction stage) before re-running this script
I get this after trying both 3dmerge and fslmaths -Tmean to average my 2 magnitude field map scans into one.
This process works for about 90% of the subject scans.
Any thoughts on what might be going wrong would be greatly appreciated.
Best,
Daniel Callow
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