Tours#
Corrections applied to the data before reconstruction or to the image after it, each shown on its own and independent of the course: removal of readout oversampling and apodization, EPI Nyquist-ghost correction and regridding of ramp-sampled readouts, receive bias-field correction, correction of the geometric distortion caused by gradient nonlinearity, off-resonance deblurring of spiral images, rigid head-motion tracking from navigators, and correction of susceptibility distortion in EPI. The first six tours simulate the artefact from a known ground truth, so that the correction is evaluated against it; the seventh corrects measured data and evaluates the correction against an independent field map.
The first tour removes readout oversampling and compares Fermi and Hann apodization by their Gibbs ringing and resolution. The second corrects the Nyquist ghost of an EPI train from a three-line navigator and resamples a ramp-sampled readout. The third estimates the receive bias field of a head array with N4. The fourth corrects the geometric distortion and intensity error of gradient nonlinearity from the coil’s spherical-harmonic coefficients. The fifth deblurs a spiral image off resonance by multifrequency interpolation and by a time-segmented reconstruction. The sixth measures rigid head motion from three orthogonal navigator planes and filters it across a scan. The seventh corrects the susceptibility distortion of a 3 T EPI pair with reversed phase encoding, downloaded from OpenNeuro.
The section additionally requires the following packages, and the seventh tour
downloads about 2 MB of data into ~/.cache/bartorch-examples:
pip install SimpleITK PyHySCO
