def main(self):
with tempfile.TemporaryDirectory() as tmpdir:
tmpdir = local.path(tmpdir)
b0masked = tmpdir / "b0masked.nii.gz" # Sylvain wants both
b0maskedbrain = tmpdir / "b0maskedbrain.nii.gz"
t2masked = tmpdir / 't2masked.nii.gz'
print('Masking the T2')
ImageMath(3, t2masked, 'm', self.t2, self.t2mask)
brain = tmpdir / "brain.nii.gz"
wmparc = tmpdir / "wmparc.nii.gz"
brainmgz = self.parent.fsdir / 'mri/brain.mgz'
wmparcmgz = self.parent.fsdir / 'mri/wmparc.mgz'
wmparcindwi = tmpdir / 'wmparcInDwi.nii.gz' # Sylvain wants both
wmparcinbrain = tmpdir / 'wmparcInBrain.nii.gz'
print(
"Making brain.nii.gz and wmparc.nii.gz from their mgz versions"
)
vol2vol = local[self.parent.fshome / 'bin/mri_vol2vol']
label2vol = local[self.parent.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)
print('Extracting B0 from DWI and masking it')
check_call((' ').join([
pjoin(FILEDIR, 'bse.py'), '-i', self.parent.dwi, '-m',
self.parent.dwimask, '-o', b0masked
]),
shell=True)
print('Made masked B0')
# rigid registration from t2 to brain.nii.gz
pre = tmpdir / 'BrainToT2'
BrainToT2Affine = pre + '0GenericAffine.mat'
print('Computing rigid registration from brain.nii.gz to t2')
rigid_registration(3, brain, t2masked, pre)
# generates three files for rigid registration:
# pre0GenericAffine.mat preInverseWarped.nii.gz preWarped.nii.gz
# generates five files for default(rigid+affine+deformable syn) registration:
# pre0GenericAffine.mat pre1Warp.nii.gz preWarped.nii.gz pre1InverseWarp.nii.gz preInverseWarped.nii.gz
dwi_res = load_nifti(
str(b0masked)).header['pixdim'][1:4].round(decimals=2)
brain_res = load_nifti(
str(brain)).header['pixdim'][1:4].round(decimals=2)
print(f'DWI resolution: {dwi_res}')
print(f'FreeSurfer brain resolution: {brain_res}')
print('Registering wmparc to B0 through T2')
registerFs2Dwi_T2(tmpdir, 'fsbrainToT2ToB0', b0masked, t2masked,
BrainToT2Affine, wmparc, wmparcindwi)
if (dwi_res != brain_res).any():
print(
'DWI resolution is different from FreeSurfer brain resolution'
)
print(
'wmparc wil be registered to both DWI and brain resolution'
)
print(
'Check output files wmparcInDwi.nii.gz and wmparcInBrain.nii.gz'
)
print('Resampling B0 to brain resolution')
ResampleImageBySpacing('3', b0masked, b0maskedbrain,
brain_res.tolist())
print('Registering wmparc to resampled B0')
registerFs2Dwi_T2(tmpdir, 'fsbrainToT2ToResampledB0',
b0maskedbrain, t2masked, BrainToT2Affine,
wmparc, wmparcinbrain)
# copying images to outDir
b0masked.copy(self.parent.out)
wmparcindwi.copy(self.parent.out)
if b0maskedbrain.exists():
b0maskedbrain.copy(self.parent.out)
wmparcinbrain.copy(self.parent.out)
if self.parent.debug:
tmpdir.copy(self.parent.out,
'fs2dwi-debug-' + str(os.getpid()))
print('See output files in ', self.parent.out._path)
def main(self):
with tempfile.TemporaryDirectory() as tmpdir:
tmpdir = local.path(tmpdir)
b0masked = tmpdir / "b0masked.nii.gz" # Sylvain wants both
b0maskedbrain = tmpdir / "b0maskedbrain.nii.gz"
brain = tmpdir / "brain.nii.gz"
wmparc = tmpdir / "wmparc.nii.gz"
brainmgz = self.parent.fsdir / 'mri/brain.mgz'
wmparcmgz = self.parent.fsdir / 'mri/wmparc.mgz'
wmparcindwi = tmpdir / 'wmparcInDwi.nii.gz' # Sylvain wants both
wmparcinbrain = tmpdir / 'wmparcInBrain.nii.gz'
print(
"Making brain.nii.gz and wmparc.nii.gz from their mgz versions"
)
vol2vol = local[self.parent.fshome / 'bin/mri_vol2vol']
label2vol = local[self.parent.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)
print('Extracting B0 from DWI and masking it')
check_call((' ').join([
pjoin(FILEDIR, 'bse.py'), '-i', self.parent.dwi, '-m',
self.parent.dwimask, '-o', b0masked
]),
shell=True)
print('Made masked B0')
dwi_res = load_nifti(
str(b0masked)).header['pixdim'][1:4].round(decimals=2)
brain_res = load_nifti(
str(brain)).header['pixdim'][1:4].round(decimals=2)
print(f'DWI resolution: {dwi_res}')
print(f'FreeSurfer brain resolution: {brain_res}')
print('Registering wmparc to B0')
registerFs2Dwi(tmpdir, 'fsbrainToB0', b0masked, brain, wmparc,
wmparcindwi)
if (dwi_res != brain_res).any():
print(
'DWI resolution is different from FreeSurfer brain resolution'
)
print(
'wmparc wil be registered to both DWI and brain resolution'
)
print(
'Check output files wmparcInDwi.nii.gz and wmparcInBrain.nii.gz'
)
print('Resampling B0 to brain resolution')
ResampleImageBySpacing('3', b0masked, b0maskedbrain,
brain_res.tolist())
print('Registering wmparc to resampled B0')
registerFs2Dwi(tmpdir, 'fsbrainToResampledB0', b0maskedbrain,
brain, wmparc, wmparcinbrain)
# copying images to outDir
b0masked.copy(self.parent.out)
wmparcindwi.copy(self.parent.out)
if b0maskedbrain.exists():
b0maskedbrain.copy(self.parent.out)
wmparcinbrain.copy(self.parent.out)
if self.parent.debug:
tmpdir.copy(self.parent.out,
'fs2dwi-debug-' + str(os.getpid()))
print('See output files in ', self.parent.out._path)