This page contains information relevant to B0 field map un-warping, using the HUP6, Siemens 3T scanner and FSL FUGUE program.
FSL_FUGUE

The b0 field map acquisition is a Gradient Echo fieldmap sequence that takes 1 min. 4 sec. to run. Though this sequence can probably be found in other places, I recommend using the sequence that is in the protocol named below.

1. Add the b0 field map sequence to your protocol by copying it over from this protocol: \user\research\thompson-schill\COLORADAPTATIONS_bomap. The name of the sequence is 'B0map“.
2. After adding the sequence has been added to your protocol, make sure that these parameters match: (number of) slices, slice thickness, field of view (FoV), and shim mode. All of these can be found on the “Routine” page of the sequence parameters, except for shim mode. Shim mode can be found on the “System” page of the sequence parameters. It should either read “standard” or “advanced”. Most protocols are set to “standard”, but this b0 map sequence is set to “advanced”- It does not need to be. Just make sure that all of the epi runs' shim mode matches the b0 shim mode. Here is an example of the scanner protocol parameters with relevant fields highlighted: b0map.pdf
3. Head coil does NOT matter. Use whichever you prefer.

External Link

These commands can be implented as a bash script, or added into your existing processing scripts.