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
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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 imagejacobian
: Jacobian associated with warp imagesenscorr
: Sensitivity correction
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oxasl.corrections.
run
(wsp)[source]¶ Apply distortion and motion corrections to ASL and calibration data
asldata_orig
: Uncorrected ASL data image
calib_orig
: Calibration imagecref_orig
: Calibration reference imagecblip_orig
: Calibration BLIP imageasldata_mc_mats
: ASL motion correction matricescalib2asl
: Calibration -> ASL transformation matrixdistcorr_warp
: Distortion correction warp imagegdc_warp
: Gradient distortion correction warp image
asldata
: Corrected ASL datacalib
: Corrected calibration imagecref
: Corrected calibration reference imagecblip
: Corrected calibration BLIP image