def registerFs2Dwi_T2(tmpdir, namePrefix, b0masked, t2masked, T2toBrainAffine, wmparc, wmparc_out):
print('Registering wmparc to B0')
pre = tmpdir / namePrefix
affine = pre + '0GenericAffine.mat'
warp = pre + '1Warp.nii.gz'
print('Computing warp from t2 to (resampled) baseline')
check_call((' ').join(['antsRegistrationSyNMI.sh', '-d', '3', '-m', t2masked, '-f', b0masked, '-o', pre,
'-n', N_CPU]), shell=True)
print('Applying warp to wmparc.nii.gz to create (resampled) wmparcindwi.nii.gz')
antsApplyTransforms('-d', '3', '-i', wmparc, '-t', warp, affine, T2toBrainAffine,
'-r', b0masked, '-o', wmparc_out,
'--interpolation', 'NearestNeighbor')
print('Made ' + wmparc_out)
def registerFs2Dwi(tmpdir, namePrefix, b0masked, brain, wmparc, wmparc_out):
pre = tmpdir / namePrefix
affine = pre + '0GenericAffine.mat'
warp = pre + '1Warp.nii.gz'
print('Computing warp from brain.nii.gz to (resampled) baseline')
check_call((' ').join([
pjoin(FILEDIR, 'antsRegistrationSyNMI.sh'), '-d', '3', '-m', brain,
'-f', b0masked, '-o', pre, '-n', ANTSREG_THREADS
]),
shell=True)
print(
'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')
print('Made ' + wmparc_out)
def main(self):
self.out = local.path(self.out)
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.nii.gz'
t2masked = tmpdir / 'maskedt2.nii.gz'
t2inbse = tmpdir / 't2inbse.nii.gz'
epiwarp = tmpdir / 'epiwarp.nii.gz'
t2tobse_rigid = tmpdir / 't2tobse_rigid'
affine = tmpdir / 't2tobse_rigid0GenericAffine.mat'
logging.info('1. Extract B0 and and mask it')
check_call((' ').join([
pjoin(FILEDIR, 'bse.py'), '-m', self.dwimask, '-i', self.dwi,
'-o', bse
]),
shell=True)
logging.info('2. Mask the T2')
fslmaths(self.t2mask, '-mul', self.t2, t2masked)
logging.info(
'3. Compute a rigid registration from the T2 to the DWI baseline'
)
rigid_registration(3, t2masked, bse, t2tobse_rigid)
antsApplyTransforms('-d', '3', '-i', t2masked, '-o', t2inbse, '-r',
bse, '-t', affine)
logging.info(
'4. Compute 1d nonlinear registration from the DWI to T2-in-bse along the phase direction'
)
moving = bse
fixed = t2inbse
pre = tmpdir / 'epi'
dwiepi = tmpdir / 'dwiepi.nii.gz'
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')
check_call((' ').join([
pjoin(FILEDIR,
'antsApplyTransformsDWI.py'), '-i', self.dwi, '-m',
self.dwimask, '-t', epiwarp, '-o', dwiepi, '-n', self.nproc
]),
shell=True)
# WarpTimeSeriesImageMultiTransform can also be used
# dwimasked = tmpdir / 'masked_dwi.nii.gz'
# fslmaths(self.dwi, '-mul', self.dwimask, dwimasked)
# WarpTimeSeriesImageMultiTransform('4', dwimasked, dwiepi, '-R', dwimasked, '-i', epiwarp)
logging.info('6. Apply warp to the DWI mask')
epimask = self.out._path + '-mask.nii.gz'
antsApplyTransforms('-d', '3', '-i', self.dwimask, '-o', epimask,
'-n', 'NearestNeighbor', '-r', bse, '-t',
epiwarp)
fslmaths(epimask, '-mul', '1', epimask, '-odt', 'char')
dwiepi.move(self.out._path + '.nii.gz')
self.bvals_file.copy(self.out._path + '.bval')
self.bvecs_file.copy(self.out._path + '.bvec')
if self.debug:
tmpdir.copy(self.out.dirname / ('epidebug-' + str(getpid())))