Research Overview
Standard functional images, using the EPI sequence, are distorted due to magnetic field inhomogeneities. These inhomogeneities are caused by magnetic susceptibility differences in neighbouring tissues within the head - particularly for air/bone or air/tissue interfaces in the sinuses. Consequently, the functional (EPI) images suffer from geometrical distortion and signal loss, particularly in the inferior frontal and temporal regions. It is possible to measure the field inhomogeneities with a fieldmap sequence, use the measured field values to calculate the geometric distortion and signal loss, and then use the calculated information to compensate for these artefacts. Compensating for these artefacts is done by geometrically unwarping the EPI images and by applying cost-function masking in registrations to ignore areas of signal loss. Note that areas where signal loss has occurred cannot be restored with any form of post-processing, as the signal has been lost - only different acquisition techniques can restore signal in these areas.
Furthermore, there are two situations where dealing with these distortions: (1) for correcting motion-dependent changes; and (2) for registration with non-distorted images (e.g. structurals). With FUGUE, only the second case is dealt with. The issue of motion-dependent signal changes (due to motion-dependent changes in field inhomogeneity and distortion directions) is not dealt with in the current version.
Fieldmap Acquisition
Unfortunately, there is no standard sequence for fieldmap acquisitions and different scanners return different images. Normally these images require processing before they represent images with field values in the desired units (of radians/second) in each voxel. The most common sequence acquires two images with different echo times. The change in MR phase from one image to the other is proportional to both the field inhomogeneity in that voxel and the echo time difference. The field value is therefore given by the difference in phase between these two images divided by the echo time difference. This is true for Spin Echo, Gradient Echo or EPI sequences. However, EPI-based fieldmaps suffer from the same distortions (more or less) as the functional images, while Spin Echo or Gradient Echo based fieldmap images do not. Within FSL you cannot use EPI-based fieldmaps with the standard processing, and their use in general is very problematic. We strongly recommend that Spin Echo or Gradient Echo fieldmap sequences are used to acquire the images.
MR phase is the most important quantity in a fieldmap sequence, whereas in normal imaging this phase is not of interest and is normally not saved when reconstructing the images. As a consequence, raw fieldmap scans are somewhat different from most scans, and may contain images of complex values, or separate phase and magnitude images. Furthermore, some scanners/sites may do the full reconstruction of acquired scans to yield a real-valued map of field inhomogeneities (in units of Hz, radians per second, Tesla or ppm). Alternatively no reconstruction may be done, and the raw phase and magnitude (or complex) images may be saved instead. It is important for each different scanner/site/sequence to know what form your data is in. If they have been converted to NIFTI or ANALYZE format, then you can use the FSL tools (particularly fslinfo) to determine the types of images present. To obtain fieldmaps that can be used within FSL using the FSL tools (in particular, PRELUDE and FUGUE), please refer to the page on preparing fieldmaps for FEAT.