def main():
time_start = ph.start_timing()
np.set_printoptions(precision=3)
input_parser = InputArgparser(
description="Register an obtained reconstruction (moving) "
"to a template image/space (fixed) using rigid registration. "
"The resulting registration can optionally be applied to previously "
"obtained motion correction slice transforms so that a volumetric "
"reconstruction is possible in the (standard anatomical) space "
"defined by the fixed.", )
input_parser.add_fixed(required=True)
input_parser.add_moving(required=True)
input_parser.add_output(help="Path to registration transform (.txt)",
required=True)
input_parser.add_fixed_mask(required=False)
input_parser.add_moving_mask(required=False)
input_parser.add_option(
option_string="--initial-transform",
type=str,
help="Path to initial transform. "
"If not provided, registration will be initialized based on "
"rigid alignment of eigenbasis of the fixed/moving image masks "
"using principal component analysis",
default=None)
input_parser.add_v2v_method(
option_string="--method",
help="Registration method used for the registration.",
default="RegAladin",
)
input_parser.add_argument(
"--refine-pca",
"-refine-pca",
action='store_true',
help="If given, PCA-based initializations will be refined using "
"RegAladin registrations.")
input_parser.add_dir_input_mc()
input_parser.add_verbose(default=0)
input_parser.add_log_config(default=1)
args = input_parser.parse_args()
input_parser.print_arguments(args)
if args.log_config:
input_parser.log_config(os.path.abspath(__file__))
if not args.output.endswith(".txt"):
raise IOError("output transformation path must end in '.txt'")
dir_output = os.path.dirname(args.output)
ph.create_directory(dir_output)
# --------------------------------Read Data--------------------------------
ph.print_title("Read Data")
fixed = st.Stack.from_filename(file_path=args.fixed,
file_path_mask=args.fixed_mask,
extract_slices=False)
moving = st.Stack.from_filename(file_path=args.moving,
file_path_mask=args.moving_mask,
extract_slices=False)
path_to_tmp_output = os.path.join(
DIR_TMP, ph.append_to_filename(os.path.basename(args.moving),
"_warped"))
# ---------------------------- Initialization ----------------------------
if args.initial_transform is None:
ph.print_title("Estimate initial transform using PCA")
if args.moving_mask is None or args.fixed_mask is None:
ph.print_warning("Fixed and moving masks are strongly recommended")
transform_initializer = tinit.TransformInitializer(
fixed=fixed,
moving=moving,
similarity_measure="NMI",
refine_pca_initializations=args.refine_pca,
)
transform_initializer.run()
transform_init_sitk = transform_initializer.get_transform_sitk()
else:
transform_init_sitk = sitkh.read_transform_sitk(args.initial_transform)
sitk.WriteTransform(transform_init_sitk, args.output)
# -------------------Register Reconstruction to Template-------------------
ph.print_title("Registration")
if args.method == "RegAladin":
path_to_transform_regaladin = os.path.join(DIR_TMP,
"transform_regaladin.txt")
# Convert SimpleITK to RegAladin transform
cmd = "simplereg_transform -sitk2nreg %s %s" % (
args.output, path_to_transform_regaladin)
ph.execute_command(cmd, verbose=False)
# Run NiftyReg
cmd_args = ["reg_aladin"]
cmd_args.append("-ref '%s'" % args.fixed)
cmd_args.append("-flo '%s'" % args.moving)
cmd_args.append("-res '%s'" % path_to_tmp_output)
cmd_args.append("-inaff '%s'" % path_to_transform_regaladin)
cmd_args.append("-aff '%s'" % path_to_transform_regaladin)
cmd_args.append("-rigOnly")
cmd_args.append("-ln 2") # seems to perform better for spina bifida
cmd_args.append("-voff")
if args.fixed_mask is not None:
cmd_args.append("-rmask '%s'" % args.fixed_mask)
# To avoid error "0 correspondences between blocks were found" that can
# occur for some cases. Also, disable moving mask, as this would be ignored
# anyway
cmd_args.append("-noSym")
# if args.moving_mask is not None:
# cmd_args.append("-fmask '%s'" % args.moving_mask)
ph.print_info("Run Registration (RegAladin) ... ", newline=False)
ph.execute_command(" ".join(cmd_args), verbose=False)
print("done")
# Convert RegAladin to SimpleITK transform
cmd = "simplereg_transform -nreg2sitk '%s' '%s'" % (
path_to_transform_regaladin, args.output)
ph.execute_command(cmd, verbose=False)
else:
path_to_transform_flirt = os.path.join(DIR_TMP, "transform_flirt.txt")
# Convert SimpleITK into FLIRT transform
cmd = "simplereg_transform -sitk2flirt '%s' '%s' '%s' '%s'" % (
args.output, args.fixed, args.moving, path_to_transform_flirt)
ph.execute_command(cmd, verbose=False)
# Define search angle ranges for FLIRT in all three dimensions
search_angles = [
"-searchr%s -%d %d" % (x, 180, 180) for x in ["x", "y", "z"]
]
cmd_args = ["flirt"]
cmd_args.append("-in '%s'" % args.moving)
cmd_args.append("-ref '%s'" % args.fixed)
if args.initial_transform is not None:
cmd_args.append("-init '%s'" % path_to_transform_flirt)
cmd_args.append("-omat '%s'" % path_to_transform_flirt)
cmd_args.append("-out '%s'" % path_to_tmp_output)
cmd_args.append("-dof 6")
cmd_args.append((" ").join(search_angles))
if args.moving_mask is not None:
cmd_args.append("-inweight '%s'" % args.moving_mask)
if args.fixed_mask is not None:
cmd_args.append("-refweight '%s'" % args.fixed_mask)
ph.print_info("Run Registration (FLIRT) ... ", newline=False)
ph.execute_command(" ".join(cmd_args), verbose=False)
print("done")
# Convert FLIRT to SimpleITK transform
cmd = "simplereg_transform -flirt2sitk '%s' '%s' '%s' '%s'" % (
path_to_transform_flirt, args.fixed, args.moving, args.output)
ph.execute_command(cmd, verbose=False)
if args.dir_input_mc is not None:
ph.print_title("Update Motion-Correction Transformations")
transform_sitk = sitkh.read_transform_sitk(args.output, inverse=1)
if args.dir_input_mc.endswith("/"):
subdir_mc = args.dir_input_mc.split("/")[-2]
else:
subdir_mc = args.dir_input_mc.split("/")[-1]
dir_output_mc = os.path.join(dir_output, subdir_mc)
ph.create_directory(dir_output_mc, delete_files=True)
pattern = REGEX_FILENAMES + "[.]tfm"
p = re.compile(pattern)
trafos = [t for t in os.listdir(args.dir_input_mc) if p.match(t)]
for t in trafos:
path_to_input_transform = os.path.join(args.dir_input_mc, t)
path_to_output_transform = os.path.join(dir_output_mc, t)
t_sitk = sitkh.read_transform_sitk(path_to_input_transform)
t_sitk = sitkh.get_composite_sitk_affine_transform(
transform_sitk, t_sitk)
sitk.WriteTransform(t_sitk, path_to_output_transform)
ph.print_info("%d transformations written to '%s'" %
(len(trafos), dir_output_mc))
if args.verbose:
ph.show_niftis([args.fixed, path_to_tmp_output])
elapsed_time_total = ph.stop_timing(time_start)
# Summary
ph.print_title("Summary")
print("Computational Time: %s" % (elapsed_time_total))
return 0
def main():
time_start = ph.start_timing()
np.set_printoptions(precision=3)
input_parser = InputArgparser(
description="Register an obtained reconstruction (moving) "
"to a template image/space (fixed) using rigid registration. "
"The resulting registration can optionally be applied to previously "
"obtained motion correction slice transforms so that a volumetric "
"reconstruction is possible in the (standard anatomical) space "
"defined by the fixed.", )
input_parser.add_fixed(required=True)
input_parser.add_moving(required=True)
input_parser.add_output(help="Path to registration transform (.txt)",
required=True)
input_parser.add_fixed_mask()
input_parser.add_moving_mask()
input_parser.add_dir_input_mc()
input_parser.add_search_angle(default=180)
input_parser.add_option(option_string="--initial-transform",
type=str,
help="Path to initial transform.",
default=None)
input_parser.add_option(
option_string="--test-ap-flip",
type=int,
help="Turn on/off functionality to run an additional registration "
"after an AP-flip. Seems to be more robust to find a better "
"registration outcome in general.",
default=1)
input_parser.add_option(
option_string="--use-flirt",
type=int,
help="Turn on/off functionality to use FLIRT for the registration.",
default=1)
input_parser.add_option(
option_string="--use-regaladin",
type=int,
help="Turn on/off functionality to use RegAladin for the "
"registration.",
default=1)
input_parser.add_verbose(default=0)
input_parser.add_log_config(default=1)
args = input_parser.parse_args()
input_parser.print_arguments(args)
debug = 0
if args.log_config:
input_parser.log_config(os.path.abspath(__file__))
if not args.use_regaladin and not args.use_flirt:
raise IOError("Either RegAladin or FLIRT must be activated.")
if not args.output.endswith(".txt"):
raise IOError("output transformation path must end in '.txt'")
dir_output = os.path.dirname(args.output)
# --------------------------------Read Data--------------------------------
ph.print_title("Read Data")
fixed = st.Stack.from_filename(file_path=args.fixed,
file_path_mask=args.fixed_mask,
extract_slices=False)
moving = st.Stack.from_filename(file_path=args.moving,
file_path_mask=args.moving_mask,
extract_slices=False)
if args.initial_transform is not None:
transform_sitk = sitkh.read_transform_sitk(args.initial_transform)
else:
transform_sitk = sitk.AffineTransform(fixed.sitk.GetDimension())
sitk.WriteTransform(transform_sitk, args.output)
path_to_tmp_output = os.path.join(
DIR_TMP, ph.append_to_filename(os.path.basename(args.moving),
"_warped"))
# -------------------Register Reconstruction to Template-------------------
ph.print_title("Register Reconstruction to Template")
if args.use_flirt:
path_to_transform_flirt = os.path.join(DIR_TMP, "transform_flirt.txt")
# Convert SimpleITK into FLIRT transform
cmd = "simplereg_transform -sitk2flirt %s %s %s %s" % (
args.output, args.fixed, args.moving, path_to_transform_flirt)
ph.execute_command(cmd, verbose=False)
# Define search angle ranges for FLIRT in all three dimensions
search_angles = [
"-searchr%s -%d %d" % (x, args.search_angle, args.search_angle)
for x in ["x", "y", "z"]
]
# flt = nipype.interfaces.fsl.FLIRT()
# flt.inputs.in_file = args.moving
# flt.inputs.reference = args.fixed
# if args.initial_transform is not None:
# flt.inputs.in_matrix_file = path_to_transform_flirt
# flt.inputs.out_matrix_file = path_to_transform_flirt
# # flt.inputs.output_type = "NIFTI_GZ"
# flt.inputs.out_file = path_to_tmp_output
# flt.inputs.args = "-dof 6"
# flt.inputs.args += " %s" % " ".join(search_angles)
# if args.moving_mask is not None:
# flt.inputs.in_weight = args.moving_mask
# if args.fixed_mask is not None:
# flt.inputs.ref_weight = args.fixed_mask
# ph.print_info("Run Registration (FLIRT) ... ", newline=False)
# flt.run()
# print("done")
cmd_args = ["flirt"]
cmd_args.append("-in %s" % args.moving)
cmd_args.append("-ref %s" % args.fixed)
if args.initial_transform is not None:
cmd_args.append("-init %s" % path_to_transform_flirt)
cmd_args.append("-omat %s" % path_to_transform_flirt)
cmd_args.append("-out %s" % path_to_tmp_output)
cmd_args.append("-dof 6")
cmd_args.append((" ").join(search_angles))
if args.moving_mask is not None:
cmd_args.append("-inweight %s" % args.moving_mask)
if args.fixed_mask is not None:
cmd_args.append("-refweight %s" % args.fixed_mask)
ph.print_info("Run Registration (FLIRT) ... ", newline=False)
ph.execute_command(" ".join(cmd_args), verbose=False)
print("done")
# Convert FLIRT to SimpleITK transform
cmd = "simplereg_transform -flirt2sitk %s %s %s %s" % (
path_to_transform_flirt, args.fixed, args.moving, args.output)
ph.execute_command(cmd, verbose=False)
if debug:
ph.show_niftis([args.fixed, path_to_tmp_output])
# Additionally, use RegAladin for more accurate alignment
# Rationale: FLIRT has better capture range, but RegAladin seems to
# find better alignment once it is within its capture range.
if args.use_regaladin:
path_to_transform_regaladin = os.path.join(DIR_TMP,
"transform_regaladin.txt")
# Convert SimpleITK to RegAladin transform
cmd = "simplereg_transform -sitk2nreg %s %s" % (
args.output, path_to_transform_regaladin)
ph.execute_command(cmd, verbose=False)
# nreg = nipype.interfaces.niftyreg.RegAladin()
# nreg.inputs.ref_file = args.fixed
# nreg.inputs.flo_file = args.moving
# nreg.inputs.res_file = path_to_tmp_output
# nreg.inputs.in_aff_file = path_to_transform_regaladin
# nreg.inputs.aff_file = path_to_transform_regaladin
# nreg.inputs.args = "-rigOnly -voff"
# if args.moving_mask is not None:
# nreg.inputs.fmask_file = args.moving_mask
# if args.fixed_mask is not None:
# nreg.inputs.rmask_file = args.fixed_mask
# ph.print_info("Run Registration (RegAladin) ... ", newline=False)
# nreg.run()
# print("done")
cmd_args = ["reg_aladin"]
cmd_args.append("-ref %s" % args.fixed)
cmd_args.append("-flo %s" % args.moving)
cmd_args.append("-res %s" % path_to_tmp_output)
if args.initial_transform is not None or args.use_flirt == 1:
cmd_args.append("-inaff %s" % path_to_transform_regaladin)
cmd_args.append("-aff %s" % path_to_transform_regaladin)
# cmd_args.append("-cog")
# cmd_args.append("-ln 2")
cmd_args.append("-rigOnly")
cmd_args.append("-voff")
if args.moving_mask is not None:
cmd_args.append("-fmask %s" % args.moving_mask)
if args.fixed_mask is not None:
cmd_args.append("-rmask %s" % args.fixed_mask)
ph.print_info("Run Registration (RegAladin) ... ", newline=False)
ph.execute_command(" ".join(cmd_args), verbose=False)
print("done")
# Convert RegAladin to SimpleITK transform
cmd = "simplereg_transform -nreg2sitk %s %s" % (
path_to_transform_regaladin, args.output)
ph.execute_command(cmd, verbose=False)
if debug:
ph.show_niftis([args.fixed, path_to_tmp_output])
if args.test_ap_flip:
path_to_transform_flip = os.path.join(DIR_TMP, "transform_flip.txt")
path_to_tmp_output_flip = os.path.join(DIR_TMP, "output_flip.nii.gz")
# Get AP-flip transform
transform_ap_flip_sitk = get_ap_flip_transform(args.fixed)
path_to_transform_flip_regaladin = os.path.join(
DIR_TMP, "transform_flip_regaladin.txt")
sitk.WriteTransform(transform_ap_flip_sitk, path_to_transform_flip)
# Compose current transform with AP flip transform
cmd = "simplereg_transform -c %s %s %s" % (
args.output, path_to_transform_flip, path_to_transform_flip)
ph.execute_command(cmd, verbose=False)
# Convert SimpleITK to RegAladin transform
cmd = "simplereg_transform -sitk2nreg %s %s" % (
path_to_transform_flip, path_to_transform_flip_regaladin)
ph.execute_command(cmd, verbose=False)
# nreg = nipype.interfaces.niftyreg.RegAladin()
# nreg.inputs.ref_file = args.fixed
# nreg.inputs.flo_file = args.moving
# nreg.inputs.res_file = path_to_tmp_output_flip
# nreg.inputs.in_aff_file = path_to_transform_flip_regaladin
# nreg.inputs.aff_file = path_to_transform_flip_regaladin
# nreg.inputs.args = "-rigOnly -voff"
# if args.moving_mask is not None:
# nreg.inputs.fmask_file = args.moving_mask
# if args.fixed_mask is not None:
# nreg.inputs.rmask_file = args.fixed_mask
# ph.print_info("Run Registration AP-flipped (RegAladin) ... ",
# newline=False)
# nreg.run()
# print("done")
cmd_args = ["reg_aladin"]
cmd_args.append("-ref %s" % args.fixed)
cmd_args.append("-flo %s" % args.moving)
cmd_args.append("-res %s" % path_to_tmp_output_flip)
cmd_args.append("-inaff %s" % path_to_transform_flip_regaladin)
cmd_args.append("-aff %s" % path_to_transform_flip_regaladin)
cmd_args.append("-rigOnly")
# cmd_args.append("-ln 2")
cmd_args.append("-voff")
if args.moving_mask is not None:
cmd_args.append("-fmask %s" % args.moving_mask)
if args.fixed_mask is not None:
cmd_args.append("-rmask %s" % args.fixed_mask)
ph.print_info("Run Registration AP-flipped (RegAladin) ... ",
newline=False)
ph.execute_command(" ".join(cmd_args), verbose=False)
print("done")
if debug:
ph.show_niftis(
[args.fixed, path_to_tmp_output, path_to_tmp_output_flip])
warped_moving = st.Stack.from_filename(path_to_tmp_output,
extract_slices=False)
warped_moving_flip = st.Stack.from_filename(path_to_tmp_output_flip,
extract_slices=False)
fixed = st.Stack.from_filename(args.fixed, args.fixed_mask)
stacks = [warped_moving, warped_moving_flip]
image_similarity_evaluator = ise.ImageSimilarityEvaluator(
stacks=stacks, reference=fixed)
image_similarity_evaluator.compute_similarities()
similarities = image_similarity_evaluator.get_similarities()
if similarities["NMI"][1] > similarities["NMI"][0]:
ph.print_info("AP-flipped outcome better")
# Convert RegAladin to SimpleITK transform
cmd = "simplereg_transform -nreg2sitk %s %s" % (
path_to_transform_flip_regaladin, args.output)
ph.execute_command(cmd, verbose=False)
# Copy better outcome
cmd = "cp -p %s %s" % (path_to_tmp_output_flip, path_to_tmp_output)
ph.execute_command(cmd, verbose=False)
else:
ph.print_info("AP-flip does not improve outcome")
if args.dir_input_mc is not None:
transform_sitk = sitkh.read_transform_sitk(args.output, inverse=1)
if args.dir_input_mc.endswith("/"):
subdir_mc = args.dir_input_mc.split("/")[-2]
else:
subdir_mc = args.dir_input_mc.split("/")[-1]
dir_output_mc = os.path.join(dir_output, subdir_mc)
ph.create_directory(dir_output_mc, delete_files=True)
pattern = REGEX_FILENAMES + "[.]tfm"
p = re.compile(pattern)
trafos = [t for t in os.listdir(args.dir_input_mc) if p.match(t)]
for t in trafos:
path_to_input_transform = os.path.join(args.dir_input_mc, t)
path_to_output_transform = os.path.join(dir_output_mc, t)
t_sitk = sitkh.read_transform_sitk(path_to_input_transform)
t_sitk = sitkh.get_composite_sitk_affine_transform(
transform_sitk, t_sitk)
sitk.WriteTransform(t_sitk, path_to_output_transform)
if args.verbose:
ph.show_niftis([args.fixed, path_to_tmp_output])
elapsed_time_total = ph.stop_timing(time_start)
# Summary
ph.print_title("Summary")
print("Computational Time: %s" % (elapsed_time_total))
return 0
