def main(self):
with TemporaryDirectory() as tmpdir:
tmpdir = local.path(tmpdir)
pre = tmpdir / 'ants'
rigidxfm = pre + '0GenericAffine.mat'
antsRegistrationSyN_sh['-t', 'r', '-m', self.infile, '-f',
self.target, '-o', pre, '-n', 32] & FG
antsApplyTransforms('-d', '3', '-i', self.labelmap, '-t', rigidxfm,
'-r', self.target, '-o', self.out,
'--interpolation', 'NearestNeighbor')
def main(self):
fshome = local.path(os.getenv('FREESURFER_HOME'))
if not fshome:
logging.error('Set FREESURFER_HOME first.')
sys.exit(1)
with TemporaryDirectory() as tmpdir:
tmpdir = local.path(tmpdir)
b0masked = tmpdir / "b0masked.nrrd"
b0masked1mm = tmpdir / "b0masked1mm.nrrd"
brain = tmpdir / "brain.nii.gz"
wmparc = tmpdir / "wmparc.nii.gz"
brainmgz = self.parent.fsdir / 'mri/brain.mgz'
wmparcmgz = self.parent.fsdir / 'mri/wmparc.mgz'
wmparcindwi1mm = tmpdir / 'wmparcInDwi1mm.nii.gz'
logging.info(
"Make brain.nii.gz and wmparc.nii.gz from their mgz versions")
vol2vol = local[fshome / 'bin/mri_vol2vol']
label2vol = local[fshome / 'bin/mri_label2vol']
with local.env(SUBJECTS_DIR=''):
vol2vol('--mov', brainmgz, '--targ', brainmgz, '--regheader',
'--o', brain)
label2vol('--seg', wmparcmgz, '--temp', brainmgz,
'--regheader', wmparcmgz, '--o', wmparc)
logging.info('Extract B0 from DWI and mask')
bse_py('-i', self.parent.dwi, '-m', self.parent.dwimask, '-o',
b0masked)
logging.info('Made masked B0')
logging.info('Upsample masked baseline to 1x1x1')
ResampleImageBySpacing('3', b0masked, b0masked1mm, '1', '1', '1')
logging.info('Made 1x1x1 baseline')
logging.info('Register wmparc to B0')
pre = tmpdir / 'fsbrain_to_b0'
affine = pre + '0GenericAffine.mat'
warp = pre + '1Warp.nii.gz'
antsRegistrationSyNMI_sh['-m', brain, '-f', b0masked1mm, '-o', pre,
'-n', 32] & FG
antsApplyTransforms('-d', '3', '-i', wmparc, '-t', warp, affine,
'-r', b0masked1mm, '-o', wmparcindwi1mm,
'--interpolation', 'NearestNeighbor')
logging.info('Made ' + wmparcindwi1mm)
logging.info('Make output directory')
self.parent.out.mkdir()
b0masked.copy(self.parent.out)
b0masked1mm.copy(self.parent.out)
wmparcindwi1mm.copy(self.parent.out)
def main(self):
if not self.force and self.out.exists():
logging.error("'{}' already exists, use '--force' to force overwrite.".format(self.out))
sys.exit(1)
with TemporaryDirectory() as tmpdir:
tmpdir = local.path(tmpdir)
bse = tmpdir / "maskedbse.nrrd"
t2masked = tmpdir / "maskedt2.nrrd"
t2inbse = tmpdir / "t2inbse.nrrd"
epiwarp = tmpdir / "epiwarp.nii.gz"
t2tobse_rigid = tmpdir / "t2tobse_rigid"
logging.info('1. Extract and mask the DWI b0')
bse_py('-m', self.dwimask, '-i', self.dwi, '-o', bse)
logging.info("2. Mask the T2")
unu("3op", "ifelse", self.t2mask, self.t2, "0", "-o", t2masked)
logging.info(
"3. Compute a rigid registration from the T2 to the DWI baseline")
antsRegistrationSyN_sh("-d", "3", "-f", bse, "-m", t2masked, "-t",
"r", "-o", tmpdir / "t2tobse_rigid")
antsApplyTransforms("-d", "3", "-i", t2masked, "-o", t2inbse, "-r",
bse, "-t",
tmpdir / "t2tobse_rigid0GenericAffine.mat")
logging.info(
"4. Compute 1d nonlinear registration from the DWI to the T2 along the phase direction")
moving = bse
fixed = t2inbse
pre = tmpdir / "epi"
dwiepi = tmpdir / ("dwiepi" + ''.join(self.out.suffixes))
antsRegistration("-d", "3", "-m",
"cc[" + str(fixed) + "," + str(moving) + ",1,2]", "-t",
"SyN[0.25,3,0]", "-c", "50x50x10", "-f", "4x2x1",
"-s", "2x1x0", "--restrict-deformation", "0x1x0",
"-v", "1", "-o", pre)
local.path(str(pre) + "0Warp.nii.gz").move(epiwarp)
logging.info("5. Apply warp to the DWI")
antsApplyTransformsDWI_py('-i', self.dwi, '-m', self.dwimask, '-t', epiwarp, '-o', dwiepi)
if '.nhdr' in dwiepi.suffixes:
unu("save", "-e", "gzip", "-f", "nrrd", "-i", dwiepi, self.out)
else:
dwiepi.move(self.out)
if self.debug:
tmpdir.copy(self.out.dirname / ("epidebug-" + str(getpid())))
def applyWarp(moving, warp, reference, out, interpolation='Linear'):
'''Interpolation options:
Linear
NearestNeighbor
MultiLabel[<sigma=imageSpacing>,<alpha=4.0>]
Gaussian[<sigma=imageSpacing>,<alpha=1.0>]
BSpline[<order=3>]
CosineWindowedSinc
WelchWindowedSinc
HammingWindowedSinc
LanczosWindowedSinc
GenericLabel[<interpolator=Linear>]
'''
from util.antspath import antsApplyTransforms
antsApplyTransforms('-d', '3', '-i', moving, '-t', warp, '-r', reference,
'-o', out, '--interpolation', interpolation)
def registerFs2Dwi(tmpdir, namePrefix, b0masked, brain, wmparc, wmparc_out):
logging.info('Registering wmparc to B0')
pre = tmpdir / namePrefix
affine = pre + '0GenericAffine.mat'
warp = pre + '1Warp.nii.gz'
logging.info('Computing warp from brain.nii.gz to (resampled) baseline')
antsRegistrationSyNMI_sh['-m', brain, '-f', b0masked, '-o', pre, '-n',
N_CPU] & FG
logging.info(
'Applying warp to wmparc.nii.gz to create (resampled) wmparcindwi.nii.gz'
)
antsApplyTransforms('-d', '3', '-i', wmparc, '-t', warp, affine, '-r',
b0masked, '-o', wmparc_out, '--interpolation',
'NearestNeighbor')
logging.info('Made ' + wmparc_out)
def main(self):
if not self.force and self.out.exists():
logging.error(
"'{}' already exists, use '--force' to force overwrite.".
format(self.out))
sys.exit(1)
with TemporaryDirectory() as tmpdir:
tmpdir = local.path(tmpdir)
bse = tmpdir / "maskedbse.nrrd"
t2masked = tmpdir / "maskedt2.nrrd"
t2inbse = tmpdir / "t2inbse.nrrd"
epiwarp = tmpdir / "epiwarp.nii.gz"
t2tobse_rigid = tmpdir / "t2tobse_rigid"
affine = tmpdir / "t2tobse_rigid0GenericAffine.mat"
logging.info('1. Extract and mask the DWI b0')
bse_py('-m', self.dwimask, '-i', self.dwi, '-o', bse)
logging.info("2. Mask the T2")
unu("3op", "ifelse", self.t2mask, self.t2, "0", "-o", t2masked)
logging.info(
"3. Compute a rigid registration from the T2 to the DWI baseline"
)
antsRegistrationSyN_sh("-d", "3", "-f", bse, "-m", t2masked, "-t",
"r", "-o", tmpdir / "t2tobse_rigid")
antsApplyTransforms("-d", "3", "-i", t2masked, "-o", t2inbse, "-r",
bse, "-t", affine)
logging.info(
"4. Compute 1d nonlinear registration from the DWI to the T2 along the phase direction"
)
moving = bse
fixed = t2inbse
pre = tmpdir / "epi"
dwiepi = tmpdir / ("dwiepi" + ''.join(self.out.suffixes))
antsRegistration("-d", "3", "-m",
"cc[" + str(fixed) + "," + str(moving) + ",1,2]",
"-t", "SyN[0.25,3,0]", "-c", "50x50x10", "-f",
"4x2x1", "-s", "2x1x0", "--restrict-deformation",
"0x1x0", "-v", "1", "-o", pre)
local.path(str(pre) + "0Warp.nii.gz").move(epiwarp)
logging.info("5. Apply warp to the DWI")
antsApplyTransformsDWI_py['-i', self.dwi, '-m', self.dwimask, '-t',
epiwarp, '-o', dwiepi, '-n',
str(self.nproc)] & FG
logging.info('6. Apply warp to the DWI mask')
epimask = self.out.dirname / self.out.basename.split(
'.')[0] + '-mask.nrrd'
antsApplyTransforms('-d', '3', '-i', self.dwimask, '-o', epimask,
'-n', 'NearestNeighbor', '-r', bse, '-t',
epiwarp)
unu('convert', '-t', 'uchar', '-i', epimask, '-o', epimask)
if '.nhdr' in dwiepi.suffixes:
unu("save", "-e", "gzip", "-f", "nrrd", "-i", dwiepi, "-o",
self.out)
else:
dwiepi.move(self.out)
# FIXME: the following conversion is only for UKFTractography, should be removed in future
if self.typeCast:
unu('convert', '-t', 'int16', '-i', self.out, '-o', self.out)
if self.debug:
tmpdir.copy(self.out.dirname / ("epidebug-" + str(getpid())))