Preprocessing: Realigning and Unwarping
Regarding the question of why two field map images are acquired... this paper is useful in explaining this. Brief extract from the paper ...
A ﬁeld map can be computed from the phase of the complex image data. By collecting more than one echo spaced in time it is possible to measure changes in the phase (and therefore the magnetic ﬁeld) that are independent of imaging gradients and artefacts caused by the excitation pulse. Image processing techniques are required to convert the phase change map into a map of voxel shifts that can then be used to unwarp the distorted images.
Below is a list of web resources used in the talk
Jody Culham's fMRI for newbies
Cusack, R., Brett, M. & Osswald, K. (2003) "An evaluation of the use of magnetic field maps to undistort echo-planar images" Neuroimage 18, 127-142.
Cusack, R., & Papadakis, N. (2002) "New robust 3-d phase unwrapping algorithms: application to magnetic field mapping and undistorting echoplanar images" Neuroimage 16, 754-764.
Jezzard, P. and Balaban, R.S. (1995). "Correction for Geometric Distortion in Echo Planar Images from B0 Field Variations" Magnetic Resonance in Medicine 34: 65-73.