def create_workflow(config: AttrDict, resource_pool: ResourcePool,
context: Context):
for _, rp in resource_pool[['T1w']]:
anat_image = rp[R('T1w')]
anat_deoblique = NipypeJob(interface=afni.Refit(deoblique=True),
reference='anat_deoblique')
anat_deoblique.in_file = anat_image
output_node = anat_deoblique.out_file
if config.non_local_means_filtering:
denoise = NipypeJob(interface=ants.DenoiseImage(),
reference='anat_denoise')
denoise.input_image = output_node
output_node = denoise.output_image
if config.n4_bias_field_correction:
n4 = NipypeJob(interface=ants.N4BiasFieldCorrection(
dimension=3, shrink_factor=2, copy_header=True),
reference='anat_n4')
n4.input_image = output_node
output_node = n4.output_image
anat_reorient = NipypeJob(interface=afni.Resample(
orientation='RPI', outputtype='NIFTI_GZ'),
reference='anat_reorient')
anat_reorient.in_file = output_node
rp[R('T1w', label='reorient')] = anat_reorient.out_file
def lesion_preproc(lesion_mask: str):
lesion_deoblique = NipypeJob(interface=afni.Refit(deoblique=True),
reference='lesion_deoblique')
lesion_inverted = PythonJob(function=inverse_lesion,
reference='inverse_lesion')
lesion_reorient = NipypeJob(interface=afni.Resample(orientation='RPI',
outputtype='NIFTI_GZ'),
reference='lesion_reorient')
lesion_inverted.lesion_path = S3Resource(lesion_mask) if lesion_mask.lower(
).startswith('s3://') else lesion_mask
lesion_deoblique.in_file = lesion_inverted.lesion_out
lesion_reorient.in_file = lesion_deoblique.out_file
return lesion_reorient.out_file
def create_workflow(config: AttrDict, resource_pool: ResourcePool, context: Context):
for _, rp in resource_pool[['T1w']]:
anat_image = rp[R('T1w')]
anat_deoblique = NipypeJob(
interface=afni.Refit(deoblique=True),
reference='deoblique'
)
anat_deoblique.in_file = anat_image
output_node = anat_deoblique.out_file
anat_reorient = NipypeJob(
interface=afni.Resample(orientation='RPI', outputtype='NIFTI_GZ'),
reference='reorient'
)
anat_reorient.in_file = output_node
rp[R('T1w', label='reorient')] = anat_reorient.out_file
def create_workflow(config: AttrDict, resource_pool: ResourcePool,
context: Context):
for _, rp in resource_pool[['brain', 'label-reorient_T1w']]:
# TODO: disable skullstrip
linear_reg = NipypeJob(interface=fsl.FLIRT(cost='corratio'),
reference='linear_reg_0')
inv_flirt_xfm = NipypeJob(
interface=fsl.utils.ConvertXFM(invert_xfm=True),
reference='inv_linear_reg0_xfm')
linear_reg.in_file = rp[R('brain')]
linear_reg.reference = config.template_brain
linear_reg.interp = config.interpolation
inv_flirt_xfm.in_file = linear_reg.out_matrix_file
if config.linear_only:
rp[R('brain', space='MNI')] = linear_reg.out_file
# other xfm
return
else:
nonlinear_reg = NipypeJob(interface=fsl.FNIRT(fieldcoeff_file=True,
jacobian_file=True),
reference='nonlinear_reg_1')
brain_warp = NipypeJob(interface=fsl.ApplyWarp(),
reference='brain_warp')
nonlinear_reg.in_file = rp[R('T1w', label='reorient')]
nonlinear_reg.ref_file = config.template_skull
nonlinear_reg.refmask_file = config.ref_mask
nonlinear_reg.config_file = config.fnirt_config
nonlinear_reg.affine_file = linear_reg.out_matrix_file
brain_warp.interp = config.interpolation
brain_warp.in_file = rp[R('brain')]
brain_warp.field_file = nonlinear_reg.fieldcoeff_file
brain_warp.ref_file = config.template_brain
rp[R('brain', space='MNI')] = brain_warp.out_file
def create_workflow(config: AttrDict, resource_pool: ResourcePool,
context: Context):
for _, rp in resource_pool[['label-reorient_T1w']]:
anat = rp[R('T1w', label='reorient')]
anat_skullstrip = NipypeJob(interface=fsl.BET(output_type='NIFTI_GZ',
**config),
reference='anat_skullstrip')
anat_skullstrip.in_file = anat
anat_skullstrip_orig_vol = NipypeJob(
interface=afni.Calc(expr='a*step(b)', outputtype='NIFTI_GZ'),
reference='anat_skullstrip_orig_vol')
anat_skullstrip_orig_vol.in_file_a = anat
anat_skullstrip_orig_vol.in_file_b = anat_skullstrip.out_file
rp[R('T1w', desc='skullstrip-fsl',
suffix='mask')] = anat_skullstrip.mask_file
rp[R('T1w', desc='skullstrip-fsl',
suffix='brain')] = anat_skullstrip_orig_vol.out_file
def create_workflow(config: AttrDict, resource_pool: ResourcePool,
context: Context):
for _, rp in resource_pool[['label-reorient_T1w']]:
anat_image = rp[R('T1w', label='reorient')]
anat_skullstrip = NipypeJob(interface=afni.SkullStrip(
outputtype='NIFTI_GZ',
args=create_3dskullstrip_arg_string(**config)),
reference='anat_skullstrip')
anat_skullstrip.in_file = anat_image
anat_brain_mask = NipypeJob(interface=afni.Calc(expr='step(a)',
outputtype='NIFTI_GZ'),
reference='anat_brain_mask')
anat_skullstrip_orig_vol = NipypeJob(
interface=afni.Calc(expr='a*step(b)', outputtype='NIFTI_GZ'),
reference='anat_skullstrip_orig_vol')
anat_brain_mask.in_file_a = anat_skullstrip.out_file
anat_skullstrip_orig_vol.in_file_a = anat_image
anat_skullstrip_orig_vol.in_file_b = anat_brain_mask.out_file
rp[R('T1w', desc='skullstrip-afni',
suffix='mask')] = anat_brain_mask.out_file
rp[R('T1w', desc='skullstrip-afni',
suffix='brain')] = anat_skullstrip_orig_vol.out_file
def create_workflow(config: AttrDict, resource_pool: ResourcePool,
context: Context):
for _, rp in resource_pool[['label-reorient_T1w']]:
anat = rp[R('T1w', label='reorient')]
train_model = UNet2d(dim_in=config.dim_in,
num_conv_block=config.num_conv_block,
kernel_root=config.kernel_root)
if config.unet_model.lower().startswith('s3://'):
unet_path = S3Resource(config.unet_model,
working_dir=tempfile.mkdtemp())()
else:
unet_path = config.unet_model
checkpoint = torch.load(unet_path, map_location={'cuda:0': 'cpu'})
train_model.load_state_dict(checkpoint['state_dict'])
model = nn.Sequential(train_model, nn.Softmax2d())
# create a node called unet_mask
unet_mask = PythonJob(function=predict_volumes, reference='unet_mask')
unet_mask.model = Resource(model)
unet_mask.cimg_in = anat
"""
Revised mask with ANTs
"""
# fslmaths <whole head> -mul <mask> brain.nii.gz
unet_masked_brain = NipypeJob(
interface=fsl.MultiImageMaths(op_string="-mul %s"),
reference='unet_masked_brain')
unet_masked_brain.in_file = anat
unet_masked_brain.operand_files = unet_mask.output_path
# flirt -v -dof 6 -in brain.nii.gz -ref NMT_SS_0.5mm.nii.gz -o brain_rot2atl -omat brain_rot2atl.mat -interp sinc
# TODO change it to ANTs linear transform
native_brain_to_template_brain = NipypeJob(
interface=fsl.FLIRT(reference=config.template_brain_only_for_anat,
dof=6,
interp='sinc'),
reference='native_brain_to_template_brain')
native_brain_to_template_brain.in_file = unet_masked_brain.out_file
# flirt -in head.nii.gz -ref NMT_0.5mm.nii.gz -o head_rot2atl -applyxfm -init brain_rot2atl.mat
# TODO change it to ANTs linear transform
native_head_to_template_head = NipypeJob(
interface=fsl.FLIRT(reference=config.template_skull_for_anat,
apply_xfm=True),
reference='native_head_to_template_head')
native_head_to_template_head.in_file = anat
native_head_to_template_head.in_matrix_file = native_brain_to_template_brain.out_matrix_file
# fslmaths NMT_SS_0.5mm.nii.gz -bin templateMask.nii.gz
template_brain_mask = NipypeJob(
interface=fsl.maths.MathsCommand(args='-bin'),
reference='template_brain_mask')
template_brain_mask.in_file = config.template_brain_only_for_anat
# ANTS 3 -m CC[head_rot2atl.nii.gz,NMT_0.5mm.nii.gz,1,5] -t SyN[0.25] -r Gauss[3,0] -o atl2T1rot -i 60x50x20 --use-Histogram-Matching --number-of-affine-iterations 10000x10000x10000x10000x10000 --MI-option 32x16000
ants_template_head_to_template = NipypeJob(
interface=ants.Registration(),
reference='template_head_to_template')
ants_template_head_to_template.metric = ['CC']
ants_template_head_to_template.metric_weight = [1, 5]
ants_template_head_to_template.moving_image = config.template_skull_for_anat
ants_template_head_to_template.transforms = ['SyN']
ants_template_head_to_template.transform_parameters = [(0.25, )]
ants_template_head_to_template.interpolation = 'NearestNeighbor'
ants_template_head_to_template.number_of_iterations = [[60, 50, 20]]
ants_template_head_to_template.smoothing_sigmas = [[0.6, 0.2, 0.0]]
ants_template_head_to_template.shrink_factors = [[4, 2, 1]]
ants_template_head_to_template.convergence_threshold = [1.e-8]
ants_template_head_to_template.fixed_image = native_head_to_template_head.out_file
# antsApplyTransforms -d 3 -i templateMask.nii.gz -t atl2T1rotWarp.nii.gz atl2T1rotAffine.txt -r brain_rot2atl.nii.gz -o brain_rot2atl_mask.nii.gz
template_head_transform_to_template = NipypeJob(
interface=ants.ApplyTransforms(dimension=3),
reference='template_head_transform_to_template')
template_head_transform_to_template.input_image = template_brain_mask.out_file
template_head_transform_to_template.reference_image = native_brain_to_template_brain.out_file
template_head_transform_to_template.transforms = ants_template_head_to_template.forward_transforms
# convert_xfm -omat brain_rot2native.mat -inverse brain_rot2atl.mat
invt = NipypeJob(interface=fsl.ConvertXFM(invert_xfm=True),
reference='convert_xfm')
invt.in_file = native_brain_to_template_brain.out_matrix_file
# flirt -in brain_rot2atl_mask.nii.gz -ref brain.nii.gz -o brain_mask.nii.gz -applyxfm -init brain_rot2native.mat
template_brain_to_native_brain = NipypeJob(
interface=fsl.FLIRT(apply_xfm=True),
reference='template_brain_to_native_brain')
template_brain_to_native_brain.in_file = template_head_transform_to_template.output_image
template_brain_to_native_brain.reference = unet_masked_brain.out_file
template_brain_to_native_brain.in_matrix_file = invt.out_file
# fslmaths brain_mask.nii.gz -thr .5 -bin brain_mask_thr.nii.gz
refined_mask = NipypeJob(interface=fsl.Threshold(thresh=0.5,
args='-bin'),
reference='refined_mask')
refined_mask.in_file = template_brain_to_native_brain.out_file
# get a new brain with mask
refined_brain = NipypeJob(
interface=fsl.MultiImageMaths(op_string="-mul %s"),
reference='refined_brain')
refined_brain.in_file = anat
refined_brain.operand_files = refined_mask.out_file
rp[R('T1w', desc='skullstrip-unet',
suffix='mask')] = refined_mask.out_file
rp[R('T1w', desc='skullstrip-unet',
suffix='brain')] = refined_brain.out_file