Corrections module

OXASL - Module to apply Moco/Distortion/sensitivity corrections

This module generates corrected ASL/calibration data from previously calculated corrections with the minimum of interpolation

Currently the following sources of transformation exist:

  • Motion correction of the ASL data. This generates a series of linear (rigid body) transformations in ASL space, one for each ASL volume. If calibration data is also present a calibration->ASL transform is also generated as part of this process
  • Fieldmap-based distortion correction. This generates a nonlinear warp image in structural space which is then transformed to ASL space
  • Phase encoding reversed (CBLIP) distortion correction using TOPUP. This generates a nonlinear warp image in ASL space FIXME calibration space?
  • User-supplied nonlinear warp image for gradient distortion corection
  • Sensitivity correction

Except for the TOPUP correction, all of the above can be combined in a single transformation to minimise interpolation of the ASL data

Copyright (c) 2008-2020 Univerisity of Oxford

class oxasl.corrections.Options[source]

Options for corrections of the input data

groups(parser)[source]
Parameters:parser – OptionParser instance
Returns:Sequence of OptionGroup instances for this category of options
oxasl.corrections.correct_img(wsp, img, linear_mat)[source]

Apply combined warp/linear transformations to an image in ASL space

Parameters:
  • img – fsl.data.image.Image to correct
  • linear_mat – img->ASL space linear transformation matrix.
Returns:

Corrected Image

If a jacobian is present, also corrects for quantitative signal magnitude as volume has been locally scaled

FIXME there are slight differences to oxford_asl here due to use of spline interpolation rather than applyxfm4D which uses sinc interpolation.

  • asldata_mean : Mean ASL image used as reference space
  • total_warp : Combined warp image
  • jacobian : Jacobian associated with warp image
  • senscorr : Sensitivity correction
oxasl.corrections.run(wsp)[source]

Apply distortion and motion corrections to ASL and calibration data

  • asldata_orig : Uncorrected ASL data image
  • calib_orig : Calibration image
  • cref_orig : Calibration reference image
  • cblip_orig : Calibration BLIP image
  • asldata_mc_mats : ASL motion correction matrices
  • calib2asl : Calibration -> ASL transformation matrix
  • distcorr_warp : Distortion correction warp image
  • gdc_warp : Gradient distortion correction warp image
  • asldata : Corrected ASL data
  • calib : Corrected calibration image
  • cref : Corrected calibration reference image
  • cblip : Corrected calibration BLIP image