The latest versions of fsl_prepare_fieldmap do have some code to account for images where the intensity range of the input is not 4096 but twice this, and it adjusts for that automatically. This is what your fslmaths command is doing. So I think that
the current version should accept your original input without problem. Do you find that you get the same result with and without your pre-processing step? If so, then that would definitely confirm this.
Note that code from several years ago did not have this automatic adjustment, so at some point in the past your pre-processing call to fslmaths was probably necessary.
Hello
My question is as follows:
Is it necessary to process the phase difference image from SIEMENS scanners before usage in the fsl_prepare_fieldmap command?
I have an older analysis guide I have inherited from my supervisor, where there is a processing step on the phase difference image before usage in the fsl_prepare_fieldmap command.
It is as follows: fslmaths *_FM_phase.nii -add 4096 -mul .5 *_FM_phase_sc.nii
(*=my subjects ID)
And the *_FM_phase_sc.nii is used as input in the fsl_prepare_fieldmap command.
I have tried both with and without this processing step, and it is not obvious to me what is correct. I have not been able to find the answer on the Wiki or in the FSL course practical material.
Thanks in advance!
Iselin Meluken
MD, PhD student