def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(
parser,
[args.in_moving_tractogram, args.in_target_file, args.in_transfo],
args.in_deformation)
assert_outputs_exist(parser, args, args.out_tractogram)
moving_sft = load_tractogram_with_reference(parser,
args,
args.in_moving_tractogram,
bbox_check=False)
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))
new_sft = transform_warp_streamlines(moving_sft,
transfo,
args.in_target_file,
inverse=args.inverse,
deformation_data=deformation_data,
remove_invalid=args.remove_invalid,
cut_invalid=args.cut_invalid)
if args.keep_invalid:
if not new_sft.is_bbox_in_vox_valid():
logging.warning('Saving tractogram with invalid streamlines.')
save_tractogram(new_sft, args.out_tractogram, bbox_valid_check=False)
else:
save_tractogram(new_sft, args.out_tractogram)
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.streamlines._data -= get_axis_shift_vector(flip_axis)
sft_fix = StatefulTractogram(sft.streamlines, args.in_dsi_fa,
Space.VOX)
sft_flip = flip_sft(sft_fix, flip_axis)
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_streamlines(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)