def reg_bbr(wsp):
"""
Perform BBR registration
:param reg_img: Data to register, e.g. PWI or calibration image. Normally would be brain extracted
:param struc_img: Structural image
:param struc_brain_img: Brain-extracted structural image
Optional keyword arguments:
:param inweight:
:param init: Initial transform matrix
Optional keyword arguments for fieldmap distortion correction:
:param fmap: Fieldmap image
:param fmapmag: Fieldmap magnitude image
:param fmapmagbrain: Fieldmap magnitude image - brain extracted
:param pedir: Phase encoding direction (x, -x, y, -y, z, -z)
:param echospacing: Echo spacing
:return Tuple of registered image, transform matrix
"""
struc.segment(wsp)
wsp.log.write(" - BBR registration using epi_reg...")
# Windows can't run epi_reg as it's a batch script. Use our experimental python
# implementation but use the standard epi_reg on other platforms until the python
# version is better tested
if sys.platform.startswith("win"):
import oxasl.epi_reg as pyepi
result = pyepi.epi_reg(wsp, wsp.reg.nativeref)
else:
result = epi_reg(epi=wsp.reg.nativeref,
t1=wsp.structural.struc,
t1brain=wsp.structural.brain,
out=fsl.LOAD,
wmseg=wsp.structural.wm_seg,
init=wsp.reg.asl2struc,
inweight=wsp.inweight,
log=wsp.fsllog)
wsp.log.write(" DONE\n")
return result["out%s" % defaultExt()], result["out"]
def get_fieldmap_correction(wsp):
"""
Get the fieldmap based distortion correction warp
Required workspace attributes
-----------------------------
- ``pwi`` : Perfusion weighted image (generated by preproc_asl)
- ``fmap`` : Fieldmap image
- ``fmapmag`` : Fieldmap magnitude image
- ``fmapmagbrain`` : Fieldmap magnitude brain image
- ``echospacing`` :
- ``pedir`` :
Optional workspace attributes
-----------------------------
- ``nofmapreg`` : If True assume fieldmap in structural space
Updated workspace attributes
----------------------------
- ``fmap_warp`` : Fieldmap distortion correction warp image in ASL space
"""
if wsp.fmap is None or wsp.fmapmag is None or wsp.fmapmagbrain is None:
wsp.log.write(" - No fieldmap images for distortion correction\n")
return
elif wsp.pedir is None or wsp.echospacing is None:
wsp.log.write(
" -WARNING: Fieldmap images supplied but pedir and echospacing required for distortion correction\n"
)
return
wsp.sub("fieldmap")
wsp.log.write(
" - Calculating distortion correction from fieldmap images using EPI_REG\n"
)
epi_reg_opts = {
"inweight": wsp.inweight,
"init": wsp.reg.asl2struc,
"fmap": wsp.fmap,
"fmapmag": wsp.fmapmag,
"fmapmagbrain": wsp.fmapmagbrain,
"pedir": wsp.pedir,
"echospacing": wsp.echospacing,
"nofmapreg": wsp.ifnone("nofmapreg", False),
}
# Windows can't run epi_reg as it's a batch script. Use our experimental python
# implementation but use the standard epi_reg on other platforms until the python
# version is better tested
if sys.platform.startswith("win"):
import oxasl.epi_reg as pyepi
result = pyepi.epi_reg(wsp, epi=wsp.reg.nativeref, **epi_reg_opts)
else:
result = epi_reg(epi=wsp.asldata.perf_weighted(),
t1=wsp.structural.struc,
t1brain=wsp.structural.brain,
out=fsl.LOAD,
wmseg=wsp.structural.wm_seg,
log=wsp.fsllog,
**epi_reg_opts)
# Occasionally we end up with NaN in the output of epi_reg and this will ruin the entire distcorr warp.
# So remove any NaN values and replace with zero.
warp_struc = result["out_warp"]
wsp.fieldmap.warp_struc = Image(np.nan_to_num(warp_struc.data, nan=0),
header=warp_struc.header)
wsp.fieldmap.asl2struc = result["out"]
wsp.fieldmap.struc2asl = np.linalg.inv(wsp.fieldmap.asl2struc)
result = fsl.convertwarp(out=fsl.LOAD,
ref=wsp.reg.nativeref,
warp1=wsp.fieldmap.warp_struc,
postmat=wsp.fieldmap.struc2asl,
rel=True,
log=wsp.fsllog)
wsp.fieldmap.warp = result["out"]
page = wsp.report.page("fmap")
page.heading("Fieldmap distortion correction", level=0)
page.text("PE direction: %s" % wsp.pedir)
page.text("Echo spacing: %f s" % wsp.echospacing)
page.heading("Correction warps", level=1)
for dim in range(3):
img = Image(wsp.fieldmap.warp.data[..., dim],
header=wsp.fieldmap.warp.header)
page.text("Dimension %i" % dim)
page.image("fmap_warp%i" % dim, LightboxImage(img))