def oxasl_preproc(wsp):
"""
Run standard processing on ASL data
This method requires wsp to be a Workspace containing certain standard information.
As a minimum, the attribute ``asldata`` must contain an AslImage object.
"""
if wsp.calib_first_vol and wsp.calib is None:
wsp.input.calib = wsp.asldata.calib
report_asl(wsp)
struc.init(wsp)
corrections.apply_corrections(wsp)
corrections.get_motion_correction(wsp)
corrections.apply_corrections(wsp)
reg.reg_asl2calib(wsp)
reg.reg_asl2struc(wsp, True, False)
reg.reg_asl2custom(wsp)
corrections.get_fieldmap_correction(wsp)
corrections.get_cblip_correction(wsp)
corrections.get_sensitivity_correction(wsp)
corrections.apply_corrections(wsp)
mask.generate_mask(wsp)
if oxasl_enable and wsp.use_enable:
wsp.sub("enable")
oxasl_enable.enable(wsp.enable)
wsp.corrected.asldata = wsp.enable.asldata_enable
def get_mask(wsp):
if wsp.mask is None:
mask.generate_mask(wsp.deblur)
wsp.mask = wsp.rois.mask
else:
wsp.mask = wsp.mask
def model_basil(wsp):
"""
Do model fitting on TC/CT or subtracted data
Workspace attributes updated
----------------------------
- ``basil`` - Contains model fitting output on data without partial volume correction
- ``basil_pvcorr`` - Contains model fitting output with partial volume correction if
``wsp.pvcorr`` is ``True``
- ``output.native`` - Native (ASL) space output from last Basil modelling output
- ``output.struc`` - Structural space output
"""
wsp.basil_options = wsp.ifnone("basil_options", {})
basil.basil(wsp, output_wsp=wsp.sub("basil"))
redo_reg(wsp, wsp.basil.finalstep.mean_ftiss)
wsp.sub("output")
output_native(wsp.output, wsp.basil)
output_trans(wsp.output)
# If the user has provided manual PV maps (pvgm and pvgm) then do PVEc, even if they
# have not explicitly given the --pvcorr option
user_pv_flag = ((wsp.pvwm is not None) and (wsp.pvgm is not None))
if (wsp.pvcorr) or (wsp.surf_pvcorr) or user_pv_flag:
# Partial volume correction is very sensitive to the mask, so recreate it
# if it came from the structural image as this requires accurate ASL->Struc registration
if wsp.rois.mask_src == "struc":
wsp.rois.mask_orig = wsp.rois.mask
wsp.rois.mask = None
mask.generate_mask(wsp)
if wsp.pvcorr or user_pv_flag:
# Do partial volume correction fitting
#
# FIXME: We could at this point re-apply all corrections derived from structural space?
# But would need to make sure corrections module re-transforms things like sensitivity map
# Prepare GM and WM partial volume maps from FAST segmentation
if user_pv_flag:
wsp.log.write("\nUsing user-supplied PV estimates\n")
wsp.structural.wm_pv_asl = wsp.pvwm
wsp.structural.gm_pv_asl = wsp.pvgm
else:
struc.segment(wsp)
wsp.structural.wm_pv_asl = reg.struc2asl(
wsp, wsp.structural.wm_pv)
wsp.structural.gm_pv_asl = reg.struc2asl(
wsp, wsp.structural.gm_pv)
wsp.basil_options.update({
"pwm": wsp.structural.wm_pv_asl,
"pgm": wsp.structural.gm_pv_asl
})
basil.basil(wsp, output_wsp=wsp.sub("basil_pvcorr"), prefit=False)
wsp.sub("output_pvcorr")
output_native(wsp.output_pvcorr, wsp.basil_pvcorr)
output_trans(wsp.output_pvcorr)
if wsp.surf_pvcorr:
if oxasl_surfpvc is None:
raise RuntimeError(
"Surface-based PVC requested but oxasl_surfpvc is not installed"
)
if user_pv_flag:
wsp.log.write(
" - WARNING: Performing surface based PVC ignores user-specified PV maps\n"
)
# Prepare GM and WM partial volume maps from surface using Toblerone plugin
# Then reform the ASL ROI mask - Toblerone does not handle the cerebellum so need
# to mask it out
oxasl_surfpvc.prepare_surf_pvs(wsp)
wsp.rois.mask_pvcorr = wsp.rois.mask
min_pv = 0.01
new_roi = (wsp.basil_options["pwm"].data >
min_pv) | (wsp.basil_options["pgm"].data > min_pv)
wsp.rois.mask = Image(new_roi.astype(np.int8),
header=wsp.rois.mask_pvcorr.header)
basil.basil(wsp,
output_wsp=wsp.sub("basil_surf_pvcorr"),
prefit=False)
wsp.sub('output_surf_pvcorr')
output_native(wsp.output_surf_pvcorr, wsp.basil_surf_pvcorr)
output_trans(wsp.output_surf_pvcorr)