def __init__(self, in_file='path', **options):
from nipype.interfaces.fsl import ImageMaths
fslmaths = ImageMaths()
fslmaths.inputs.in_file = in_file
for ef in options:
setattr(fslmaths.inputs, ef, options[ef])
self.res = fslmaths.run()
def canonical(
subjects_participants,
regdir,
f2s,
template="~/GitHub/mriPipeline/templates/waxholm/WHS_SD_rat_T2star_v1.01_downsample3.nii.gz",
f_file_format="~/GitHub/mripipeline/base/preprocessing/generic_work/_subject_session_{subject}.{session}/_scan_type_SE_EPI/f_bru2nii/",
s_file_format="~/GitHub/mripipeline/base/preprocessing/generic_work/_subject_session_{subject}.{session}/_scan_type_T2_TurboRARE/s_bru2nii/",
):
"""Warp a functional image based on the functional-to-structural and the structural-to-template registrations.
Currently this approach is failing because the functiona-to-structural registration pushes the brain stem too far down.
This may be
"""
template = os.path.expanduser(template)
for subject_participant in subjects_participants:
func_image_dir = os.path.expanduser(
f_file_format.format(**subject_participant))
struct_image_dir = os.path.expanduser(
s_file_format.format(**subject_participant))
try:
for myfile in os.listdir(func_image_dir):
if myfile.endswith((".nii.gz", ".nii")):
func_image = os.path.join(func_image_dir, myfile)
for myfile in os.listdir(struct_image_dir):
if myfile.endswith((".nii.gz", ".nii")):
struct_image = os.path.join(struct_image_dir, myfile)
except FileNotFoundError:
pass
else:
#struct
n4 = ants.N4BiasFieldCorrection()
n4.inputs.dimension = 3
n4.inputs.input_image = struct_image
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
n4.inputs.bspline_fitting_distance = 100
n4.inputs.shrink_factor = 2
n4.inputs.n_iterations = [200, 200, 200, 200]
n4.inputs.convergence_threshold = 1e-11
n4.inputs.output_image = '{}/ss_n4_{}_ofM{}.nii.gz'.format(
regdir, participant, i)
n4_res = n4.run()
_n4 = ants.N4BiasFieldCorrection()
_n4.inputs.dimension = 3
_n4.inputs.input_image = struct_image
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
_n4.inputs.bspline_fitting_distance = 95
_n4.inputs.shrink_factor = 2
_n4.inputs.n_iterations = [500, 500, 500, 500]
_n4.inputs.convergence_threshold = 1e-14
_n4.inputs.output_image = '{}/ss__n4_{}_ofM{}.nii.gz'.format(
regdir, participant, i)
_n4_res = _n4.run()
#we do this on a separate bias-corrected image to remove hyperintensities which we have to create in order to prevent brain regions being caught by the negative threshold
struct_cutoff = ImageMaths()
struct_cutoff.inputs.op_string = "-thrP 20 -uthrp 98"
struct_cutoff.inputs.in_file = _n4_res.outputs.output_image
struct_cutoff_res = struct_cutoff.run()
struct_BET = BET()
struct_BET.inputs.mask = True
struct_BET.inputs.frac = 0.3
struct_BET.inputs.robust = True
struct_BET.inputs.in_file = struct_cutoff_res.outputs.out_file
struct_BET_res = struct_BET.run()
struct_mask = ApplyMask()
struct_mask.inputs.in_file = n4_res.outputs.output_image
struct_mask.inputs.mask_file = struct_BET_res.outputs.mask_file
struct_mask_res = struct_mask.run()
struct_registration = ants.Registration()
struct_registration.inputs.fixed_image = template
struct_registration.inputs.output_transform_prefix = "output_"
struct_registration.inputs.transforms = ['Affine', 'SyN'] ##
struct_registration.inputs.transform_parameters = [(1.0, ),
(1.0, 3.0, 5.0)
] ##
struct_registration.inputs.number_of_iterations = [[
2000, 1000, 500
], [100, 100, 100]] #
struct_registration.inputs.dimension = 3
struct_registration.inputs.write_composite_transform = True
struct_registration.inputs.collapse_output_transforms = True
struct_registration.inputs.initial_moving_transform_com = True
# Tested on Affine transform: CC takes too long; Demons does not tilt, but moves the slices too far caudally; GC tilts too much on
struct_registration.inputs.metric = ['MeanSquares', 'Mattes']
struct_registration.inputs.metric_weight = [1, 1]
struct_registration.inputs.radius_or_number_of_bins = [16, 32] #
struct_registration.inputs.sampling_strategy = ['Random', None]
struct_registration.inputs.sampling_percentage = [0.3, 0.3]
struct_registration.inputs.convergence_threshold = [1.e-11,
1.e-8] #
struct_registration.inputs.convergence_window_size = [20, 20]
struct_registration.inputs.smoothing_sigmas = [[4, 2, 1],
[4, 2, 1]]
struct_registration.inputs.sigma_units = ['vox', 'vox']
struct_registration.inputs.shrink_factors = [[3, 2, 1], [3, 2, 1]]
struct_registration.inputs.use_estimate_learning_rate_once = [
True, True
]
# if the fixed_image is not acquired similarly to the moving_image (e.g. RARE to histological (e.g. AMBMC)) this should be False
struct_registration.inputs.use_histogram_matching = [False, False]
struct_registration.inputs.winsorize_lower_quantile = 0.005
struct_registration.inputs.winsorize_upper_quantile = 0.98
struct_registration.inputs.args = '--float'
struct_registration.inputs.num_threads = 6
struct_registration.inputs.moving_image = struct_mask_res.outputs.out_file
struct_registration.inputs.output_warped_image = '{}/s_{}_ofM{}.nii.gz'.format(
regdir, participant, i)
struct_registration_res = struct_registration.run()
#func
func_n4 = ants.N4BiasFieldCorrection()
func_n4.inputs.dimension = 3
func_n4.inputs.input_image = func_image
func_n4.inputs.bspline_fitting_distance = 100
func_n4.inputs.shrink_factor = 2
func_n4.inputs.n_iterations = [200, 200, 200, 200]
func_n4.inputs.convergence_threshold = 1e-11
func_n4.inputs.output_image = '{}/f_n4_{}_ofM{}.nii.gz'.format(
regdir, participant, i)
func_n4_res = func_n4.run()
func_registration = ants.Registration()
func_registration.inputs.fixed_image = n4_res.outputs.output_image
func_registration.inputs.output_transform_prefix = "func_"
func_registration.inputs.transforms = [f2s]
func_registration.inputs.transform_parameters = [(0.1, )]
func_registration.inputs.number_of_iterations = [[40, 20, 10]]
func_registration.inputs.dimension = 3
func_registration.inputs.write_composite_transform = True
func_registration.inputs.collapse_output_transforms = True
func_registration.inputs.initial_moving_transform_com = True
func_registration.inputs.metric = ['MeanSquares']
func_registration.inputs.metric_weight = [1]
func_registration.inputs.radius_or_number_of_bins = [16]
func_registration.inputs.sampling_strategy = ["Regular"]
func_registration.inputs.sampling_percentage = [0.3]
func_registration.inputs.convergence_threshold = [1.e-2]
func_registration.inputs.convergence_window_size = [8]
func_registration.inputs.smoothing_sigmas = [[4, 2,
1]] # [1,0.5,0]
func_registration.inputs.sigma_units = ['vox']
func_registration.inputs.shrink_factors = [[3, 2, 1]]
func_registration.inputs.use_estimate_learning_rate_once = [True]
func_registration.inputs.use_histogram_matching = [False]
func_registration.inputs.winsorize_lower_quantile = 0.005
func_registration.inputs.winsorize_upper_quantile = 0.995
func_registration.inputs.args = '--float'
func_registration.inputs.num_threads = 6
func_registration.inputs.moving_image = func_n4_res.outputs.output_image
func_registration.inputs.output_warped_image = '{}/f_{}_ofM{}.nii.gz'.format(
regdir, participant, i)
func_registration_res = func_registration.run()
warp = ants.ApplyTransforms()
warp.inputs.reference_image = template
warp.inputs.input_image_type = 3
warp.inputs.interpolation = 'Linear'
warp.inputs.invert_transform_flags = [False, False]
warp.inputs.terminal_output = 'file'
warp.inputs.output_image = '{}/{}_ofM{}.nii.gz'.format(
regdir, participant, i)
warp.num_threads = 6
warp.inputs.input_image = func_image
warp.inputs.transforms = [
func_registration_res.outputs.composite_transform,
struct_registration_res.outputs.composite_transform
]
warp.run()
def structural_to_functional_per_participant_test(
subjects_sessions,
template="~/GitHub/mriPipeline/templates/waxholm/new/WHS_SD_masked.nii.gz",
f_file_format="~/GitHub/mripipeline/base/preprocessing/generic_work/_subject_session_{subject}.{session}/_scan_type_SE_EPI/f_bru2nii/",
s_file_format="~/GitHub/mripipeline/base/preprocessing/generic_work/_subject_session_{subject}.{session}/_scan_type_T2_TurboRARE/s_bru2nii/",
num_threads=3,
):
template = os.path.expanduser(template)
for subject_session in subjects_sessions:
func_image_dir = os.path.expanduser(
f_file_format.format(**subject_session))
struct_image_dir = os.path.expanduser(
s_file_format.format(**subject_session))
try:
for myfile in os.listdir(func_image_dir):
if myfile.endswith((".nii.gz", ".nii")):
func_image = os.path.join(func_image_dir, myfile)
for myfile in os.listdir(struct_image_dir):
if myfile.endswith((".nii.gz", ".nii")):
struct_image = os.path.join(struct_image_dir, myfile)
except FileNotFoundError:
pass
else:
n4 = ants.N4BiasFieldCorrection()
n4.inputs.dimension = 3
n4.inputs.input_image = struct_image
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
n4.inputs.bspline_fitting_distance = 100
n4.inputs.shrink_factor = 2
n4.inputs.n_iterations = [200, 200, 200, 200]
n4.inputs.convergence_threshold = 1e-11
n4.inputs.output_image = '{}_{}_1_biasCorrection_forRegistration.nii.gz'.format(
*subject_session.values())
n4_res = n4.run()
_n4 = ants.N4BiasFieldCorrection()
_n4.inputs.dimension = 3
_n4.inputs.input_image = struct_image
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
_n4.inputs.bspline_fitting_distance = 95
_n4.inputs.shrink_factor = 2
_n4.inputs.n_iterations = [500, 500, 500, 500]
_n4.inputs.convergence_threshold = 1e-14
_n4.inputs.output_image = '{}_{}_1_biasCorrection_forMasking.nii.gz'.format(
*subject_session.values())
_n4_res = _n4.run()
#we do this on a separate bias-corrected image to remove hyperintensities which we have to create in order to prevent brain regions being caught by the negative threshold
struct_cutoff = ImageMaths()
struct_cutoff.inputs.op_string = "-thrP 20 -uthrp 98"
struct_cutoff.inputs.in_file = _n4_res.outputs.output_image
struct_cutoff_res = struct_cutoff.run()
struct_BET = BET()
struct_BET.inputs.mask = True
struct_BET.inputs.frac = 0.3
struct_BET.inputs.robust = True
struct_BET.inputs.in_file = struct_cutoff_res.outputs.out_file
struct_BET.inputs.out_file = '{}_{}_2_brainExtraction.nii.gz'.format(
*subject_session.values())
struct_BET_res = struct_BET.run()
# we need/can not apply a fill, because the "holes" if any, will be at the rostral edge (touching it, and thus not counting as holes)
struct_mask = ApplyMask()
struct_mask.inputs.in_file = n4_res.outputs.output_image
struct_mask.inputs.mask_file = struct_BET_res.outputs.mask_file
struct_mask.inputs.out_file = '{}_{}_3_brainMasked.nii.gz'.format(
*subject_session.values())
struct_mask_res = struct_mask.run()
struct_registration = ants.Registration()
struct_registration.inputs.fixed_image = template
struct_registration.inputs.output_transform_prefix = "output_"
struct_registration.inputs.transforms = ['Affine', 'SyN'] ##
struct_registration.inputs.transform_parameters = [(1.0, ),
(1.0, 3.0, 5.0)
] ##
struct_registration.inputs.number_of_iterations = [[
2000, 1000, 500
], [100, 100, 100]] #
struct_registration.inputs.dimension = 3
struct_registration.inputs.write_composite_transform = True
struct_registration.inputs.collapse_output_transforms = True
struct_registration.inputs.initial_moving_transform_com = True
# Tested on Affine transform: CC takes too long; Demons does not tilt, but moves the slices too far caudally; GC tilts too much on
struct_registration.inputs.metric = ['MeanSquares', 'Mattes']
struct_registration.inputs.metric_weight = [1, 1]
struct_registration.inputs.radius_or_number_of_bins = [16, 32] #
struct_registration.inputs.sampling_strategy = ['Random', None]
struct_registration.inputs.sampling_percentage = [0.3, 0.3]
struct_registration.inputs.convergence_threshold = [1.e-11,
1.e-8] #
struct_registration.inputs.convergence_window_size = [20, 20]
struct_registration.inputs.smoothing_sigmas = [[4, 2, 1],
[4, 2, 1]]
struct_registration.inputs.sigma_units = ['vox', 'vox']
struct_registration.inputs.shrink_factors = [[3, 2, 1], [3, 2, 1]]
struct_registration.inputs.use_estimate_learning_rate_once = [
True, True
]
# if the fixed_image is not acquired similarly to the moving_image (e.g. RARE to histological (e.g. AMBMC)) this should be False
struct_registration.inputs.use_histogram_matching = [False, False]
struct_registration.inputs.winsorize_lower_quantile = 0.005
struct_registration.inputs.winsorize_upper_quantile = 0.98
struct_registration.inputs.args = '--float'
struct_registration.inputs.num_threads = num_threads
struct_registration.inputs.moving_image = struct_mask_res.outputs.out_file
struct_registration.inputs.output_warped_image = '{}_{}_4_structuralRegistration.nii.gz'.format(
*subject_session.values())
struct_registration_res = struct_registration.run()
warp = ants.ApplyTransforms()
warp.inputs.reference_image = template
warp.inputs.input_image_type = 3
warp.inputs.interpolation = 'Linear'
warp.inputs.invert_transform_flags = [False]
warp.inputs.terminal_output = 'file'
warp.inputs.output_image = '{}_{}_5_functionalWarp.nii.gz'.format(
*subject_session.values())
warp.num_threads = num_threads
warp.inputs.input_image = func_image
warp.inputs.transforms = struct_registration_res.outputs.composite_transform
warp.run()
def functional_per_participant_test():
for i in ["", "_aF", "_cF1", "_cF2", "_pF"]:
template = "~/ni_data/templates/ds_QBI_chr.nii.gz"
participant = "4008"
image_dir = "~/ni_data/ofM.dr/preprocessing/generic_work/_subject_session_{}.ofM{}/_scan_type_7_EPI_CBV/temporal_mean/".format(
participant, i)
try:
for myfile in os.listdir(image_dir):
if myfile.endswith(".nii.gz"):
mimage = os.path.join(image_dir, myfile)
except FileNotFoundError:
pass
else:
n4 = ants.N4BiasFieldCorrection()
n4.inputs.dimension = 3
n4.inputs.input_image = mimage
n4.inputs.bspline_fitting_distance = 100
n4.inputs.shrink_factor = 2
n4.inputs.n_iterations = [200, 200, 200, 200]
n4.inputs.convergence_threshold = 1e-11
n4.inputs.output_image = 'n4_{}_ofM{}.nii.gz'.format(
participant, i)
n4_res = n4.run()
functional_cutoff = ImageMaths()
functional_cutoff.inputs.op_string = "-thrP 30"
functional_cutoff.inputs.in_file = n4_res.outputs.output_image
functional_cutoff_res = functional_cutoff.run()
functional_BET = BET()
functional_BET.inputs.mask = True
functional_BET.inputs.frac = 0.5
functional_BET.inputs.in_file = functional_cutoff_res.outputs.out_file
functional_BET_res = functional_BET.run()
registration = ants.Registration()
registration.inputs.fixed_image = template
registration.inputs.output_transform_prefix = "output_"
registration.inputs.transforms = ['Affine', 'SyN']
registration.inputs.transform_parameters = [(0.1, ),
(3.0, 3.0, 5.0)]
registration.inputs.number_of_iterations = [[10000, 10000, 10000],
[100, 100, 100]]
registration.inputs.dimension = 3
registration.inputs.write_composite_transform = True
registration.inputs.collapse_output_transforms = True
registration.inputs.initial_moving_transform_com = True
registration.inputs.metric = ['Mattes'] * 2 + [['Mattes', 'CC']]
registration.inputs.metric_weight = [1] * 2 + [[0.5, 0.5]]
registration.inputs.radius_or_number_of_bins = [32] * 2 + [[32, 4]]
registration.inputs.sampling_strategy = ['Regular'] * 2 + [[
None, None
]]
registration.inputs.sampling_percentage = [0.3] * 2 + [[
None, None
]]
registration.inputs.convergence_threshold = [1.e-8] * 2 + [-0.01]
registration.inputs.convergence_window_size = [20] * 2 + [5]
registration.inputs.smoothing_sigmas = [[4, 2, 1]] * 2 + [[
1, 0.5, 0
]]
registration.inputs.sigma_units = ['vox'] * 3
registration.inputs.shrink_factors = [[3, 2, 1]] * 2 + [[4, 2, 1]]
registration.inputs.use_estimate_learning_rate_once = [True] * 3
registration.inputs.use_histogram_matching = [False] * 2 + [True]
registration.inputs.winsorize_lower_quantile = 0.005
registration.inputs.winsorize_upper_quantile = 0.995
registration.inputs.args = '--float'
registration.inputs.num_threads = 4
registration.plugin_args = {
'qsub_args': '-pe orte 4',
'sbatch_args': '--mem=6G -c 4'
}
registration.inputs.moving_image = functional_BET_res.outputs.out_file
registration.inputs.output_warped_image = '{}_ofM{}.nii.gz'.format(
participant, i)
res = registration.run()
def structural_per_participant_test(
participant,
conditions=["", "_aF", "_cF1", "_cF2", "_pF"],
template="/home/chymera/ni_data/templates/ds_QBI_chr.nii.gz",
):
for i in conditions:
image_dir = "/home/chymera/ni_data/ofM.dr/preprocessing/generic_work/_subject_session_{}.ofM{}/_scan_type_T2_TurboRARE/s_bru2nii/".format(
participant, i)
print(image_dir)
try:
for myfile in os.listdir(image_dir):
if myfile.endswith(".nii"):
mimage = os.path.join(image_dir, myfile)
except FileNotFoundError:
pass
else:
n4 = ants.N4BiasFieldCorrection()
n4.inputs.dimension = 3
n4.inputs.input_image = mimage
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
n4.inputs.bspline_fitting_distance = 100
n4.inputs.shrink_factor = 2
n4.inputs.n_iterations = [200, 200, 200, 200]
n4.inputs.convergence_threshold = 1e-11
n4.inputs.output_image = 'ss_n4_{}_ofM{}.nii.gz'.format(
participant, i)
n4_res = n4.run()
_n4 = ants.N4BiasFieldCorrection()
_n4.inputs.dimension = 3
_n4.inputs.input_image = mimage
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
_n4.inputs.bspline_fitting_distance = 95
_n4.inputs.shrink_factor = 2
_n4.inputs.n_iterations = [500, 500, 500, 500]
_n4.inputs.convergence_threshold = 1e-14
_n4.inputs.output_image = 'ss__n4_{}_ofM{}.nii.gz'.format(
participant, i)
_n4_res = _n4.run()
#we do this on a separate bias-corrected image to remove hyperintensities which we have to create in order to prevent brain regions being caught by the negative threshold
struct_cutoff = ImageMaths()
struct_cutoff.inputs.op_string = "-thrP 20 -uthrp 98"
struct_cutoff.inputs.in_file = _n4_res.outputs.output_image
struct_cutoff_res = struct_cutoff.run()
struct_BET = BET()
struct_BET.inputs.mask = True
struct_BET.inputs.frac = 0.3
struct_BET.inputs.robust = True
struct_BET.inputs.in_file = struct_cutoff_res.outputs.out_file
struct_BET_res = struct_BET.run()
mask = ApplyMask()
mask.inputs.in_file = n4_res.outputs.output_image
mask.inputs.mask_file = struct_BET_res.outputs.mask_file
mask_res = mask.run()
struct_registration = ants.Registration()
struct_registration.inputs.fixed_image = template
struct_registration.inputs.output_transform_prefix = "output_"
struct_registration.inputs.transforms = ['Rigid', 'Affine',
'SyN'] ##
struct_registration.inputs.transform_parameters = [(.1, ), (1.0, ),
(1.0, 3.0, 5.0)
] ##
struct_registration.inputs.number_of_iterations = [[
150, 100, 50
], [2000, 1000, 500], [100, 100, 100]] #
struct_registration.inputs.dimension = 3
struct_registration.inputs.write_composite_transform = True
struct_registration.inputs.collapse_output_transforms = True
struct_registration.inputs.initial_moving_transform_com = True
# Tested on Affine transform: CC takes too long; Demons does not tilt, but moves the slices too far caudally; GC tilts too much on
struct_registration.inputs.metric = [
'MeanSquares', 'MeanSquares', 'Mattes'
]
struct_registration.inputs.metric_weight = [1, 1, 1]
struct_registration.inputs.radius_or_number_of_bins = [16, 16,
32] #
struct_registration.inputs.sampling_strategy = [
'Random', 'Random', None
]
struct_registration.inputs.sampling_percentage = [0.3, 0.3, 0.3]
struct_registration.inputs.convergence_threshold = [
1.e-10, 1.e-11, 1.e-8
] #
struct_registration.inputs.convergence_window_size = [20, 20, 20]
struct_registration.inputs.smoothing_sigmas = [[4, 2,
1], [4, 2, 1],
[4, 2, 1]]
struct_registration.inputs.sigma_units = ['vox', 'vox', 'vox']
struct_registration.inputs.shrink_factors = [[3, 2, 1], [3, 2, 1],
[3, 2, 1]]
struct_registration.inputs.use_estimate_learning_rate_once = [
True, True, True
]
# if the fixed_image is not acquired similarly to the moving_image (e.g. RARE to histological (e.g. AMBMC)) this should be False
struct_registration.inputs.use_histogram_matching = [
False, False, False
]
struct_registration.inputs.winsorize_lower_quantile = 0.005
struct_registration.inputs.winsorize_upper_quantile = 0.98
struct_registration.inputs.args = '--float'
struct_registration.inputs.num_threads = 6
struct_registration.inputs.moving_image = mask_res.outputs.out_file
struct_registration.inputs.output_warped_image = 'ss_{}_ofM{}.nii.gz'.format(
participant, i)
res = struct_registration.run()
#load data
if amico_model == "NODDI":
mask_file = "data_brain_mask.nii.gz"
# generate scheme file from the bvals/bvecs
amico.util.fsl2scheme('data.bval', 'data.bvec')
amico_dir = opj(experiment_dir, sub, amico_model)
if not os.path.exists(amico_dir):
os.mkdir(amico_dir)
os.rename('data.scheme', amico_dir + '/noddi.scheme')
if amico_model == "CylinderZeppelinBall":
threshL = ImageMaths(op_string='-thr 2 -uthr 2')
threshL.inputs.in_file = experiment_dir + sub + '/aseg_trans.nii.gz'
threshL.inputs.out_file = experiment_dir + sub + '/wmL_mask.nii.gz'
threshL.run()
threshR = ImageMaths(op_string='-thr 41 -uthr 41')
threshR.inputs.in_file = experiment_dir + sub + '/aseg_trans.nii.gz'
threshR.inputs.out_file = experiment_dir + sub + '/wmR_mask.nii.gz'
threshR.run()
add_string = '-add ' + experiment_dir + sub + '/wmR_mask.nii.gz'
wm = ImageMaths(op_string=add_string)
wm.inputs.in_file = experiment_dir + sub + '/wmL_mask.nii.gz'
wm.inputs.out_file = experiment_dir + sub + '/wm_mask.nii.gz'
wm.run()
mask_file = "wm_mask.nii.gz"
os.remove('wmR_mask.nii.gz')
os.remove('wmL_mask.nii.gz')
ae.load_data(dwi_filename='data.nii.gz',
scheme_filename=amico_dir + "/scheme.scheme",
def canonical(subjects_participants, regdir, f2s,
template = "~/GitHub/mriPipeline/templates/waxholm/WHS_SD_rat_T2star_v1.01_downsample3.nii.gz",
f_file_format = "~/GitHub/mripipeline/base/preprocessing/generic_work/_subject_session_{subject}.{session}/_scan_type_SE_EPI/f_bru2nii/",
s_file_format = "~/GitHub/mripipeline/base/preprocessing/generic_work/_subject_session_{subject}.{session}/_scan_type_T2_TurboRARE/s_bru2nii/",
):
"""Warp a functional image based on the functional-to-structural and the structural-to-template registrations.
Currently this approach is failing because the functiona-to-structural registration pushes the brain stem too far down.
This may be
"""
template = os.path.expanduser(template)
for subject_participant in subjects_participants:
func_image_dir = os.path.expanduser(f_file_format.format(**subject_participant))
struct_image_dir = os.path.expanduser(s_file_format.format(**subject_participant))
try:
for myfile in os.listdir(func_image_dir):
if myfile.endswith((".nii.gz", ".nii")):
func_image = os.path.join(func_image_dir,myfile)
for myfile in os.listdir(struct_image_dir):
if myfile.endswith((".nii.gz", ".nii")):
struct_image = os.path.join(struct_image_dir,myfile)
except FileNotFoundError:
pass
else:
#struct
n4 = ants.N4BiasFieldCorrection()
n4.inputs.dimension = 3
n4.inputs.input_image = struct_image
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
n4.inputs.bspline_fitting_distance = 100
n4.inputs.shrink_factor = 2
n4.inputs.n_iterations = [200,200,200,200]
n4.inputs.convergence_threshold = 1e-11
n4.inputs.output_image = '{}/ss_n4_{}_ofM{}.nii.gz'.format(regdir,participant,i)
n4_res = n4.run()
_n4 = ants.N4BiasFieldCorrection()
_n4.inputs.dimension = 3
_n4.inputs.input_image = struct_image
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
_n4.inputs.bspline_fitting_distance = 95
_n4.inputs.shrink_factor = 2
_n4.inputs.n_iterations = [500,500,500,500]
_n4.inputs.convergence_threshold = 1e-14
_n4.inputs.output_image = '{}/ss__n4_{}_ofM{}.nii.gz'.format(regdir,participant,i)
_n4_res = _n4.run()
#we do this on a separate bias-corrected image to remove hyperintensities which we have to create in order to prevent brain regions being caught by the negative threshold
struct_cutoff = ImageMaths()
struct_cutoff.inputs.op_string = "-thrP 20 -uthrp 98"
struct_cutoff.inputs.in_file = _n4_res.outputs.output_image
struct_cutoff_res = struct_cutoff.run()
struct_BET = BET()
struct_BET.inputs.mask = True
struct_BET.inputs.frac = 0.3
struct_BET.inputs.robust = True
struct_BET.inputs.in_file = struct_cutoff_res.outputs.out_file
struct_BET_res = struct_BET.run()
struct_mask = ApplyMask()
struct_mask.inputs.in_file = n4_res.outputs.output_image
struct_mask.inputs.mask_file = struct_BET_res.outputs.mask_file
struct_mask_res = struct_mask.run()
struct_registration = ants.Registration()
struct_registration.inputs.fixed_image = template
struct_registration.inputs.output_transform_prefix = "output_"
struct_registration.inputs.transforms = ['Affine', 'SyN'] ##
struct_registration.inputs.transform_parameters = [(1.0,), (1.0, 3.0, 5.0)] ##
struct_registration.inputs.number_of_iterations = [[2000, 1000, 500], [100, 100, 100]] #
struct_registration.inputs.dimension = 3
struct_registration.inputs.write_composite_transform = True
struct_registration.inputs.collapse_output_transforms = True
struct_registration.inputs.initial_moving_transform_com = True
# Tested on Affine transform: CC takes too long; Demons does not tilt, but moves the slices too far caudally; GC tilts too much on
struct_registration.inputs.metric = ['MeanSquares', 'Mattes']
struct_registration.inputs.metric_weight = [1, 1]
struct_registration.inputs.radius_or_number_of_bins = [16, 32] #
struct_registration.inputs.sampling_strategy = ['Random', None]
struct_registration.inputs.sampling_percentage = [0.3, 0.3]
struct_registration.inputs.convergence_threshold = [1.e-11, 1.e-8] #
struct_registration.inputs.convergence_window_size = [20, 20]
struct_registration.inputs.smoothing_sigmas = [[4, 2, 1], [4, 2, 1]]
struct_registration.inputs.sigma_units = ['vox', 'vox']
struct_registration.inputs.shrink_factors = [[3, 2, 1],[3, 2, 1]]
struct_registration.inputs.use_estimate_learning_rate_once = [True, True]
# if the fixed_image is not acquired similarly to the moving_image (e.g. RARE to histological (e.g. AMBMC)) this should be False
struct_registration.inputs.use_histogram_matching = [False, False]
struct_registration.inputs.winsorize_lower_quantile = 0.005
struct_registration.inputs.winsorize_upper_quantile = 0.98
struct_registration.inputs.args = '--float'
struct_registration.inputs.num_threads = 6
struct_registration.inputs.moving_image = struct_mask_res.outputs.out_file
struct_registration.inputs.output_warped_image = '{}/s_{}_ofM{}.nii.gz'.format(regdir,participant,i)
struct_registration_res = struct_registration.run()
#func
func_n4 = ants.N4BiasFieldCorrection()
func_n4.inputs.dimension = 3
func_n4.inputs.input_image = func_image
func_n4.inputs.bspline_fitting_distance = 100
func_n4.inputs.shrink_factor = 2
func_n4.inputs.n_iterations = [200,200,200,200]
func_n4.inputs.convergence_threshold = 1e-11
func_n4.inputs.output_image = '{}/f_n4_{}_ofM{}.nii.gz'.format(regdir,participant,i)
func_n4_res = func_n4.run()
func_registration = ants.Registration()
func_registration.inputs.fixed_image = n4_res.outputs.output_image
func_registration.inputs.output_transform_prefix = "func_"
func_registration.inputs.transforms = [f2s]
func_registration.inputs.transform_parameters = [(0.1,)]
func_registration.inputs.number_of_iterations = [[40, 20, 10]]
func_registration.inputs.dimension = 3
func_registration.inputs.write_composite_transform = True
func_registration.inputs.collapse_output_transforms = True
func_registration.inputs.initial_moving_transform_com = True
func_registration.inputs.metric = ['MeanSquares']
func_registration.inputs.metric_weight = [1]
func_registration.inputs.radius_or_number_of_bins = [16]
func_registration.inputs.sampling_strategy = ["Regular"]
func_registration.inputs.sampling_percentage = [0.3]
func_registration.inputs.convergence_threshold = [1.e-2]
func_registration.inputs.convergence_window_size = [8]
func_registration.inputs.smoothing_sigmas = [[4, 2, 1]] # [1,0.5,0]
func_registration.inputs.sigma_units = ['vox']
func_registration.inputs.shrink_factors = [[3, 2, 1]]
func_registration.inputs.use_estimate_learning_rate_once = [True]
func_registration.inputs.use_histogram_matching = [False]
func_registration.inputs.winsorize_lower_quantile = 0.005
func_registration.inputs.winsorize_upper_quantile = 0.995
func_registration.inputs.args = '--float'
func_registration.inputs.num_threads = 6
func_registration.inputs.moving_image = func_n4_res.outputs.output_image
func_registration.inputs.output_warped_image = '{}/f_{}_ofM{}.nii.gz'.format(regdir,participant,i)
func_registration_res = func_registration.run()
warp = ants.ApplyTransforms()
warp.inputs.reference_image = template
warp.inputs.input_image_type = 3
warp.inputs.interpolation = 'Linear'
warp.inputs.invert_transform_flags = [False, False]
warp.inputs.terminal_output = 'file'
warp.inputs.output_image = '{}/{}_ofM{}.nii.gz'.format(regdir,participant,i)
warp.num_threads = 6
warp.inputs.input_image = func_image
warp.inputs.transforms = [func_registration_res.outputs.composite_transform, struct_registration_res.outputs.composite_transform]
warp.run()
def structural_to_functional_per_participant_test(subjects_sessions,
template = "~/GitHub/mriPipeline/templates/waxholm/new/WHS_SD_masked.nii.gz",
f_file_format = "~/GitHub/mripipeline/base/preprocessing/generic_work/_subject_session_{subject}.{session}/_scan_type_SE_EPI/f_bru2nii/",
s_file_format = "~/GitHub/mripipeline/base/preprocessing/generic_work/_subject_session_{subject}.{session}/_scan_type_T2_TurboRARE/s_bru2nii/",
num_threads = 3,
):
template = os.path.expanduser(template)
for subject_session in subjects_sessions:
func_image_dir = os.path.expanduser(f_file_format.format(**subject_session))
struct_image_dir = os.path.expanduser(s_file_format.format(**subject_session))
try:
for myfile in os.listdir(func_image_dir):
if myfile.endswith((".nii.gz", ".nii")):
func_image = os.path.join(func_image_dir,myfile)
for myfile in os.listdir(struct_image_dir):
if myfile.endswith((".nii.gz", ".nii")):
struct_image = os.path.join(struct_image_dir,myfile)
except FileNotFoundError:
pass
else:
n4 = ants.N4BiasFieldCorrection()
n4.inputs.dimension = 3
n4.inputs.input_image = struct_image
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
n4.inputs.bspline_fitting_distance = 100
n4.inputs.shrink_factor = 2
n4.inputs.n_iterations = [200,200,200,200]
n4.inputs.convergence_threshold = 1e-11
n4.inputs.output_image = '{}_{}_1_biasCorrection_forRegistration.nii.gz'.format(*subject_session.values())
n4_res = n4.run()
_n4 = ants.N4BiasFieldCorrection()
_n4.inputs.dimension = 3
_n4.inputs.input_image = struct_image
# correction bias is introduced (along the z-axis) if the following value is set to under 85. This is likely contingent on resolution.
_n4.inputs.bspline_fitting_distance = 95
_n4.inputs.shrink_factor = 2
_n4.inputs.n_iterations = [500,500,500,500]
_n4.inputs.convergence_threshold = 1e-14
_n4.inputs.output_image = '{}_{}_1_biasCorrection_forMasking.nii.gz'.format(*subject_session.values())
_n4_res = _n4.run()
#we do this on a separate bias-corrected image to remove hyperintensities which we have to create in order to prevent brain regions being caught by the negative threshold
struct_cutoff = ImageMaths()
struct_cutoff.inputs.op_string = "-thrP 20 -uthrp 98"
struct_cutoff.inputs.in_file = _n4_res.outputs.output_image
struct_cutoff_res = struct_cutoff.run()
struct_BET = BET()
struct_BET.inputs.mask = True
struct_BET.inputs.frac = 0.3
struct_BET.inputs.robust = True
struct_BET.inputs.in_file = struct_cutoff_res.outputs.out_file
struct_BET.inputs.out_file = '{}_{}_2_brainExtraction.nii.gz'.format(*subject_session.values())
struct_BET_res = struct_BET.run()
# we need/can not apply a fill, because the "holes" if any, will be at the rostral edge (touching it, and thus not counting as holes)
struct_mask = ApplyMask()
struct_mask.inputs.in_file = n4_res.outputs.output_image
struct_mask.inputs.mask_file = struct_BET_res.outputs.mask_file
struct_mask.inputs.out_file = '{}_{}_3_brainMasked.nii.gz'.format(*subject_session.values())
struct_mask_res = struct_mask.run()
struct_registration = ants.Registration()
struct_registration.inputs.fixed_image = template
struct_registration.inputs.output_transform_prefix = "output_"
struct_registration.inputs.transforms = ['Affine', 'SyN'] ##
struct_registration.inputs.transform_parameters = [(1.0,), (1.0, 3.0, 5.0)] ##
struct_registration.inputs.number_of_iterations = [[2000, 1000, 500], [100, 100, 100]] #
struct_registration.inputs.dimension = 3
struct_registration.inputs.write_composite_transform = True
struct_registration.inputs.collapse_output_transforms = True
struct_registration.inputs.initial_moving_transform_com = True
# Tested on Affine transform: CC takes too long; Demons does not tilt, but moves the slices too far caudally; GC tilts too much on
struct_registration.inputs.metric = ['MeanSquares', 'Mattes']
struct_registration.inputs.metric_weight = [1, 1]
struct_registration.inputs.radius_or_number_of_bins = [16, 32] #
struct_registration.inputs.sampling_strategy = ['Random', None]
struct_registration.inputs.sampling_percentage = [0.3, 0.3]
struct_registration.inputs.convergence_threshold = [1.e-11, 1.e-8] #
struct_registration.inputs.convergence_window_size = [20, 20]
struct_registration.inputs.smoothing_sigmas = [[4, 2, 1], [4, 2, 1]]
struct_registration.inputs.sigma_units = ['vox', 'vox']
struct_registration.inputs.shrink_factors = [[3, 2, 1],[3, 2, 1]]
struct_registration.inputs.use_estimate_learning_rate_once = [True, True]
# if the fixed_image is not acquired similarly to the moving_image (e.g. RARE to histological (e.g. AMBMC)) this should be False
struct_registration.inputs.use_histogram_matching = [False, False]
struct_registration.inputs.winsorize_lower_quantile = 0.005
struct_registration.inputs.winsorize_upper_quantile = 0.98
struct_registration.inputs.args = '--float'
struct_registration.inputs.num_threads = num_threads
struct_registration.inputs.moving_image = struct_mask_res.outputs.out_file
struct_registration.inputs.output_warped_image = '{}_{}_4_structuralRegistration.nii.gz'.format(*subject_session.values())
struct_registration_res = struct_registration.run()
warp = ants.ApplyTransforms()
warp.inputs.reference_image = template
warp.inputs.input_image_type = 3
warp.inputs.interpolation = 'Linear'
warp.inputs.invert_transform_flags = [False]
warp.inputs.terminal_output = 'file'
warp.inputs.output_image = '{}_{}_5_functionalWarp.nii.gz'.format(*subject_session.values())
warp.num_threads = num_threads
warp.inputs.input_image = func_image
warp.inputs.transforms = struct_registration_res.outputs.composite_transform
warp.run()
def functional_per_participant_test():
for i in ["","_aF","_cF1","_cF2","_pF"]:
template = "~/ni_data/templates/ds_QBI_chr.nii.gz"
participant = "4008"
image_dir = "~/ni_data/ofM.dr/preprocessing/generic_work/_subject_session_{}.ofM{}/_scan_type_7_EPI_CBV/temporal_mean/".format(participant,i)
try:
for myfile in os.listdir(image_dir):
if myfile.endswith(".nii.gz"):
mimage = os.path.join(image_dir,myfile)
except FileNotFoundError:
pass
else:
n4 = ants.N4BiasFieldCorrection()
n4.inputs.dimension = 3
n4.inputs.input_image = mimage
n4.inputs.bspline_fitting_distance = 100
n4.inputs.shrink_factor = 2
n4.inputs.n_iterations = [200,200,200,200]
n4.inputs.convergence_threshold = 1e-11
n4.inputs.output_image = 'n4_{}_ofM{}.nii.gz'.format(participant,i)
n4_res = n4.run()
functional_cutoff = ImageMaths()
functional_cutoff.inputs.op_string = "-thrP 30"
functional_cutoff.inputs.in_file = n4_res.outputs.output_image
functional_cutoff_res = functional_cutoff.run()
functional_BET = BET()
functional_BET.inputs.mask = True
functional_BET.inputs.frac = 0.5
functional_BET.inputs.in_file = functional_cutoff_res.outputs.out_file
functional_BET_res = functional_BET.run()
registration = ants.Registration()
registration.inputs.fixed_image = template
registration.inputs.output_transform_prefix = "output_"
registration.inputs.transforms = ['Affine', 'SyN']
registration.inputs.transform_parameters = [(0.1,), (3.0, 3.0, 5.0)]
registration.inputs.number_of_iterations = [[10000, 10000, 10000], [100, 100, 100]]
registration.inputs.dimension = 3
registration.inputs.write_composite_transform = True
registration.inputs.collapse_output_transforms = True
registration.inputs.initial_moving_transform_com = True
registration.inputs.metric = ['Mattes'] * 2 + [['Mattes', 'CC']]
registration.inputs.metric_weight = [1] * 2 + [[0.5, 0.5]]
registration.inputs.radius_or_number_of_bins = [32] * 2 + [[32, 4]]
registration.inputs.sampling_strategy = ['Regular'] * 2 + [[None, None]]
registration.inputs.sampling_percentage = [0.3] * 2 + [[None, None]]
registration.inputs.convergence_threshold = [1.e-8] * 2 + [-0.01]
registration.inputs.convergence_window_size = [20] * 2 + [5]
registration.inputs.smoothing_sigmas = [[4, 2, 1]] * 2 + [[1, 0.5, 0]]
registration.inputs.sigma_units = ['vox'] * 3
registration.inputs.shrink_factors = [[3, 2, 1]]*2 + [[4, 2, 1]]
registration.inputs.use_estimate_learning_rate_once = [True] * 3
registration.inputs.use_histogram_matching = [False] * 2 + [True]
registration.inputs.winsorize_lower_quantile = 0.005
registration.inputs.winsorize_upper_quantile = 0.995
registration.inputs.args = '--float'
registration.inputs.num_threads = 4
registration.plugin_args = {'qsub_args': '-pe orte 4', 'sbatch_args': '--mem=6G -c 4'}
registration.inputs.moving_image = functional_BET_res.outputs.out_file
registration.inputs.output_warped_image = '{}_ofM{}.nii.gz'.format(participant,i)
res = registration.run()