def reference_info_zero_affine():
header = create_nifti_header(np.zeros((4, 4)), [10, 10, 10], [1, 1, 1])
try:
get_reference_info(header)
return True
except ValueError:
return False
def compute_distance_barycenters(ref_1, ref_2, ref_2_transfo):
"""
Compare the barycenter (center of volume) of two reference object.
The provided transformation will move the reference #2 and
return the distance before and after transformation.
Parameters
----------
ref_1: reference object
Any type supported by the sft as reference (e.g .nii of .trk).
ref_2: reference object
Any type supported by the sft as reference (e.g .nii of .trk).
ref_2_transfo: np.ndarray
Transformation that modifies the barycenter of ref_2.
Returns
-------
distance: float or tuple (2,)
return a tuple containing the distance before and after
the transformation.
"""
aff_1, dim_1, _, _ = get_reference_info(ref_1)
aff_2, dim_2, _, _ = get_reference_info(ref_2)
barycenter_1 = voxel_to_world(dim_1 / 2.0, aff_1)
barycenter_2 = voxel_to_world(dim_2 / 2.0, aff_2)
distance_before = np.linalg.norm(barycenter_1 - barycenter_2)
normalized_coord = row[barycenter_2[0:3], 1.0].astype(float)
barycenter_2 = np.dot(ref_2_transfo, normalized_coord)[0:3]
distance_after = np.linalg.norm(barycenter_1 - barycenter_2)
return distance_before, distance_after
def test_reference_info_identical():
tuple_1 = get_reference_info(filepath_dix['gs.trk'])
tuple_2 = get_reference_info(filepath_dix['gs.nii'])
affine_1, dimensions_1, voxel_sizes_1, voxel_order_1 = tuple_1
affine_2, dimensions_2, voxel_sizes_2, voxel_order_2 = tuple_2
assert_allclose(affine_1, affine_2)
assert_array_equal(dimensions_1, dimensions_2)
assert_allclose(voxel_sizes_1, voxel_sizes_2)
assert voxel_order_1 == voxel_order_2
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, args.in_bundles)
output_streamlines_filename = '{}streamlines.trk'.format(
args.output_prefix)
output_voxels_filename = '{}voxels.nii.gz'.format(args.output_prefix)
assert_outputs_exist(parser, args,
[output_voxels_filename, output_streamlines_filename])
if not 0 <= args.ratio_voxels <= 1 or not 0 <= args.ratio_streamlines <= 1:
parser.error('Ratios must be between 0 and 1.')
fusion_streamlines = []
if args.reference:
reference_file = args.reference
else:
reference_file = args.in_bundles[0]
sft_list = []
for name in args.in_bundles:
tmp_sft = load_tractogram_with_reference(parser, args, name)
tmp_sft.to_vox()
tmp_sft.to_corner()
if not is_header_compatible(reference_file, tmp_sft):
raise ValueError('Headers are not compatible.')
sft_list.append(tmp_sft)
fusion_streamlines.append(tmp_sft.streamlines)
fusion_streamlines, _ = union_robust(fusion_streamlines)
transformation, dimensions, _, _ = get_reference_info(reference_file)
volume = np.zeros(dimensions)
streamlines_vote = dok_matrix(
(len(fusion_streamlines), len(args.in_bundles)))
for i in range(len(args.in_bundles)):
sft = sft_list[i]
binary = compute_tract_counts_map(sft.streamlines, dimensions)
volume[binary > 0] += 1
if args.same_tractogram:
_, indices = intersection_robust(
[fusion_streamlines, sft.streamlines])
streamlines_vote[list(indices), [i]] += 1
if args.same_tractogram:
real_indices = []
ratio_value = int(args.ratio_streamlines * len(args.in_bundles))
real_indices = np.where(
np.sum(streamlines_vote, axis=1) >= ratio_value)[0]
new_sft = StatefulTractogram.from_sft(fusion_streamlines[real_indices],
sft_list[0])
save_tractogram(new_sft, output_streamlines_filename)
volume[volume < int(args.ratio_voxels * len(args.in_bundles))] = 0
volume[volume > 0] = 1
nib.save(nib.Nifti1Image(volume.astype(np.uint8), transformation),
output_voxels_filename)
def get_seeds_from_wm(wm_path, threshold=0):
wm_file = nib.load(wm_path)
wm_img = wm_file.get_fdata()
seeds = np.argwhere(wm_img > threshold)
seeds = np.hstack([seeds, np.ones([len(seeds), 1])])
seeds = (wm_file.affine.dot(seeds.T).T)[:, :3].reshape(-1, 1, 3)
n_seeds = len(seeds)
header = TrkFile.create_empty_header()
header["voxel_to_rasmm"] = wm_file.affine
header["dimensions"] = wm_file.header["dim"][1:4]
header["voxel_sizes"] = wm_file.header["pixdim"][1:4]
header["voxel_order"] = get_reference_info(wm_file)[3]
tractogram = Tractogram(streamlines=ArraySequence(seeds),
affine_to_rasmm=np.eye(4))
save_path = os.path.join(os.path.dirname(wm_path), "seeds_from_wm.trk")
print("Saving {}".format(save_path))
TrkFile(tractogram, header).save(save_path)
def transform_anatomy(transfo, reference, moving, filename_to_save,
interp='linear', keep_dtype=False):
"""
Apply transformation to an image using Dipy's tool
Parameters
----------
transfo: numpy.ndarray
Transformation matrix to be applied
reference: str
Filename of the reference image (target)
moving: str
Filename of the moving image
filename_to_save: str
Filename of the output image
interp : string, either 'linear' or 'nearest'
the type of interpolation to be used, either 'linear'
(for k-linear interpolation) or 'nearest' for nearest neighbor
keep_dtype : bool
If True, keeps the data_type of the input moving image when saving
the output image
"""
grid2world, dim, _, _ = get_reference_info(reference)
static_data = nib.load(reference).get_fdata(dtype=np.float32)
nib_file = nib.load(moving)
curr_type = nib_file.get_data_dtype()
if keep_dtype:
moving_data = np.asanyarray(nib_file.dataobj).astype(curr_type)
else:
moving_data = nib_file.get_fdata(dtype=np.float32)
moving_affine = nib_file.affine
if moving_data.ndim == 3 and isinstance(moving_data[0, 0, 0],
np.ScalarType):
orig_type = moving_data.dtype
affine_map = AffineMap(np.linalg.inv(transfo),
dim, grid2world,
moving_data.shape, moving_affine)
resampled = affine_map.transform(moving_data.astype(np.float64),
interpolation=interp)
nib.save(nib.Nifti1Image(resampled.astype(orig_type), grid2world),
filename_to_save)
elif len(moving_data[0, 0, 0]) > 1:
if isinstance(moving_data[0, 0, 0], np.void):
raise ValueError('Does not support TrackVis RGB')
affine_map = AffineMap(np.linalg.inv(transfo),
dim[0:3], grid2world,
moving_data.shape[0:3], moving_affine)
orig_type = moving_data.dtype
resampled = transform_dwi(affine_map, static_data, moving_data,
interpolation=interp)
nib.save(nib.Nifti1Image(resampled.astype(orig_type), grid2world),
filename_to_save)
else:
raise ValueError('Does not support this dataset (shape, type, etc)')
def assert_same_resolution(images):
"""
Check the resolution of multiple images.
Parameters
----------
images : array of string or string
List of images or an image.
"""
if isinstance(images, str):
images = [images]
if len(images) == 0:
raise Exception("Can't check if images are of the same "
"resolution/affine. No image has been given")
aff_1, shape_1, _, _ = get_reference_info(images[0])
for i in images[1:]:
aff_2, shape_2, _, _ = get_reference_info(i)
if not (shape_1 == shape_2) and (aff_1 == aff_2).any():
raise Exception("Images are not of the same resolution/affine")
def __init__(self, nb_vertices=None, nb_streamlines=None, init_as=None,
reference=None):
""" Initialize an empty TrxFile, support preallocation """
if init_as is not None:
affine = init_as.header['VOXEL_TO_RASMM']
dimensions = init_as.header['DIMENSIONS']
elif reference is not None:
affine, dimensions, _, _ = get_reference_info(reference)
else:
logging.debug('No reference provided, using blank space '
'attributes, please update them later.')
affine = np.eye(4).astype(np.float32)
dimensions = np.array([1, 1, 1], dtype=np.uint16)
if nb_vertices is None and nb_streamlines is None:
if init_as is not None:
raise ValueError('Cant use init_as without declaring '
'nb_vertices AND nb_streamlines')
logging.debug('Intializing empty TrxFile.')
self.header = {}
# Using the new format default type
tmp_strs = ArraySequence()
tmp_strs._data = tmp_strs._data.astype(np.float16)
tmp_strs._offsets = tmp_strs._offsets.astype(np.uint64)
tmp_strs._lengths = tmp_strs._lengths.astype(np.uint32)
self.streamlines = tmp_strs
self.groups = {}
self.data_per_streamline = {}
self.data_per_vertex = {}
self.data_per_group = {}
self._uncompressed_folder_handle = None
nb_vertices = 0
nb_streamlines = 0
elif nb_vertices is not None and nb_streamlines is not None:
logging.debug('Preallocating TrxFile with size {} streamlines'
'and {} vertices.'.format(nb_streamlines, nb_vertices))
trx = self._initialize_empty_trx(nb_streamlines, nb_vertices,
init_as=init_as)
self.__dict__ = trx.__dict__
else:
raise ValueError('You must declare both nb_vertices AND '
'NB_STREAMLINES')
self.header['VOXEL_TO_RASMM'] = affine
self.header['DIMENSIONS'] = dimensions
self.header['NB_VERTICES'] = nb_vertices
self.header['NB_STREAMLINES'] = nb_streamlines
self._copy_safe = True
def to_bin_mask(tractogram):
affine, dimensions, voxel_sizes, voxel_order = get_reference_info(
reference_anatomy)
low_res = (2.5, 2.5, 2.5)
mask = np.zeros(dimensions, dtype=np.float)
tractogram.to_vox()
try:
streams = np.vstack(tractogram.streamlines).astype(np.int32)
mask[streams[:, 0], streams[:, 1], streams[:, 2]] = 1
except:
print('Trivial mask!')
return mask, affine
def density_map(tractogram, n_sls=None, to_vox=False, normalize=False):
"""
Create a streamline density map.
based on:
https://dipy.org/documentation/1.1.1./examples_built/streamline_formats/
Parameters
----------
tractogram : StatefulTractogram
Stateful tractogram whose streamlines are used to make
the density map.
n_sls : int or None, optional
n_sls to randomly select to make the density map.
If None, all streamlines are used.
Default: None
to_vox : bool, optional
Whether to put the stateful tractogram in VOX space before making
the density map.
Default: False
normalize : bool, optional
Whether to normalize maximum values to 1.
Default: False
Returns
-------
Nifti1Image containing the density map.
"""
if to_vox:
tractogram.to_vox()
sls = tractogram.streamlines
if n_sls is not None:
sls = select_random_set_of_streamlines(sls, n_sls)
affine, vol_dims, voxel_sizes, voxel_order = get_reference_info(tractogram)
tractogram_density = dtu.density_map(sls, np.eye(4), vol_dims)
if normalize:
tractogram_density = tractogram_density / tractogram_density.max()
nifti_header = create_nifti_header(affine, vol_dims, voxel_sizes)
density_map_img = nib.Nifti1Image(tractogram_density, affine, nifti_header)
return density_map_img
def load_node_nifti(directory, in_label, out_label, ref_filename):
in_filename_1 = os.path.join(directory,
'{}_{}.nii.gz'.format(in_label, out_label))
in_filename_2 = os.path.join(directory,
'{}_{}.nii.gz'.format(out_label, in_label))
in_filename = None
if os.path.isfile(in_filename_1):
in_filename = in_filename_1
elif os.path.isfile(in_filename_2):
in_filename = in_filename_2
if in_filename is not None:
if not is_header_compatible(in_filename, ref_filename):
logging.error('{} and {} do not have a compatible header'.format(
in_filename, ref_filename))
raise IOError
return nib.load(in_filename).get_fdata()
_, dims, _, _ = get_reference_info(ref_filename)
return np.zeros(dims)
def from_tractogram(tractogram, reference, cast_position=np.float16):
""" Generate a valid TrxFile from a Nibabel Tractogram """
if not np.issubdtype(cast_position, np.floating):
logging.warning('Casting as {}, considering using a floating point '
'dtype.'.format(cast_position))
trx = TrxFile(nb_vertices=len(tractogram.streamlines._data),
nb_streamlines=len(tractogram.streamlines))
affine, dimensions, _, _ = get_reference_info(reference)
trx.header = {'DIMENSIONS': dimensions,
'VOXEL_TO_RASMM': affine,
'NB_VERTICES': len(tractogram.streamlines._data),
'NB_STREAMLINES': len(tractogram.streamlines)}
if cast_position != np.float32:
tmp_streamlines = deepcopy(tractogram.streamlines)
else:
tmp_streamlines = tractogram.streamlines
# Cast the int64 of Nibabel to uint64
tmp_streamlines._offsets = tmp_streamlines._offsets.astype(np.uint64)
if cast_position != np.float32:
tmp_streamlines._data = tmp_streamlines._data.astype(cast_position)
trx.streamlines = tmp_streamlines
trx.data_per_streamline = tractogram.data_per_streamline
trx.data_per_vertex = tractogram.data_per_point
# For safety and for RAM, convert the whole object to memmaps
tmpdir = tempfile.TemporaryDirectory()
save(trx, tmpdir.name)
trx = load_from_directory(tmpdir.name)
trx._uncompressed_folder_handle = tmpdir
return trx
def get_ismrm_seeds(data_dir, source, keep, weighted, threshold, voxel):
trk_dir = os.path.join(data_dir, "bundles")
if source in ["wm", "trk"]:
anat_path = os.path.join(data_dir, "masks", "wm.nii.gz")
resized_path = os.path.join(data_dir, "masks",
"wm_{}.nii.gz".format(voxel))
elif source == "brain":
anat_path = os.path.join("subjects", "ismrm_gt",
"dwi_brain_mask.nii.gz")
resized_path = os.path.join("subjects", "ismrm_gt",
"dwi_brain_mask_125.nii.gz")
sp.call([
"mrresize", "-voxel", "{:1.2f}".format(voxel / 100), anat_path,
resized_path
])
if source == "trk":
print("Running Tractconverter...")
sp.call([
"python", "tractconverter/scripts/WalkingTractConverter.py", "-i",
trk_dir, "-a", resized_path, "-vtk2trk"
])
print("Loading seed bundles...")
seed_bundles = []
for i, trk_path in enumerate(glob.glob(os.path.join(trk_dir,
"*.trk"))):
trk_file = nib.streamlines.load(trk_path)
endpoints = []
for fiber in trk_file.tractogram.streamlines:
endpoints.append(fiber[0])
endpoints.append(fiber[-1])
seed_bundles.append(endpoints)
if i == 0:
header = trk_file.header
n_seeds = sum([len(b) for b in seed_bundles])
n_bundles = len(seed_bundles)
print("Loaded {} seeds from {} bundles.".format(n_seeds, n_bundles))
seeds = np.array([[seed] for bundle in seed_bundles
for seed in bundle])
if keep < 1:
if weighted:
p = np.zeros(n_seeds)
offset = 0
for b in seed_bundles:
l = len(b)
p[offset:offset + l] = 1 / (l * n_bundles)
offset += l
else:
p = np.ones(n_seeds) / n_seeds
elif source in ["brain", "wm"]:
weighted = False
wm_file = nib.load(resized_path)
wm_img = wm_file.get_fdata()
seeds = np.argwhere(wm_img > threshold)
seeds = np.hstack([seeds, np.ones([len(seeds), 1])])
seeds = (wm_file.affine.dot(seeds.T).T)[:, :3].reshape(-1, 1, 3)
n_seeds = len(seeds)
if keep < 1:
p = np.ones(n_seeds) / n_seeds
header = TrkFile.create_empty_header()
header["voxel_to_rasmm"] = wm_file.affine
header["dimensions"] = wm_file.header["dim"][1:4]
header["voxel_sizes"] = wm_file.header["pixdim"][1:4]
header["voxel_order"] = get_reference_info(wm_file)[3]
if keep < 1:
keep_n = int(keep * n_seeds)
print("Subsampling from {} seeds to {} seeds".format(n_seeds, keep_n))
np.random.seed(42)
keep_idx = np.random.choice(len(seeds),
size=keep_n,
replace=False,
p=p)
seeds = seeds[keep_idx]
tractogram = Tractogram(streamlines=ArraySequence(seeds),
affine_to_rasmm=np.eye(4))
save_dir = os.path.join(data_dir, "seeds")
if not os.path.exists(save_dir):
os.makedirs(save_dir)
save_path = os.path.join(save_dir, "seeds_from_{}_{}_vox{:03d}.trk")
save_path = save_path.format(
source, "W" + str(int(100 * keep)) if weighted else "all", voxel)
print("Saving {}".format(save_path))
TrkFile(tractogram, header).save(save_path)
os.remove(resized_path)
for file in glob.glob(os.path.join(trk_dir, "*.trk")):
os.remove(file)
def main():
parser = _build_args_parser()
args = parser.parse_args()
assert_inputs_exist(parser, args.in_bundles)
output_streamlines_filename = '{}streamlines.trk'.format(
args.output_prefix)
output_voxels_filename = '{}voxels.nii.gz'.format(args.output_prefix)
assert_outputs_exist(parser, args,
[output_voxels_filename, output_streamlines_filename])
if not 0 <= args.ratio_voxels <= 1 or not 0 <= args.ratio_streamlines <= 1:
parser.error('Ratios must be between 0 and 1.')
fusion_streamlines = []
for name in args.in_bundles:
fusion_streamlines.extend(
load_tractogram_with_reference(parser, args, name).streamlines)
fusion_streamlines, _ = perform_streamlines_operation(
union, [fusion_streamlines], 0)
fusion_streamlines = ArraySequence(fusion_streamlines)
if args.reference:
reference_file = args.reference
else:
reference_file = args.in_bundles[0]
transformation, dimensions, _, _ = get_reference_info(reference_file)
volume = np.zeros(dimensions)
streamlines_vote = dok_matrix(
(len(fusion_streamlines), len(args.in_bundles)))
for i, name in enumerate(args.in_bundles):
if not is_header_compatible(reference_file, name):
raise ValueError('Both headers are not the same')
sft = load_tractogram_with_reference(parser, args, name)
bundle = sft.get_streamlines_copy()
sft.to_vox()
bundle_vox_space = sft.get_streamlines_copy()
binary = compute_tract_counts_map(bundle_vox_space, dimensions)
volume[binary > 0] += 1
if args.same_tractogram:
_, indices = perform_streamlines_operation(
intersection, [fusion_streamlines, bundle], 0)
streamlines_vote[list(indices), i] += 1
if args.same_tractogram:
real_indices = []
for i in range(len(fusion_streamlines)):
ratio_value = int(args.ratio_streamlines * len(args.in_bundles))
if np.sum(streamlines_vote[i]) >= ratio_value:
real_indices.append(i)
new_streamlines = fusion_streamlines[real_indices]
sft = StatefulTractogram(new_streamlines, reference_file, Space.RASMM)
save_tractogram(sft, output_streamlines_filename)
volume[volume < int(args.ratio_streamlines * len(args.in_bundles))] = 0
volume[volume > 0] = 1
nib.save(nib.Nifti1Image(volume.astype(np.uint8), transformation),
output_voxels_filename)
"""
The function ``load_tractogram`` requires a reference, any of the following
inputs is considered valid (as long as they are in the same share space)
- Nifti filename
- Trk filename
- nib.nifti1.Nifti1Image
- nib.streamlines.trk.TrkFile
- nib.nifti1.Nifti1Header
- Trk header (dict)
- Stateful Tractogram
The reason why this parameter is required is to guarantee all information
related to space attributes is always present.
"""
affine, dimensions, voxel_sizes, voxel_order = get_reference_info(
reference_anatomy)
print(affine)
print(dimensions)
print(voxel_sizes)
print(voxel_order)
"""
If you have a Trk file that was generated using a particular anatomy,
to be considered valid all fields must correspond between the headers.
It can be easily verified using this function, which also accept
the same variety of input as ``get_reference_info``
"""
print(is_header_compatible(reference_anatomy, bundles_filename[0]))
"""
If a TRK was generated with a valid header, but the reference NIFTI was lost
a header can be generated to then generate a fake NIFTI file.
def __init__(self, streamlines, reference, space,
origin=Origin.NIFTI,
data_per_point=None, data_per_streamline=None):
""" Create a strict, state-aware, robust tractogram
Parameters
----------
streamlines : list or ArraySequence
Streamlines of the tractogram
reference : Nifti or Trk filename, Nifti1Image or TrkFile,
Nifti1Header, trk.header (dict) or another Stateful Tractogram
Reference that provides the spatial attributes.
Typically a nifti-related object from the native diffusion used for
streamlines generation
space : Enum (dipy.io.stateful_tractogram.Space)
Current space in which the streamlines are (vox, voxmm or rasmm)
After tracking the space is VOX, after loading with nibabel
the space is RASMM
origin : Enum (dipy.io.stateful_tractogram.Origin), optional
Current origin in which the streamlines are (center or corner)
After loading with nibabel the origin is CENTER
data_per_point : dict, optional
Dictionary in which each key has X items, each items has Y_i items
X being the number of streamlines
Y_i being the number of points on streamlines #i
data_per_streamline : dict, optional
Dictionary in which each key has X items
X being the number of streamlines
Notes
-----
Very important to respect the convention, verify that streamlines
match the reference and are effectively in the right space.
Any change to the number of streamlines, data_per_point or
data_per_streamline requires particular verification.
In a case of manipulation not allowed by this object, use Nibabel
directly and be careful.
"""
if data_per_point is None:
data_per_point = {}
if data_per_streamline is None:
data_per_streamline = {}
if isinstance(streamlines, Streamlines):
streamlines = streamlines.copy()
self._tractogram = Tractogram(streamlines,
data_per_point=data_per_point,
data_per_streamline=data_per_streamline)
if isinstance(reference, type(self)):
logger.warning('Using a StatefulTractogram as reference, this '
'will copy only the space_attributes, not '
'the state. The variables space and origin '
'must be specified separately.')
logger.warning('To copy the state from another StatefulTractogram '
'you may want to use the function from_sft '
'(static function of the StatefulTractogram).')
if isinstance(reference, tuple) and len(reference) == 4:
if is_reference_info_valid(*reference):
space_attributes = reference
else:
raise TypeError('The provided space attributes are not '
'considered valid, please correct before '
'using them with StatefulTractogram.')
else:
space_attributes = get_reference_info(reference)
if space_attributes is None:
raise TypeError('Reference MUST be one of the following:\n'
'Nifti or Trk filename, Nifti1Image or '
'TrkFile, Nifti1Header or trk.header (dict).')
(self._affine, self._dimensions,
self._voxel_sizes, self._voxel_order) = space_attributes
self._inv_affine = np.linalg.inv(self._affine)
if space not in Space:
raise ValueError('Space MUST be from Space enum, e.g Space.VOX.')
self._space = space
if origin not in Origin:
raise ValueError('Origin MUST be from Origin enum, '
'e.g Origin.NIFTI.')
self._origin = origin
logger.debug(self)
def main():
t_init = perf_counter()
parser = _build_arg_parser()
args = parser.parse_args()
if args.verbose:
logging.basicConfig(level=logging.INFO)
assert_inputs_exist(parser, [args.in_odf, args.in_mask, args.in_seed])
assert_outputs_exist(parser, args, args.out_tractogram)
if args.compress is not None:
verify_compression_th(args.compress)
odf_sh_img = nib.load(args.in_odf)
mask = get_data_as_mask(nib.load(args.in_mask))
seed_mask = get_data_as_mask(nib.load(args.in_seed))
odf_sh = odf_sh_img.get_fdata(dtype=np.float32)
t0 = perf_counter()
if args.npv:
nb_seeds = args.npv
seed_per_vox = True
elif args.nt:
nb_seeds = args.nt
seed_per_vox = False
else:
nb_seeds = 1
seed_per_vox = True
# Seeds are returned with origin `center`.
# However, GPUTracker expects origin to be `corner`.
# Therefore, we need to shift the seed positions by half voxel.
seeds = random_seeds_from_mask(seed_mask,
np.eye(4),
seeds_count=nb_seeds,
seed_count_per_voxel=seed_per_vox,
random_seed=args.rng_seed) + 0.5
logging.info('Generated {0} seed positions in {1:.2f}s.'.format(
len(seeds),
perf_counter() - t0))
voxel_size = odf_sh_img.header.get_zooms()[0]
vox_step_size = args.step_size / voxel_size
vox_max_length = args.max_length / voxel_size
vox_min_length = args.min_length / voxel_size
min_strl_len = int(vox_min_length / vox_step_size) + 1
max_strl_len = int(vox_max_length / vox_step_size) + 1
# initialize tracking
tracker = GPUTacker(odf_sh, mask, seeds, vox_step_size, min_strl_len,
max_strl_len, args.theta, args.sh_basis,
args.batch_size, args.forward_only, args.rng_seed)
# wrapper for tracker.track() yielding one TractogramItem per
# streamline for use with the LazyTractogram.
def tracks_generator_wrapper():
for strl, seed in tracker.track():
# seed must be saved in voxel space, with origin `center`.
dps = {'seeds': seed - 0.5} if args.save_seeds else {}
# TODO: Investigate why the streamline must NOT be shifted to
# origin `corner` for LazyTractogram.
strl *= voxel_size # in mm.
if args.compress:
strl = compress_streamlines(strl, args.compress)
yield TractogramItem(strl, dps, {})
# instantiate tractogram
tractogram = LazyTractogram.from_data_func(tracks_generator_wrapper)
tractogram.affine_to_rasmm = odf_sh_img.affine
filetype = nib.streamlines.detect_format(args.out_tractogram)
reference = get_reference_info(odf_sh_img)
header = create_tractogram_header(filetype, *reference)
# Use generator to save the streamlines on-the-fly
nib.streamlines.save(tractogram, args.out_tractogram, header=header)
logging.info('Saved tractogram to {0}.'.format(args.out_tractogram))
# Total runtime
logging.info('Total runtime of {0:.2f}s.'.format(perf_counter() - t_init))
def __init__(self,
streamlines,
reference,
space,
shifted_origin=False,
data_per_point=None,
data_per_streamline=None):
""" Create a strict, state-aware, robust tractogram
Parameters
----------
streamlines : list or ArraySequence
Streamlines of the tractogram
reference : Nifti or Trk filename, Nifti1Image or TrkFile,
Nifti1Header, trk.header (dict) or another Stateful Tractogram
Reference that provides the spatial attributes.
Typically a nifti-related object from the native diffusion used for
streamlines generation
space : Enum (dipy.io.stateful_tractogram.Space)
Current space in which the streamlines are (vox, voxmm or rasmm)
Typically after tracking the space is VOX, after nibabel loading
the space is RASMM
shifted_origin : bool
Information on the position of the origin,
False is Trackvis standard, default (center of the voxel)
True is NIFTI standard (corner of the voxel)
data_per_point : dict
Dictionary in which each key has X items, each items has Y_i items
X being the number of streamlines
Y_i being the number of points on streamlines #i
data_per_streamline : dict
Dictionary in which each key has X items
X being the number of streamlines
Notes
-----
Very important to respect the convention, verify that streamlines
match the reference and are effectively in the right space.
Any change to the number of streamlines, data_per_point or
data_per_streamline requires particular verification.
In a case of manipulation not allowed by this object, use Nibabel
directly and be careful.
"""
if data_per_point is None:
data_per_point = {}
if data_per_streamline is None:
data_per_streamline = {}
if isinstance(streamlines, Streamlines):
streamlines = streamlines.copy()
self._tractogram = Tractogram(streamlines,
data_per_point=data_per_point,
data_per_streamline=data_per_streamline)
space_attributes = get_reference_info(reference)
if space_attributes is None:
raise TypeError('Reference MUST be one of the following:\n' +
'Nifti or Trk filename, Nifti1Image or TrkFile, ' +
'Nifti1Header or trk.header (dict)')
(self._affine, self._dimensions, self._voxel_sizes,
self._voxel_order) = space_attributes
self._inv_affine = np.linalg.inv(self._affine)
if space not in Space:
raise ValueError('Space MUST be from Space enum, e.g Space.VOX')
self._space = space
if not isinstance(shifted_origin, bool):
raise TypeError('shifted_origin MUST be a boolean')
self._shifted_origin = shifted_origin
logging.debug(self)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
if args.verbose:
logging.basicConfig(level=logging.DEBUG)
assert_inputs_exist(parser, [args.in_odf, args.in_seed, args.in_mask])
assert_outputs_exist(parser, args, args.out_tractogram)
if not nib.streamlines.is_supported(args.out_tractogram):
parser.error('Invalid output streamline file format (must be trk or ' +
'tck): {0}'.format(args.out_tractogram))
verify_streamline_length_options(parser, args)
verify_compression_th(args.compress)
verify_seed_options(parser, args)
mask_img = nib.load(args.in_mask)
mask_data = get_data_as_mask(mask_img, dtype=bool)
# Make sure the data is isotropic. Else, the strategy used
# when providing information to dipy (i.e. working as if in voxel space)
# will not yield correct results.
odf_sh_img = nib.load(args.in_odf)
if not np.allclose(np.mean(odf_sh_img.header.get_zooms()[:3]),
odf_sh_img.header.get_zooms()[0], atol=1e-03):
parser.error(
'ODF SH file is not isotropic. Tracking cannot be ran robustly.')
if args.npv:
nb_seeds = args.npv
seed_per_vox = True
elif args.nt:
nb_seeds = args.nt
seed_per_vox = False
else:
nb_seeds = 1
seed_per_vox = True
voxel_size = odf_sh_img.header.get_zooms()[0]
vox_step_size = args.step_size / voxel_size
seed_img = nib.load(args.in_seed)
seeds = track_utils.random_seeds_from_mask(
seed_img.get_fdata(dtype=np.float32),
np.eye(4),
seeds_count=nb_seeds,
seed_count_per_voxel=seed_per_vox,
random_seed=args.seed)
# Tracking is performed in voxel space
max_steps = int(args.max_length / args.step_size) + 1
streamlines_generator = LocalTracking(
_get_direction_getter(args),
BinaryStoppingCriterion(mask_data),
seeds, np.eye(4),
step_size=vox_step_size, max_cross=1,
maxlen=max_steps,
fixedstep=True, return_all=True,
random_seed=args.seed,
save_seeds=args.save_seeds)
scaled_min_length = args.min_length / voxel_size
scaled_max_length = args.max_length / voxel_size
if args.save_seeds:
filtered_streamlines, seeds = \
zip(*((s, p) for s, p in streamlines_generator
if scaled_min_length <= length(s) <= scaled_max_length))
data_per_streamlines = {'seeds': lambda: seeds}
else:
filtered_streamlines = \
(s for s in streamlines_generator
if scaled_min_length <= length(s) <= scaled_max_length)
data_per_streamlines = {}
if args.compress:
filtered_streamlines = (
compress_streamlines(s, args.compress)
for s in filtered_streamlines)
tractogram = LazyTractogram(lambda: filtered_streamlines,
data_per_streamlines,
affine_to_rasmm=seed_img.affine)
filetype = nib.streamlines.detect_format(args.out_tractogram)
reference = get_reference_info(seed_img)
header = create_tractogram_header(filetype, *reference)
# Use generator to save the streamlines on-the-fly
nib.streamlines.save(tractogram, args.out_tractogram, header=header)
def _processing_wrapper(args):
hdf5_filename = args[0]
labels_img = args[1]
in_label, out_label = args[2]
measures_to_compute = copy.copy(args[3])
if args[4] is not None:
similarity_directory = args[4][0]
weighted = args[5]
include_dps = args[6]
hdf5_file = h5py.File(hdf5_filename, 'r')
key = '{}_{}'.format(in_label, out_label)
if key not in hdf5_file:
return
streamlines = reconstruct_streamlines_from_hdf5(hdf5_file, key)
affine, dimensions, voxel_sizes, _ = get_reference_info(labels_img)
measures_to_return = {}
if not (np.allclose(hdf5_file.attrs['affine'], affine, atol=1e-03)
and np.array_equal(hdf5_file.attrs['dimensions'], dimensions)):
raise ValueError('Provided hdf5 have incompatible headers.')
# Precompute to save one transformation, insert later
if 'length' in measures_to_compute:
streamlines_copy = list(streamlines)
# scil_decompose_connectivity.py requires isotropic voxels
mean_length = np.average(length(streamlines_copy)) * voxel_sizes[0]
# If density is not required, do not compute it
# Only required for volume, similarity and any metrics
if not ((len(measures_to_compute) == 1 and
('length' in measures_to_compute
or 'streamline_count' in measures_to_compute)) or
(len(measures_to_compute) == 2 and
('length' in measures_to_compute
and 'streamline_count' in measures_to_compute))):
density = compute_tract_counts_map(streamlines, dimensions)
if 'volume' in measures_to_compute:
measures_to_return['volume'] = np.count_nonzero(density) * \
np.prod(voxel_sizes)
measures_to_compute.remove('volume')
if 'streamline_count' in measures_to_compute:
measures_to_return['streamline_count'] = len(streamlines)
measures_to_compute.remove('streamline_count')
if 'length' in measures_to_compute:
measures_to_return['length'] = mean_length
measures_to_compute.remove('length')
if 'similarity' in measures_to_compute and similarity_directory:
density_sim = load_node_nifti(similarity_directory, in_label,
out_label, labels_img)
if density_sim is None:
ba_vox = 0
else:
ba_vox = compute_bundle_adjacency_voxel(density, density_sim)
measures_to_return['similarity'] = ba_vox
measures_to_compute.remove('similarity')
for measure in measures_to_compute:
if isinstance(measure, str) and os.path.isdir(measure):
map_dirname = measure
map_data = load_node_nifti(map_dirname, in_label, out_label,
labels_img)
measures_to_return[map_dirname] = np.average(
map_data[map_data > 0])
elif isinstance(measure, tuple) and os.path.isfile(measure[0]):
metric_filename = measure[0]
metric_img = measure[1]
if not is_header_compatible(metric_img, labels_img):
logging.error('{} do not have a compatible header'.format(
metric_filename))
raise IOError
metric_data = metric_img.get_fdata(dtype=np.float64)
if weighted:
density = density / np.max(density)
voxels_value = metric_data * density
voxels_value = voxels_value[voxels_value > 0]
else:
voxels_value = metric_data[density > 0]
measures_to_return[metric_filename] = np.average(voxels_value)
if include_dps:
for dps_key in hdf5_file[key].keys():
if dps_key not in ['data', 'offsets', 'lengths']:
out_file = os.path.join(include_dps, dps_key)
measures_to_return[out_file] = np.average(
hdf5_file[key][dps_key])
return {(in_label, out_label): measures_to_return}
def main():
parser = _build_arg_parser()
args = parser.parse_args()
if args.verbose:
logging.basicConfig(level=logging.DEBUG)
assert_inputs_exist(parser, [args.sh_file, args.seed_file, args.mask_file])
assert_outputs_exist(parser, args, args.output_file)
if not nib.streamlines.is_supported(args.output_file):
parser.error('Invalid output streamline file format (must be trk or ' +
'tck): {0}'.format(args.output_file))
if not args.min_length > 0:
parser.error('minL must be > 0, {}mm was provided.'.format(
args.min_length))
if args.max_length < args.min_length:
parser.error(
'maxL must be > than minL, (minL={}mm, maxL={}mm).'.format(
args.min_length, args.max_length))
if args.compress:
if args.compress < 0.001 or args.compress > 1:
logging.warning(
'You are using an error rate of {}.\nWe recommend setting it '
'between 0.001 and 1.\n0.001 will do almost nothing to the '
'tracts while 1 will higly compress/linearize the tracts'.
format(args.compress))
if args.npv and args.npv <= 0:
parser.error('Number of seeds per voxel must be > 0.')
if args.nt and args.nt <= 0:
parser.error('Total number of seeds must be > 0.')
mask_img = nib.load(args.mask_file)
mask_data = mask_img.get_fdata()
# Make sure the mask is isotropic. Else, the strategy used
# when providing information to dipy (i.e. working as if in voxel space)
# will not yield correct results.
fodf_sh_img = nib.load(args.sh_file)
if not np.allclose(np.mean(fodf_sh_img.header.get_zooms()[:3]),
fodf_sh_img.header.get_zooms()[0],
atol=1.e-3):
parser.error(
'SH file is not isotropic. Tracking cannot be ran robustly.')
if args.npv:
nb_seeds = args.npv
seed_per_vox = True
elif args.nt:
nb_seeds = args.nt
seed_per_vox = False
else:
nb_seeds = 1
seed_per_vox = True
voxel_size = fodf_sh_img.header.get_zooms()[0]
vox_step_size = args.step_size / voxel_size
seed_img = nib.load(args.seed_file)
seeds = track_utils.random_seeds_from_mask(
seed_img.get_fdata(),
np.eye(4),
seeds_count=nb_seeds,
seed_count_per_voxel=seed_per_vox,
random_seed=args.seed)
# Tracking is performed in voxel space
max_steps = int(args.max_length / args.step_size) + 1
streamlines = LocalTracking(_get_direction_getter(args, mask_data),
BinaryStoppingCriterion(mask_data),
seeds,
np.eye(4),
step_size=vox_step_size,
max_cross=1,
maxlen=max_steps,
fixedstep=True,
return_all=True,
random_seed=args.seed,
save_seeds=args.save_seeds)
scaled_min_length = args.min_length / voxel_size
scaled_max_length = args.max_length / voxel_size
if args.save_seeds:
filtered_streamlines, seeds = \
zip(*((s, p) for s, p in streamlines
if scaled_min_length <= length(s) <= scaled_max_length))
data_per_streamlines = {'seeds': lambda: seeds}
else:
filtered_streamlines = \
(s for s in streamlines
if scaled_min_length <= length(s) <= scaled_max_length)
data_per_streamlines = {}
if args.compress:
filtered_streamlines = (compress_streamlines(s, args.compress)
for s in filtered_streamlines)
tractogram = LazyTractogram(lambda: filtered_streamlines,
data_per_streamlines,
affine_to_rasmm=seed_img.affine)
filetype = nib.streamlines.detect_format(args.output_file)
reference = get_reference_info(seed_img)
header = create_tractogram_header(filetype, *reference)
# Use generator to save the streamlines on-the-fly
nib.streamlines.save(tractogram, args.output_file, header=header)
def _processing_wrapper(args):
hdf5_filename = args[0]
labels_img = args[1]
in_label, out_label = args[2]
measures_to_compute = copy.copy(args[3])
if args[4] is not None:
similarity_directory = args[4][0]
weighted = args[5]
include_dps = args[6]
min_lesion_vol = args[7]
hdf5_file = h5py.File(hdf5_filename, 'r')
key = '{}_{}'.format(in_label, out_label)
if key not in hdf5_file:
return
streamlines = reconstruct_streamlines_from_hdf5(hdf5_file, key)
if len(streamlines) == 0:
return
affine, dimensions, voxel_sizes, _ = get_reference_info(labels_img)
measures_to_return = {}
if not (np.allclose(hdf5_file.attrs['affine'], affine, atol=1e-03)
and np.array_equal(hdf5_file.attrs['dimensions'], dimensions)):
raise ValueError('Provided hdf5 have incompatible headers.')
# Precompute to save one transformation, insert later
if 'length' in measures_to_compute:
streamlines_copy = list(streamlines)
# scil_decompose_connectivity.py requires isotropic voxels
mean_length = np.average(length(streamlines_copy))*voxel_sizes[0]
# If density is not required, do not compute it
# Only required for volume, similarity and any metrics
if not ((len(measures_to_compute) == 1 and
('length' in measures_to_compute or
'streamline_count' in measures_to_compute)) or
(len(measures_to_compute) == 2 and
('length' in measures_to_compute and
'streamline_count' in measures_to_compute))):
density = compute_tract_counts_map(streamlines,
dimensions)
if 'volume' in measures_to_compute:
measures_to_return['volume'] = np.count_nonzero(density) * \
np.prod(voxel_sizes)
measures_to_compute.remove('volume')
if 'streamline_count' in measures_to_compute:
measures_to_return['streamline_count'] = len(streamlines)
measures_to_compute.remove('streamline_count')
if 'length' in measures_to_compute:
measures_to_return['length'] = mean_length
measures_to_compute.remove('length')
if 'similarity' in measures_to_compute and similarity_directory:
density_sim = load_node_nifti(similarity_directory,
in_label, out_label,
labels_img)
if density_sim is None:
ba_vox = 0
else:
ba_vox = compute_bundle_adjacency_voxel(density, density_sim)
measures_to_return['similarity'] = ba_vox
measures_to_compute.remove('similarity')
for measure in measures_to_compute:
# Maps
if isinstance(measure, str) and os.path.isdir(measure):
map_dirname = measure
map_data = load_node_nifti(map_dirname,
in_label, out_label,
labels_img)
measures_to_return[map_dirname] = np.average(
map_data[map_data > 0])
elif isinstance(measure, tuple):
if not isinstance(measure[0], tuple) \
and os.path.isfile(measure[0]):
metric_filename = measure[0]
metric_img = measure[1]
if not is_header_compatible(metric_img, labels_img):
logging.error('{} do not have a compatible header'.format(
metric_filename))
raise IOError
metric_data = metric_img.get_fdata(dtype=np.float64)
if weighted:
avg_value = np.average(metric_data, weights=density)
else:
avg_value = np.average(metric_data[density > 0])
measures_to_return[metric_filename] = avg_value
# lesion
else:
lesion_filename = measure[0][0]
computed_lesion_labels = measure[0][1]
lesion_img = measure[1]
if not is_header_compatible(lesion_img, labels_img):
logging.error('{} do not have a compatible header'.format(
lesion_filename))
raise IOError
voxel_sizes = lesion_img.header.get_zooms()[0:3]
lesion_img.set_filename('tmp.nii.gz')
lesion_atlas = get_data_as_label(lesion_img)
tmp_dict = compute_lesion_stats(
density.astype(bool), lesion_atlas,
voxel_sizes=voxel_sizes, single_label=True,
min_lesion_vol=min_lesion_vol,
precomputed_lesion_labels=computed_lesion_labels)
tmp_ind = _streamlines_in_mask(list(streamlines),
lesion_atlas.astype(np.uint8),
np.eye(3), [0, 0, 0])
streamlines_count = len(
np.where(tmp_ind == [0, 1][True])[0].tolist())
if tmp_dict:
measures_to_return[lesion_filename+'vol'] = \
tmp_dict['lesion_total_volume']
measures_to_return[lesion_filename+'count'] = \
tmp_dict['lesion_count']
measures_to_return[lesion_filename+'sc'] = \
streamlines_count
else:
measures_to_return[lesion_filename+'vol'] = 0
measures_to_return[lesion_filename+'count'] = 0
measures_to_return[lesion_filename+'sc'] = 0
if include_dps:
for dps_key in hdf5_file[key].keys():
if dps_key not in ['data', 'offsets', 'lengths']:
out_file = os.path.join(include_dps, dps_key)
if 'commit' in dps_key:
measures_to_return[out_file] = np.sum(
hdf5_file[key][dps_key])
else:
measures_to_return[out_file] = np.average(
hdf5_file[key][dps_key])
return {(in_label, out_label): measures_to_return}
def compute_all_measures(args):
tuple_1, tuple_2 = args[0]
filename_1, reference_1 = tuple_1
filename_2, reference_2 = tuple_2
streamline_dice = args[1]
disable_streamline_distance = args[2]
if not is_header_compatible(reference_1, reference_2):
raise ValueError('{} and {} have incompatible headers'.format(
filename_1, filename_2))
data_tuple_1 = load_data_tmp_saving([filename_1, reference_1, False,
disable_streamline_distance])
if data_tuple_1 is None:
return None
density_1, endpoints_density_1, bundle_1, \
centroids_1 = data_tuple_1
data_tuple_2 = load_data_tmp_saving([filename_2, reference_2, False,
disable_streamline_distance])
if data_tuple_2 is None:
return None
density_2, endpoints_density_2, bundle_2, \
centroids_2 = data_tuple_2
_, _, voxel_size, _ = get_reference_info(reference_1)
voxel_size = np.product(voxel_size)
# These measures are in mm^3
binary_1 = copy.copy(density_1)
binary_1[binary_1 > 0] = 1
binary_2 = copy.copy(density_2)
binary_2[binary_2 > 0] = 1
volume_overlap = np.count_nonzero(binary_1 * binary_2)
volume_overlap_endpoints = np.count_nonzero(
endpoints_density_1 * endpoints_density_2)
volume_overreach = np.abs(np.count_nonzero(
binary_1 + binary_2) - volume_overlap)
volume_overreach_endpoints = np.abs(np.count_nonzero(
endpoints_density_1 + endpoints_density_2) - volume_overlap_endpoints)
# These measures are in mm
bundle_adjacency_voxel = compute_bundle_adjacency_voxel(density_1,
density_2,
non_overlap=True)
if streamline_dice and not disable_streamline_distance:
bundle_adjacency_streamlines = \
compute_bundle_adjacency_streamlines(bundle_1,
bundle_2,
non_overlap=True)
elif not disable_streamline_distance:
bundle_adjacency_streamlines = \
compute_bundle_adjacency_streamlines(bundle_1,
bundle_2,
centroids_1=centroids_1,
centroids_2=centroids_2,
non_overlap=True)
# These measures are between 0 and 1
dice_vox, w_dice_vox = compute_dice_voxel(density_1, density_2)
dice_vox_endpoints, w_dice_vox_endpoints = compute_dice_voxel(
endpoints_density_1,
endpoints_density_2)
density_correlation = compute_correlation(density_1, density_2)
density_correlation_endpoints = compute_correlation(endpoints_density_1,
endpoints_density_2)
measures_name = ['bundle_adjacency_voxels',
'dice_voxels', 'w_dice_voxels',
'volume_overlap',
'volume_overreach',
'dice_voxels_endpoints',
'w_dice_voxels_endpoints',
'volume_overlap_endpoints',
'volume_overreach_endpoints',
'density_correlation',
'density_correlation_endpoints']
measures = [bundle_adjacency_voxel,
dice_vox, w_dice_vox,
volume_overlap * voxel_size,
volume_overreach * voxel_size,
dice_vox_endpoints,
w_dice_vox_endpoints,
volume_overlap_endpoints * voxel_size,
volume_overreach_endpoints * voxel_size,
density_correlation,
density_correlation_endpoints]
if not disable_streamline_distance:
measures_name += ['bundle_adjacency_streamlines']
measures += [bundle_adjacency_streamlines]
# Only when the tractograms are exactly the same
if streamline_dice:
dice_streamlines, streamlines_intersect, streamlines_union = \
compute_dice_streamlines(bundle_1, bundle_2)
streamlines_count_overlap = len(streamlines_intersect)
streamlines_count_overreach = len(
streamlines_union) - len(streamlines_intersect)
measures_name += ['dice_streamlines',
'streamlines_count_overlap',
'streamlines_count_overreach']
measures += [dice_streamlines,
streamlines_count_overlap,
streamlines_count_overreach]
return dict(zip(measures_name, measures))
def __init__(self, init_as=None, reference=None, store=None):
""" Initialize an empty TrxFile, support preallocation """
if init_as is not None:
affine = init_as._zcontainer.attrs['VOXEL_TO_RASMM']
dimensions = init_as._zcontainer.attrs['DIMENSIONS']
elif reference is not None:
affine, dimensions, _, _ = get_reference_info(reference)
else:
logging.debug('No reference provided, using blank space '
'attributes, please update them later.')
affine = np.eye(4).astype(np.float32)
dimensions = [1, 1, 1]
if store is None:
store = zarr.storage.TempStore()
self._zcontainer = zarr.group(store=store, overwrite=True)
self.voxel_to_rasmm = affine
self.dimensions = dimensions
self.nb_points = 0
self.nb_streamlines = 0
self._zstore = store
if init_as:
positions_dtype = init_as._zpos.dtype
else:
positions_dtype = np.float16
self._zcontainer.create_dataset('positions',
shape=(0, 3),
chunks=(1000000, None),
dtype=positions_dtype)
self._zcontainer.create_dataset('offsets',
shape=(0, ),
chunks=(100000, ),
dtype=np.uint64)
self._zcontainer.create_group('data_per_point')
self._zcontainer.create_group('data_per_streamline')
self._zcontainer.create_group('data_per_group')
self._zcontainer.create_group('groups')
if init_as is None:
return
for dpp_key in init_as._zdpp.array_keys():
empty_shape = list(init_as._zdpp[dpp_key].shape)
empty_shape[0] = 0
dtype = init_as._zdpp[dpp_key].dtype
chunks = [1000000]
for _ in range(len(empty_shape) - 1):
chunks.append(None)
self._zdpp.create_dataset(dpp_key,
shape=empty_shape,
chunks=chunks,
dtype=dtype)
for dps_key in init_as._zdps.array_keys():
empty_shape = list(init_as._zdps[dps_key].shape)
empty_shape[0] = 0
dtype = init_as._zdps[dps_key].dtype
chunks = [100000]
for _ in range(len(empty_shape) - 1):
chunks.append(None)
self._zdps.create_dataset(dps_key,
shape=empty_shape,
chunks=chunks,
dtype=dtype)
for grp_key in init_as._zgrp.array_keys():
empty_shape = list(init_as._zgrp[grp_key].shape)
empty_shape[0] = 0
dtype = init_as._zgrp[grp_key].dtype
self._zgrp.create_dataset(grp_key,
shape=empty_shape,
chunks=(10000, ),
dtype=dtype)
for grp_key in init_as._zdpg.group_keys():
if len(init_as._zdpg[grp_key]):
self._zdpg.create_group(grp_key)
for dpg_key in init_as._zdpg[grp_key].array_keys():
empty_shape = list(init_as._zdpg[grp_key][dpg_key].shape)
empty_shape[0] = 0
dtype = init_as._zdpg[grp_key][dpg_key].dtype
self._zdpg[grp_key].create_dataset(dpg_key,
shape=empty_shape,
chunks=None,
dtype=dtype)
def transform_warp_streamlines(sft,
linear_transfo,
target,
inverse=False,
deformation_data=None,
remove_invalid=True,
cut_invalid=False):
# TODO rename transform_warp_sft
""" Transform tractogram using a affine Subsequently apply a warp from
antsRegistration (optional).
Remove/Cut invalid streamlines to preserve sft validity.
Parameters
----------
sft: StatefulTractogram
Stateful tractogram object containing the streamlines to transform.
linear_transfo: numpy.ndarray
Linear transformation matrix to apply to the tractogram.
target: Nifti filepath, image object, header
Final reference for the tractogram after registration.
inverse: boolean
Apply the inverse linear transformation.
deformation_data: np.ndarray
4D array containing a 3D displacement vector in each voxel.
remove_invalid: boolean
Remove the streamlines landing out of the bounding box.
cut_invalid: boolean
Cut invalid streamlines rather than removing them. Keep the longest
segment only.
Return
----------
new_sft : StatefulTractogram
"""
sft.to_rasmm()
sft.to_center()
if inverse:
linear_transfo = np.linalg.inv(linear_transfo)
streamlines = transform_streamlines(sft.streamlines, linear_transfo)
if deformation_data is not None:
affine, _, _, _ = get_reference_info(target)
# Because of duplication, an iteration over chunks of points is
# necessary for a big dataset (especially if not compressed)
streamlines = ArraySequence(streamlines)
nb_points = len(streamlines._data)
cur_position = 0
chunk_size = 1000000
nb_iteration = int(np.ceil(nb_points / chunk_size))
inv_affine = np.linalg.inv(affine)
while nb_iteration > 0:
max_position = min(cur_position + chunk_size, nb_points)
points = streamlines._data[cur_position:max_position]
# To access the deformation information, we need to go in VOX space
# No need for corner shift since we are doing interpolation
cur_points_vox = np.array(transform_streamlines(
points, inv_affine)).T
x_def = map_coordinates(deformation_data[..., 0],
cur_points_vox.tolist(),
order=1)
y_def = map_coordinates(deformation_data[..., 1],
cur_points_vox.tolist(),
order=1)
z_def = map_coordinates(deformation_data[..., 2],
cur_points_vox.tolist(),
order=1)
# ITK is in LPS and nibabel is in RAS, a flip is necessary for ANTs
final_points = np.array([-1 * x_def, -1 * y_def, z_def])
final_points += np.array(points).T
streamlines._data[cur_position:max_position] = final_points.T
cur_position = max_position
nb_iteration -= 1
new_sft = StatefulTractogram(streamlines,
target,
Space.RASMM,
data_per_point=sft.data_per_point,
data_per_streamline=sft.data_per_streamline)
if cut_invalid:
new_sft, _ = cut_invalid_streamlines(new_sft)
elif remove_invalid:
new_sft.remove_invalid_streamlines()
return new_sft
def main():
parser = _build_arg_parser()
args = parser.parse_args()
if args.verbose:
logging.basicConfig(level=logging.DEBUG)
assert_inputs_exist(
parser,
[args.in_sh, args.in_seed, args.in_map_include, args.map_exclude_file])
assert_outputs_exist(parser, args, args.out_tractogram)
if not nib.streamlines.is_supported(args.out_tractogram):
parser.error('Invalid output streamline file format (must be trk or ' +
'tck): {0}'.format(args.out_tractogram))
if not args.min_length > 0:
parser.error('minL must be > 0, {}mm was provided.'.format(
args.min_length))
if args.max_length < args.min_length:
parser.error(
'maxL must be > than minL, (minL={}mm, maxL={}mm).'.format(
args.min_length, args.max_length))
if args.compress:
if args.compress < 0.001 or args.compress > 1:
logging.warning(
'You are using an error rate of {}.\nWe recommend setting it '
'between 0.001 and 1.\n0.001 will do almost nothing to the '
'tracts while 1 will higly compress/linearize the tracts'.
format(args.compress))
if args.particles <= 0:
parser.error('--particles must be >= 1.')
if args.back_tracking <= 0:
parser.error('PFT backtracking distance must be > 0.')
if args.forward_tracking <= 0:
parser.error('PFT forward tracking distance must be > 0.')
if args.npv and args.npv <= 0:
parser.error('Number of seeds per voxel must be > 0.')
if args.nt and args.nt <= 0:
parser.error('Total number of seeds must be > 0.')
fodf_sh_img = nib.load(args.in_sh)
if not np.allclose(np.mean(fodf_sh_img.header.get_zooms()[:3]),
fodf_sh_img.header.get_zooms()[0],
atol=1.e-3):
parser.error(
'SH file is not isotropic. Tracking cannot be ran robustly.')
tracking_sphere = HemiSphere.from_sphere(get_sphere('repulsion724'))
# Check if sphere is unit, since we couldn't find such check in Dipy.
if not np.allclose(np.linalg.norm(tracking_sphere.vertices, axis=1), 1.):
raise RuntimeError('Tracking sphere should be unit normed.')
sh_basis = args.sh_basis
if args.algo == 'det':
dgklass = DeterministicMaximumDirectionGetter
else:
dgklass = ProbabilisticDirectionGetter
theta = get_theta(args.theta, args.algo)
# Reminder for the future:
# pmf_threshold == clip pmf under this
# relative_peak_threshold is for initial directions filtering
# min_separation_angle is the initial separation angle for peak extraction
dg = dgklass.from_shcoeff(fodf_sh_img.get_fdata(dtype=np.float32),
max_angle=theta,
sphere=tracking_sphere,
basis_type=sh_basis,
pmf_threshold=args.sf_threshold,
relative_peak_threshold=args.sf_threshold_init)
map_include_img = nib.load(args.in_map_include)
map_exclude_img = nib.load(args.map_exclude_file)
voxel_size = np.average(map_include_img.header['pixdim'][1:4])
if not args.act:
tissue_classifier = CmcStoppingCriterion(
map_include_img.get_fdata(dtype=np.float32),
map_exclude_img.get_fdata(dtype=np.float32),
step_size=args.step_size,
average_voxel_size=voxel_size)
else:
tissue_classifier = ActStoppingCriterion(
map_include_img.get_fdata(dtype=np.float32),
map_exclude_img.get_fdata(dtype=np.float32))
if args.npv:
nb_seeds = args.npv
seed_per_vox = True
elif args.nt:
nb_seeds = args.nt
seed_per_vox = False
else:
nb_seeds = 1
seed_per_vox = True
voxel_size = fodf_sh_img.header.get_zooms()[0]
vox_step_size = args.step_size / voxel_size
seed_img = nib.load(args.in_seed)
seeds = track_utils.random_seeds_from_mask(
get_data_as_mask(seed_img, dtype=np.bool),
np.eye(4),
seeds_count=nb_seeds,
seed_count_per_voxel=seed_per_vox,
random_seed=args.seed)
# Note that max steps is used once for the forward pass, and
# once for the backwards. This doesn't, in fact, control the real
# max length
max_steps = int(args.max_length / args.step_size) + 1
pft_streamlines = ParticleFilteringTracking(
dg,
tissue_classifier,
seeds,
np.eye(4),
max_cross=1,
step_size=vox_step_size,
maxlen=max_steps,
pft_back_tracking_dist=args.back_tracking,
pft_front_tracking_dist=args.forward_tracking,
particle_count=args.particles,
return_all=args.keep_all,
random_seed=args.seed,
save_seeds=args.save_seeds)
scaled_min_length = args.min_length / voxel_size
scaled_max_length = args.max_length / voxel_size
if args.save_seeds:
filtered_streamlines, seeds = \
zip(*((s, p) for s, p in pft_streamlines
if scaled_min_length <= length(s) <= scaled_max_length))
data_per_streamlines = {'seeds': lambda: seeds}
else:
filtered_streamlines = \
(s for s in pft_streamlines
if scaled_min_length <= length(s) <= scaled_max_length)
data_per_streamlines = {}
if args.compress:
filtered_streamlines = (compress_streamlines(s, args.compress)
for s in filtered_streamlines)
tractogram = LazyTractogram(lambda: filtered_streamlines,
data_per_streamlines,
affine_to_rasmm=seed_img.affine)
filetype = nib.streamlines.detect_format(args.out_tractogram)
reference = get_reference_info(seed_img)
header = create_tractogram_header(filetype, *reference)
# Use generator to save the streamlines on-the-fly
nib.streamlines.save(tractogram, args.out_tractogram, header=header)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.in_tractogram, args.in_labels],
args.reference)
assert_outputs_exist(parser, args, args.out_hdf5)
# HDF5 will not overwrite the file
if os.path.isfile(args.out_hdf5):
os.remove(args.out_hdf5)
if (args.save_raw_connections or args.save_intermediate
or args.save_discarded) and not args.out_dir:
parser.error('To save outputs in the streamlines form, provide the '
'output directory using --out_dir.')
if args.out_dir:
if os.path.abspath(args.out_dir) == os.getcwd():
parser.error('Do not use the current path as output directory.')
assert_output_dirs_exist_and_empty(parser,
args,
args.out_dir,
create_dir=True)
log_level = logging.WARNING
if args.verbose:
log_level = logging.INFO
logging.basicConfig(level=log_level)
coloredlogs.install(level=log_level)
set_sft_logger_level('WARNING')
img_labels = nib.load(args.in_labels)
data_labels = get_data_as_label(img_labels)
real_labels = np.unique(data_labels)[1:]
if args.out_labels_list:
np.savetxt(args.out_labels_list, real_labels, fmt='%i')
# Voxel size must be isotropic, for speed/performance considerations
vox_sizes = img_labels.header.get_zooms()
if not np.allclose(np.mean(vox_sizes), vox_sizes, atol=1e-03):
parser.error('Labels must be isotropic')
logging.info('*** Loading streamlines ***')
time1 = time.time()
sft = load_tractogram_with_reference(parser,
args,
args.in_tractogram,
bbox_check=False)
sft.remove_invalid_streamlines()
time2 = time.time()
logging.info(' Loading {} streamlines took {} sec.'.format(
len(sft), round(time2 - time1, 2)))
if not is_header_compatible(sft, img_labels):
raise IOError('{} and {}do not have a compatible header'.format(
args.in_tractogram, args.in_labels))
sft.to_vox()
sft.to_corner()
# Get all streamlines intersection indices
logging.info('*** Computing streamlines intersection ***')
time1 = time.time()
indices, points_to_idx = uncompress(sft.streamlines, return_mapping=True)
time2 = time.time()
logging.info(' Streamlines intersection took {} sec.'.format(
round(time2 - time1, 2)))
# Compute the connectivity mapping
logging.info('*** Computing connectivity information ***')
time1 = time.time()
con_info = compute_connectivity(indices, data_labels, real_labels,
extract_longest_segments_from_profile)
time2 = time.time()
logging.info(' Connectivity computation took {} sec.'.format(
round(time2 - time1, 2)))
# Prepare directories and information needed to save.
_create_required_output_dirs(args)
logging.info('*** Starting connection post-processing and saving. ***')
logging.info(' This can be long, be patient.')
time1 = time.time()
# Saving will be done from streamlines already in the right space
comb_list = list(itertools.combinations(real_labels, r=2))
comb_list.extend(zip(real_labels, real_labels))
iteration_counter = 0
with h5py.File(args.out_hdf5, 'w') as hdf5_file:
affine, dimensions, voxel_sizes, voxel_order = get_reference_info(sft)
hdf5_file.attrs['affine'] = affine
hdf5_file.attrs['dimensions'] = dimensions
hdf5_file.attrs['voxel_sizes'] = voxel_sizes
hdf5_file.attrs['voxel_order'] = voxel_order
# Each connections is processed independently. Multiprocessing would be
# a burden on the I/O of most SSD/HD
for in_label, out_label in comb_list:
if iteration_counter > 0 and iteration_counter % 100 == 0:
logging.info('Split {} nodes out of {}'.format(
iteration_counter, len(comb_list)))
iteration_counter += 1
pair_info = []
if in_label not in con_info:
continue
elif out_label in con_info[in_label]:
pair_info.extend(con_info[in_label][out_label])
if out_label not in con_info:
continue
elif in_label in con_info[out_label]:
pair_info.extend(con_info[out_label][in_label])
if not len(pair_info):
continue
connecting_streamlines = []
connecting_ids = []
for connection in pair_info:
strl_idx = connection['strl_idx']
curr_streamlines = compute_streamline_segment(
sft.streamlines[strl_idx], indices[strl_idx],
connection['in_idx'], connection['out_idx'],
points_to_idx[strl_idx])
connecting_streamlines.append(curr_streamlines)
connecting_ids.append(strl_idx)
# Each step is processed from the previous 'success'
# 1. raw -> length pass/fail
# 2. length pass -> loops pass/fail
# 3. loops pass -> outlier detection pass/fail
# 4. outlier detection pass -> qb curvature pass/fail
# 5. qb curvature pass == final connections
connecting_streamlines = ArraySequence(connecting_streamlines)
raw_dps = sft.data_per_streamline[connecting_ids]
raw_sft = StatefulTractogram.from_sft(connecting_streamlines,
sft,
data_per_streamline=raw_dps,
data_per_point={})
_save_if_needed(raw_sft, hdf5_file, args, 'raw', 'raw', in_label,
out_label)
# Doing all post-processing
if not args.no_pruning:
valid_length_ids, invalid_length_ids = _prune_segments(
raw_sft.streamlines, args.min_length, args.max_length,
vox_sizes[0])
invalid_length_sft = raw_sft[invalid_length_ids]
valid_length = connecting_streamlines[valid_length_ids]
_save_if_needed(invalid_length_sft, hdf5_file, args,
'discarded', 'invalid_length', in_label,
out_label)
else:
valid_length = connecting_streamlines
valid_length_ids = range(len(connecting_streamlines))
if not len(valid_length):
continue
valid_length_sft = raw_sft[valid_length_ids]
_save_if_needed(valid_length_sft, hdf5_file, args, 'intermediate',
'valid_length', in_label, out_label)
if not args.no_remove_loops:
no_loop_ids = remove_loops_and_sharp_turns(
valid_length, args.loop_max_angle)
loop_ids = np.setdiff1d(np.arange(len(valid_length)),
no_loop_ids)
loops_sft = valid_length_sft[loop_ids]
no_loops = valid_length[no_loop_ids]
_save_if_needed(loops_sft, hdf5_file, args, 'discarded',
'loops', in_label, out_label)
else:
no_loops = valid_length
no_loop_ids = range(len(valid_length))
if not len(no_loops):
continue
no_loops_sft = valid_length_sft[no_loop_ids]
_save_if_needed(no_loops_sft, hdf5_file, args, 'intermediate',
'no_loops', in_label, out_label)
if not args.no_remove_outliers:
outliers_ids, inliers_ids = remove_outliers(
no_loops,
args.outlier_threshold,
nb_samplings=10,
fast_approx=True)
outliers_sft = no_loops_sft[outliers_ids]
inliers = no_loops[inliers_ids]
_save_if_needed(outliers_sft, hdf5_file, args, 'discarded',
'outliers', in_label, out_label)
else:
inliers = no_loops
inliers_ids = range(len(no_loops))
if not len(inliers):
continue
inliers_sft = no_loops_sft[inliers_ids]
_save_if_needed(inliers_sft, hdf5_file, args, 'intermediate',
'inliers', in_label, out_label)
if not args.no_remove_curv_dev:
no_qb_curv_ids = remove_loops_and_sharp_turns(
inliers,
args.loop_max_angle,
use_qb=True,
qb_threshold=args.curv_qb_distance)
qb_curv_ids = np.setdiff1d(np.arange(len(inliers)),
no_qb_curv_ids)
qb_curv_sft = inliers_sft[qb_curv_ids]
_save_if_needed(qb_curv_sft, hdf5_file, args, 'discarded',
'qb_curv', in_label, out_label)
else:
no_qb_curv_ids = range(len(inliers))
no_qb_curv_sft = inliers_sft[no_qb_curv_ids]
_save_if_needed(no_qb_curv_sft, hdf5_file, args, 'final', 'final',
in_label, out_label)
time2 = time.time()
logging.info(
' Connections post-processing and saving took {} sec.'.format(
round(time2 - time1, 2)))
def alltrks2bin(tractseg_folder):
reference_anatomy = tractseg_folder + 'reference_anatomy.nii.gz'
affine, dimensions, voxel_sizes, voxel_order = get_reference_info(
reference_anatomy)
low_res = (2.5, 2.5, 2.5)
subjects = []
for root, dirs, files in walk(tractseg_folder):
if 'average' in dirs: dirs.remove('average')
subjects.extend(dirs)
break
# assuming all subject folders contain all tracts (given for TractSeg samples)
tracts = []
for root, dirs, files in walk(tractseg_folder + subjects[0] + '/tracts'):
for f in files:
if f[-4:] == ".trk":
tracts.append(f[:-4])
# make a folder to save average masks into
try:
Path(tractseg_folder + 'average').mkdir(parents=True, exist_ok=True)
except OSError:
print('Could not create output dir. Aborting...')
return
i = 0
errs = []
for t in tracts:
print('Current tract: ', t, ' (', (i * 100) / len(tracts), '%)')
high_res_path = tractseg_folder + 'average/' + t + '.nii.gz'
low_res_path = tractseg_folder + 'average/' + t + '_low_res.nii.gz'
if not (Path(high_res_path).exists() & Path(low_res_path).exists()):
j = 0
t_ave = np.zeros(dimensions, dtype=np.float)
for s in subjects:
try:
print('Current subject: ', s, ' (',
(j * 100) / len(subjects), '%)')
trk_data = load_trk(
tractseg_folder + s + '/tracts/' + t + '.trk',
reference_anatomy)
trk_data.to_vox()
streams = np.vstack(trk_data.streamlines).astype(np.int32)
mask = np.zeros(dimensions, dtype=np.float)
mask[streams[:, 0], streams[:, 1], streams[:, 2]] = 1
save_nifti(
tractseg_folder + s + '/tracts/' + t + '.nii.gz', mask,
affine)
# make low res version
# mask_low_res, affine_low_res = reslice(mask, affine, voxel_sizes, low_res)
# save_nifti(tractseg_folder + s + '/tracts/' + t + '_low_res.nii.gz', mask_low_res, affine_low_res)
t_ave += mask
j += 1
except:
errs.append('Error with tract ' + t + ' in subject ' + s)
try:
t_ave /= len(subjects)
save_nifti(high_res_path, t_ave, affine)
t_ave_low_res, affine_low_res = reslice(
t_ave, affine, voxel_sizes, low_res)
save_nifti(low_res_path, t_ave_low_res, affine_low_res)
except:
errs.append('Error with average of tract ' + t)
i += 1
for e in errs:
print(e)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.in_hdf5, args.in_target_file,
args.in_transfo], args.in_deformation)
assert_outputs_exist(parser, args, args.out_hdf5)
# HDF5 will not overwrite the file
if os.path.isfile(args.out_hdf5):
os.remove(args.out_hdf5)
with h5py.File(args.in_hdf5, 'r') as in_hdf5_file:
shutil.copy(args.in_hdf5, args.out_hdf5)
with h5py.File(args.out_hdf5, 'a') as out_hdf5_file:
transfo = load_matrix_in_any_format(args.in_transfo)
deformation_data = None
if args.in_deformation is not None:
deformation_data = np.squeeze(nib.load(
args.in_deformation).get_fdata(dtype=np.float32))
target_img = nib.load(args.in_target_file)
for key in in_hdf5_file.keys():
affine = in_hdf5_file.attrs['affine']
dimensions = in_hdf5_file.attrs['dimensions']
voxel_sizes = in_hdf5_file.attrs['voxel_sizes']
streamlines = reconstruct_streamlines_from_hdf5(
in_hdf5_file, key)
if len(streamlines) == 0:
continue
header = create_nifti_header(affine, dimensions, voxel_sizes)
moving_sft = StatefulTractogram(streamlines, header, Space.VOX,
origin=Origin.TRACKVIS)
new_sft = transform_warp_streamlines(
moving_sft, transfo, target_img,
inverse=args.inverse,
deformation_data=deformation_data,
remove_invalid=not args.cut_invalid,
cut_invalid=args.cut_invalid)
new_sft.to_vox()
new_sft.to_corner()
affine, dimensions, voxel_sizes, voxel_order = get_reference_info(
target_img)
out_hdf5_file.attrs['affine'] = affine
out_hdf5_file.attrs['dimensions'] = dimensions
out_hdf5_file.attrs['voxel_sizes'] = voxel_sizes
out_hdf5_file.attrs['voxel_order'] = voxel_order
group = out_hdf5_file[key]
del group['data']
group.create_dataset('data',
data=new_sft.streamlines.get_data())
del group['offsets']
group.create_dataset('offsets',
data=new_sft.streamlines._offsets)
del group['lengths']
group.create_dataset('lengths',
data=new_sft.streamlines._lengths)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
if args.load_transfo and args.in_native_fa is None:
parser.error('When loading a transformation, the final reference is '
'needed, use --in_native_fa.')
assert_inputs_exist(parser, [args.in_dsi_tractogram, args.in_dsi_fa],
optional=args.in_native_fa)
assert_outputs_exist(parser, args, args.out_tractogram)
sft = load_tractogram(args.in_dsi_tractogram,
'same',
bbox_valid_check=False)
# LPS -> RAS convention in voxel space
sft.to_vox()
flip_axis = ['x', 'y']
sft_fix = StatefulTractogram(sft.streamlines, args.in_dsi_fa, Space.VOXMM)
sft_fix.to_vox()
sft_fix.streamlines._data -= get_axis_shift_vector(flip_axis)
sft_flip = flip_sft(sft_fix, flip_axis)
sft_flip.to_rasmm()
sft_flip.streamlines._data -= [0.5, 0.5, -0.5]
if not args.in_native_fa:
if args.cut_invalid:
sft_flip, _ = cut_invalid_streamlines(sft_flip)
elif args.remove_invalid:
sft_flip.remove_invalid_streamlines()
save_tractogram(sft_flip,
args.out_tractogram,
bbox_valid_check=not args.keep_invalid)
else:
static_img = nib.load(args.in_native_fa)
static_data = static_img.get_fdata()
moving_img = nib.load(args.in_dsi_fa)
moving_data = moving_img.get_fdata()
# DSI-Studio flips the volume without changing the affine (I think)
# So this has to be reversed (not the same problem as above)
vox_order = get_reference_info(moving_img)[3]
flip_axis = []
if vox_order[0] == 'L':
moving_data = moving_data[::-1, :, :]
flip_axis.append('x')
if vox_order[1] == 'P':
moving_data = moving_data[:, ::-1, :]
flip_axis.append('y')
if vox_order[2] == 'I':
moving_data = moving_data[:, :, ::-1]
flip_axis.append('z')
sft_flip_back = flip_sft(sft_flip, flip_axis)
if args.load_transfo:
transfo = np.loadtxt(args.load_transfo)
else:
# Sometimes DSI studio has quite a lot of skull left
# Dipy Median Otsu does not work with FA/GFA
if args.auto_crop:
moving_data = cube_crop_data(moving_data)
static_data = cube_crop_data(static_data)
# Since DSI Studio register to AC/PC and does not save the
# transformation We must estimate the transformation, since it's
# rigid it is 'easy'
c_of_mass = transform_centers_of_mass(static_data,
static_img.affine,
moving_data,
moving_img.affine)
nbins = 32
sampling_prop = None
level_iters = [1000, 100, 10]
sigmas = [3.0, 2.0, 1.0]
factors = [3, 2, 1]
metric = MutualInformationMetric(nbins, sampling_prop)
affreg = AffineRegistration(metric=metric,
level_iters=level_iters,
sigmas=sigmas,
factors=factors)
transform = RigidTransform3D()
rigid = affreg.optimize(static_data,
moving_data,
transform,
None,
static_img.affine,
moving_img.affine,
starting_affine=c_of_mass.affine)
transfo = rigid.affine
if args.save_transfo:
np.savetxt(args.save_transfo, transfo)
new_sft = transform_warp_sft(sft_flip_back,
transfo,
static_img,
inverse=True,
remove_invalid=args.remove_invalid,
cut_invalid=args.cut_invalid)
if args.cut_invalid:
new_sft, _ = cut_invalid_streamlines(new_sft)
elif args.remove_invalid:
new_sft.remove_invalid_streamlines()
save_tractogram(new_sft,
args.out_tractogram,
bbox_valid_check=not args.keep_invalid)
