def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_global_loglevel(verbose=verbose)
# Initialization
param = Param()
start_time = time.time()
fname_anat = arguments.i
fname_centerline = arguments.s
param.algo_fitting = arguments.algo_fitting
if arguments.smooth is not None:
sigmas = arguments.smooth
remove_temp_files = arguments.r
if arguments.o is not None:
fname_out = arguments.o
else:
fname_out = extract_fname(fname_anat)[1] + '_smooth.nii'
# Display arguments
printv('\nCheck input arguments...')
printv(' Volume to smooth .................. ' + fname_anat)
printv(' Centerline ........................ ' + fname_centerline)
printv(' Sigma (mm) ........................ ' + str(sigmas))
printv(' Verbose ........................... ' + str(verbose))
# Check that input is 3D:
nx, ny, nz, nt, px, py, pz, pt = Image(fname_anat).dim
dim = 4 # by default, will be adjusted later
if nt == 1:
dim = 3
if nz == 1:
dim = 2
if dim == 4:
printv(
'WARNING: the input image is 4D, please split your image to 3D before smoothing spinalcord using :\n'
'sct_image -i ' + fname_anat + ' -split t -o ' + fname_anat,
verbose, 'warning')
printv('4D images not supported, aborting ...', verbose, 'error')
# Extract path/file/extension
path_anat, file_anat, ext_anat = extract_fname(fname_anat)
path_centerline, file_centerline, ext_centerline = extract_fname(
fname_centerline)
path_tmp = tmp_create(basename="smooth_spinalcord")
# Copying input data to tmp folder
printv('\nCopying input data to tmp folder and convert to nii...', verbose)
copy(fname_anat, os.path.join(path_tmp, "anat" + ext_anat))
copy(fname_centerline, os.path.join(path_tmp,
"centerline" + ext_centerline))
# go to tmp folder
curdir = os.getcwd()
os.chdir(path_tmp)
# convert to nii format
im_anat = convert(Image('anat' + ext_anat))
im_anat.save('anat.nii', mutable=True, verbose=verbose)
im_centerline = convert(Image('centerline' + ext_centerline))
im_centerline.save('centerline.nii', mutable=True, verbose=verbose)
# Change orientation of the input image into RPI
printv('\nOrient input volume to RPI orientation...')
img_anat_rpi = Image("anat.nii").change_orientation("RPI")
fname_anat_rpi = add_suffix(img_anat_rpi.absolutepath, "_rpi")
img_anat_rpi.save(path=fname_anat_rpi, mutable=True)
# Change orientation of the input image into RPI
printv('\nOrient centerline to RPI orientation...')
img_centerline_rpi = Image("centerline.nii").change_orientation("RPI")
fname_centerline_rpi = add_suffix(img_centerline_rpi.absolutepath, "_rpi")
img_centerline_rpi.save(path=fname_centerline_rpi, mutable=True)
# Straighten the spinal cord
# straighten segmentation
printv('\nStraighten the spinal cord using centerline/segmentation...',
verbose)
cache_sig = cache_signature(
input_files=[fname_anat_rpi, fname_centerline_rpi],
input_params={"x": "spline"})
cachefile = os.path.join(curdir, "straightening.cache")
if cache_valid(cachefile, cache_sig) and os.path.isfile(
os.path.join(
curdir, 'warp_curve2straight.nii.gz')) and os.path.isfile(
os.path.join(
curdir,
'warp_straight2curve.nii.gz')) and os.path.isfile(
os.path.join(curdir, 'straight_ref.nii.gz')):
# if they exist, copy them into current folder
printv('Reusing existing warping field which seems to be valid',
verbose, 'warning')
copy(os.path.join(curdir, 'warp_curve2straight.nii.gz'),
'warp_curve2straight.nii.gz')
copy(os.path.join(curdir, 'warp_straight2curve.nii.gz'),
'warp_straight2curve.nii.gz')
copy(os.path.join(curdir, 'straight_ref.nii.gz'),
'straight_ref.nii.gz')
# apply straightening
run_proc([
'sct_apply_transfo', '-i', fname_anat_rpi, '-w',
'warp_curve2straight.nii.gz', '-d', 'straight_ref.nii.gz', '-o',
'anat_rpi_straight.nii', '-x', 'spline'
], verbose)
else:
run_proc([
'sct_straighten_spinalcord', '-i', fname_anat_rpi, '-o',
'anat_rpi_straight.nii', '-s', fname_centerline_rpi, '-x',
'spline', '-param', 'algo_fitting=' + param.algo_fitting
], verbose)
cache_save(cachefile, cache_sig)
# move warping fields locally (to use caching next time)
copy('warp_curve2straight.nii.gz',
os.path.join(curdir, 'warp_curve2straight.nii.gz'))
copy('warp_straight2curve.nii.gz',
os.path.join(curdir, 'warp_straight2curve.nii.gz'))
# Smooth the straightened image along z
printv('\nSmooth the straightened image...')
img = Image("anat_rpi_straight.nii")
out = img.copy()
if len(sigmas) == 1:
sigmas = [sigmas[0] for i in range(len(img.data.shape))]
elif len(sigmas) != len(img.data.shape):
raise ValueError(
"-smooth need the same number of inputs as the number of image dimension OR only one input"
)
sigmas = [sigmas[i] / img.dim[i + 4] for i in range(3)]
out.data = smooth(out.data, sigmas)
out.save(path="anat_rpi_straight_smooth.nii")
# Apply the reversed warping field to get back the curved spinal cord
printv(
'\nApply the reversed warping field to get back the curved spinal cord...'
)
run_proc([
'sct_apply_transfo', '-i', 'anat_rpi_straight_smooth.nii', '-o',
'anat_rpi_straight_smooth_curved.nii', '-d', 'anat.nii', '-w',
'warp_straight2curve.nii.gz', '-x', 'spline'
], verbose)
# replace zeroed voxels by original image (issue #937)
printv('\nReplace zeroed voxels by original image...', verbose)
nii_smooth = Image('anat_rpi_straight_smooth_curved.nii')
data_smooth = nii_smooth.data
data_input = Image('anat.nii').data
indzero = np.where(data_smooth == 0)
data_smooth[indzero] = data_input[indzero]
nii_smooth.data = data_smooth
nii_smooth.save('anat_rpi_straight_smooth_curved_nonzero.nii')
# come back
os.chdir(curdir)
# Generate output file
printv('\nGenerate output file...')
generate_output_file(
os.path.join(path_tmp, "anat_rpi_straight_smooth_curved_nonzero.nii"),
fname_out)
# Remove temporary files
if remove_temp_files == 1:
printv('\nRemove temporary files...')
rmtree(path_tmp)
# Display elapsed time
elapsed_time = time.time() - start_time
printv('\nFinished! Elapsed time: ' + str(int(np.round(elapsed_time))) +
's\n')
display_viewer_syntax([fname_anat, fname_out], verbose=verbose)
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv if argv else ['--help'])
verbose = arguments.v
set_global_loglevel(verbose=verbose)
# initializations
initz = ''
initcenter = ''
fname_initlabel = ''
file_labelz = 'labelz.nii.gz'
param = Param()
fname_in = os.path.abspath(arguments.i)
fname_seg = os.path.abspath(arguments.s)
contrast = arguments.c
path_template = os.path.abspath(arguments.t)
scale_dist = arguments.scale_dist
path_output = arguments.ofolder
param.path_qc = arguments.qc
if arguments.discfile is not None:
fname_disc = os.path.abspath(arguments.discfile)
else:
fname_disc = None
if arguments.initz is not None:
initz = arguments.initz
if len(initz) != 2:
raise ValueError(
'--initz takes two arguments: position in superior-inferior direction, label value'
)
if arguments.initcenter is not None:
initcenter = arguments.initcenter
# if user provided text file, parse and overwrite arguments
if arguments.initfile is not None:
file = open(arguments.initfile, 'r')
initfile = ' ' + file.read().replace('\n', '')
arg_initfile = initfile.split(' ')
for idx_arg, arg in enumerate(arg_initfile):
if arg == '-initz':
initz = [int(x) for x in arg_initfile[idx_arg + 1].split(',')]
if len(initz) != 2:
raise ValueError(
'--initz takes two arguments: position in superior-inferior direction, label value'
)
if arg == '-initcenter':
initcenter = int(arg_initfile[idx_arg + 1])
if arguments.initlabel is not None:
# get absolute path of label
fname_initlabel = os.path.abspath(arguments.initlabel)
if arguments.param is not None:
param.update(arguments.param[0])
remove_temp_files = arguments.r
clean_labels = arguments.clean_labels
laplacian = arguments.laplacian
path_tmp = tmp_create(basename="label_vertebrae")
# Copying input data to tmp folder
printv('\nCopying input data to tmp folder...', verbose)
Image(fname_in).save(os.path.join(path_tmp, "data.nii"))
Image(fname_seg).save(os.path.join(path_tmp, "segmentation.nii"))
# Go go temp folder
curdir = os.getcwd()
os.chdir(path_tmp)
# Straighten spinal cord
printv('\nStraighten spinal cord...', verbose)
# check if warp_curve2straight and warp_straight2curve already exist (i.e. no need to do it another time)
cache_sig = cache_signature(input_files=[fname_in, fname_seg], )
cachefile = os.path.join(curdir, "straightening.cache")
if cache_valid(cachefile, cache_sig) and os.path.isfile(
os.path.join(
curdir, "warp_curve2straight.nii.gz")) and os.path.isfile(
os.path.join(
curdir,
"warp_straight2curve.nii.gz")) and os.path.isfile(
os.path.join(curdir, "straight_ref.nii.gz")):
# if they exist, copy them into current folder
printv('Reusing existing warping field which seems to be valid',
verbose, 'warning')
copy(os.path.join(curdir, "warp_curve2straight.nii.gz"),
'warp_curve2straight.nii.gz')
copy(os.path.join(curdir, "warp_straight2curve.nii.gz"),
'warp_straight2curve.nii.gz')
copy(os.path.join(curdir, "straight_ref.nii.gz"),
'straight_ref.nii.gz')
# apply straightening
s, o = run_proc([
'sct_apply_transfo', '-i', 'data.nii', '-w',
'warp_curve2straight.nii.gz', '-d', 'straight_ref.nii.gz', '-o',
'data_straight.nii'
])
else:
sct_straighten_spinalcord.main(argv=[
'-i',
'data.nii',
'-s',
'segmentation.nii',
'-r',
str(remove_temp_files),
'-v',
str(verbose),
])
cache_save(cachefile, cache_sig)
# resample to 0.5mm isotropic to match template resolution
printv('\nResample to 0.5mm isotropic...', verbose)
s, o = run_proc([
'sct_resample', '-i', 'data_straight.nii', '-mm', '0.5x0.5x0.5', '-x',
'linear', '-o', 'data_straightr.nii'
],
verbose=verbose)
# Apply straightening to segmentation
# N.B. Output is RPI
printv('\nApply straightening to segmentation...', verbose)
run_proc(
'isct_antsApplyTransforms -d 3 -i %s -r %s -t %s -o %s -n %s' %
('segmentation.nii', 'data_straightr.nii',
'warp_curve2straight.nii.gz', 'segmentation_straight.nii', 'Linear'),
verbose=verbose,
is_sct_binary=True,
)
# Threshold segmentation at 0.5
run_proc([
'sct_maths', '-i', 'segmentation_straight.nii', '-thr', '0.5', '-o',
'segmentation_straight.nii'
], verbose)
# If disc label file is provided, label vertebrae using that file instead of automatically
if fname_disc:
# Apply straightening to disc-label
printv('\nApply straightening to disc labels...', verbose)
run_proc(
'sct_apply_transfo -i %s -d %s -w %s -o %s -x %s' %
(fname_disc, 'data_straightr.nii', 'warp_curve2straight.nii.gz',
'labeldisc_straight.nii.gz', 'label'),
verbose=verbose)
label_vert('segmentation_straight.nii',
'labeldisc_straight.nii.gz',
verbose=1)
else:
# create label to identify disc
printv('\nCreate label to identify disc...', verbose)
fname_labelz = os.path.join(path_tmp, file_labelz)
if initz or initcenter:
if initcenter:
# find z centered in FOV
nii = Image('segmentation.nii').change_orientation("RPI")
nx, ny, nz, nt, px, py, pz, pt = nii.dim # Get dimensions
z_center = int(np.round(nz / 2)) # get z_center
initz = [z_center, initcenter]
im_label = create_labels_along_segmentation(
Image('segmentation.nii'), [(initz[0], initz[1])])
im_label.data = dilate(im_label.data, 3, 'ball')
im_label.save(fname_labelz)
elif fname_initlabel:
Image(fname_initlabel).save(fname_labelz)
else:
# automatically finds C2-C3 disc
im_data = Image('data.nii')
im_seg = Image('segmentation.nii')
if not remove_temp_files: # because verbose is here also used for keeping temp files
verbose_detect_c2c3 = 2
else:
verbose_detect_c2c3 = 0
im_label_c2c3 = detect_c2c3(im_data,
im_seg,
contrast,
verbose=verbose_detect_c2c3)
ind_label = np.where(im_label_c2c3.data)
if not np.size(ind_label) == 0:
im_label_c2c3.data[ind_label] = 3
else:
printv(
'Automatic C2-C3 detection failed. Please provide manual label with sct_label_utils',
1, 'error')
sys.exit()
im_label_c2c3.save(fname_labelz)
# dilate label so it is not lost when applying warping
dilate(Image(fname_labelz), 3, 'ball').save(fname_labelz)
# Apply straightening to z-label
printv('\nAnd apply straightening to label...', verbose)
run_proc(
'isct_antsApplyTransforms -d 3 -i %s -r %s -t %s -o %s -n %s' %
(file_labelz, 'data_straightr.nii', 'warp_curve2straight.nii.gz',
'labelz_straight.nii.gz', 'NearestNeighbor'),
verbose=verbose,
is_sct_binary=True,
)
# get z value and disk value to initialize labeling
printv('\nGet z and disc values from straight label...', verbose)
init_disc = get_z_and_disc_values_from_label('labelz_straight.nii.gz')
printv('.. ' + str(init_disc), verbose)
# apply laplacian filtering
if laplacian:
printv('\nApply Laplacian filter...', verbose)
run_proc([
'sct_maths', '-i', 'data_straightr.nii', '-laplacian', '1',
'-o', 'data_straightr.nii'
], verbose)
# detect vertebral levels on straight spinal cord
init_disc[1] = init_disc[1] - 1
vertebral_detection('data_straightr.nii',
'segmentation_straight.nii',
contrast,
param,
init_disc=init_disc,
verbose=verbose,
path_template=path_template,
path_output=path_output,
scale_dist=scale_dist)
# un-straighten labeled spinal cord
printv('\nUn-straighten labeling...', verbose)
run_proc(
'isct_antsApplyTransforms -d 3 -i %s -r %s -t %s -o %s -n %s' %
('segmentation_straight_labeled.nii', 'segmentation.nii',
'warp_straight2curve.nii.gz', 'segmentation_labeled.nii',
'NearestNeighbor'),
verbose=verbose,
is_sct_binary=True,
)
if clean_labels:
# Clean labeled segmentation
printv(
'\nClean labeled segmentation (correct interpolation errors)...',
verbose)
clean_labeled_segmentation('segmentation_labeled.nii',
'segmentation.nii',
'segmentation_labeled.nii')
# label discs
printv('\nLabel discs...', verbose)
printv('\nUn-straighten labeled discs...', verbose)
run_proc(
'sct_apply_transfo -i %s -d %s -w %s -o %s -x %s' %
('segmentation_straight_labeled_disc.nii', 'segmentation.nii',
'warp_straight2curve.nii.gz', 'segmentation_labeled_disc.nii',
'label'),
verbose=verbose,
is_sct_binary=True,
)
# come back
os.chdir(curdir)
# Generate output files
path_seg, file_seg, ext_seg = extract_fname(fname_seg)
fname_seg_labeled = os.path.join(path_output,
file_seg + '_labeled' + ext_seg)
printv('\nGenerate output files...', verbose)
generate_output_file(os.path.join(path_tmp, "segmentation_labeled.nii"),
fname_seg_labeled)
generate_output_file(
os.path.join(path_tmp, "segmentation_labeled_disc.nii"),
os.path.join(path_output, file_seg + '_labeled_discs' + ext_seg))
# copy straightening files in case subsequent SCT functions need them
generate_output_file(os.path.join(path_tmp, "warp_curve2straight.nii.gz"),
os.path.join(path_output,
"warp_curve2straight.nii.gz"),
verbose=verbose)
generate_output_file(os.path.join(path_tmp, "warp_straight2curve.nii.gz"),
os.path.join(path_output,
"warp_straight2curve.nii.gz"),
verbose=verbose)
generate_output_file(os.path.join(path_tmp, "straight_ref.nii.gz"),
os.path.join(path_output, "straight_ref.nii.gz"),
verbose=verbose)
# Remove temporary files
if remove_temp_files == 1:
printv('\nRemove temporary files...', verbose)
rmtree(path_tmp)
# Generate QC report
if param.path_qc is not None:
path_qc = os.path.abspath(arguments.qc)
qc_dataset = arguments.qc_dataset
qc_subject = arguments.qc_subject
labeled_seg_file = os.path.join(path_output,
file_seg + '_labeled' + ext_seg)
generate_qc(fname_in,
fname_seg=labeled_seg_file,
args=argv,
path_qc=os.path.abspath(path_qc),
dataset=qc_dataset,
subject=qc_subject,
process='sct_label_vertebrae')
display_viewer_syntax([fname_in, fname_seg_labeled],
colormaps=['', 'subcortical'],
opacities=['1', '0.5'])
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_loglevel(verbose=verbose)
fname_in = os.path.abspath(arguments.i)
fname_seg = os.path.abspath(arguments.s)
contrast = arguments.c
path_template = os.path.abspath(arguments.t)
scale_dist = arguments.scale_dist
path_output = os.path.abspath(arguments.ofolder)
fname_disc = arguments.discfile
if fname_disc is not None:
fname_disc = os.path.abspath(fname_disc)
initz = arguments.initz
initcenter = arguments.initcenter
fname_initlabel = arguments.initlabel
if fname_initlabel is not None:
fname_initlabel = os.path.abspath(fname_initlabel)
remove_temp_files = arguments.r
clean_labels = arguments.clean_labels
path_tmp = tmp_create(basename="label_vertebrae")
# Copying input data to tmp folder
printv('\nCopying input data to tmp folder...', verbose)
Image(fname_in).save(os.path.join(path_tmp, "data.nii"))
Image(fname_seg).save(os.path.join(path_tmp, "segmentation.nii"))
# Go go temp folder
curdir = os.getcwd()
os.chdir(path_tmp)
# Straighten spinal cord
printv('\nStraighten spinal cord...', verbose)
# check if warp_curve2straight and warp_straight2curve already exist (i.e. no need to do it another time)
cache_sig = cache_signature(input_files=[fname_in, fname_seg], )
fname_cache = "straightening.cache"
if (cache_valid(os.path.join(curdir, fname_cache), cache_sig)
and os.path.isfile(
os.path.join(curdir, "warp_curve2straight.nii.gz"))
and os.path.isfile(
os.path.join(curdir, "warp_straight2curve.nii.gz"))
and os.path.isfile(os.path.join(curdir, "straight_ref.nii.gz"))):
# if they exist, copy them into current folder
printv('Reusing existing warping field which seems to be valid',
verbose, 'warning')
copy(os.path.join(curdir, "warp_curve2straight.nii.gz"),
'warp_curve2straight.nii.gz')
copy(os.path.join(curdir, "warp_straight2curve.nii.gz"),
'warp_straight2curve.nii.gz')
copy(os.path.join(curdir, "straight_ref.nii.gz"),
'straight_ref.nii.gz')
# apply straightening
s, o = run_proc([
'sct_apply_transfo', '-i', 'data.nii', '-w',
'warp_curve2straight.nii.gz', '-d', 'straight_ref.nii.gz', '-o',
'data_straight.nii'
])
else:
sct_straighten_spinalcord.main(argv=[
'-i',
'data.nii',
'-s',
'segmentation.nii',
'-r',
str(remove_temp_files),
'-v',
'0',
])
cache_save(os.path.join(path_output, fname_cache), cache_sig)
# resample to 0.5mm isotropic to match template resolution
printv('\nResample to 0.5mm isotropic...', verbose)
s, o = run_proc([
'sct_resample', '-i', 'data_straight.nii', '-mm', '0.5x0.5x0.5', '-x',
'linear', '-o', 'data_straightr.nii'
],
verbose=verbose)
# Apply straightening to segmentation
# N.B. Output is RPI
printv('\nApply straightening to segmentation...', verbose)
sct_apply_transfo.main([
'-i', 'segmentation.nii', '-d', 'data_straightr.nii', '-w',
'warp_curve2straight.nii.gz', '-o', 'segmentation_straight.nii', '-x',
'linear', '-v', '0'
])
# Threshold segmentation at 0.5
img = Image('segmentation_straight.nii')
img.data = threshold(img.data, 0.5)
img.save()
# If disc label file is provided, label vertebrae using that file instead of automatically
if fname_disc:
# Apply straightening to disc-label
printv('\nApply straightening to disc labels...', verbose)
run_proc(
'sct_apply_transfo -i %s -d %s -w %s -o %s -x %s' %
(fname_disc, 'data_straightr.nii', 'warp_curve2straight.nii.gz',
'labeldisc_straight.nii.gz', 'label'),
verbose=verbose)
label_vert('segmentation_straight.nii',
'labeldisc_straight.nii.gz',
verbose=1)
else:
printv('\nCreate label to identify disc...', verbose)
fname_labelz = os.path.join(path_tmp, 'labelz.nii.gz')
if initcenter is not None:
# find z centered in FOV
nii = Image('segmentation.nii').change_orientation("RPI")
nx, ny, nz, nt, px, py, pz, pt = nii.dim
z_center = round(nz / 2)
initz = [z_center, initcenter]
if initz is not None:
im_label = create_labels_along_segmentation(
Image('segmentation.nii'), [tuple(initz)])
im_label.save(fname_labelz)
elif fname_initlabel is not None:
Image(fname_initlabel).save(fname_labelz)
else:
# automatically finds C2-C3 disc
im_data = Image('data.nii')
im_seg = Image('segmentation.nii')
# because verbose is also used for keeping temp files
verbose_detect_c2c3 = 0 if remove_temp_files else 2
im_label_c2c3 = detect_c2c3(im_data,
im_seg,
contrast,
verbose=verbose_detect_c2c3)
ind_label = np.where(im_label_c2c3.data)
if np.size(ind_label) == 0:
printv(
'Automatic C2-C3 detection failed. Please provide manual label with sct_label_utils',
1, 'error')
sys.exit(1)
im_label_c2c3.data[ind_label] = 3
im_label_c2c3.save(fname_labelz)
# dilate label so it is not lost when applying warping
dilate(Image(fname_labelz), 3, 'ball').save(fname_labelz)
# Apply straightening to z-label
printv('\nAnd apply straightening to label...', verbose)
sct_apply_transfo.main([
'-i', 'labelz.nii.gz', '-d', 'data_straightr.nii', '-w',
'warp_curve2straight.nii.gz', '-o', 'labelz_straight.nii.gz', '-x',
'nn', '-v', '0'
])
# get z value and disk value to initialize labeling
printv('\nGet z and disc values from straight label...', verbose)
init_disc = get_z_and_disc_values_from_label('labelz_straight.nii.gz')
printv('.. ' + str(init_disc), verbose)
# apply laplacian filtering
if arguments.laplacian:
printv('\nApply Laplacian filter...', verbose)
img = Image("data_straightr.nii")
# apply std dev to each axis of the image
sigmas = [1 for i in range(len(img.data.shape))]
# adjust sigma based on voxel size
sigmas = [sigmas[i] / img.dim[i + 4] for i in range(3)]
# smooth data
img.data = laplacian(img.data, sigmas)
img.save()
# detect vertebral levels on straight spinal cord
init_disc[1] = init_disc[1] - 1
vertebral_detection('data_straightr.nii',
'segmentation_straight.nii',
contrast,
arguments.param,
init_disc=init_disc,
verbose=verbose,
path_template=path_template,
path_output=path_output,
scale_dist=scale_dist)
# un-straighten labeled spinal cord
printv('\nUn-straighten labeling...', verbose)
sct_apply_transfo.main([
'-i', 'segmentation_straight_labeled.nii', '-d', 'segmentation.nii',
'-w', 'warp_straight2curve.nii.gz', '-o', 'segmentation_labeled.nii',
'-x', 'nn', '-v', '0'
])
if clean_labels >= 1:
printv('\nCleaning labeled segmentation:', verbose)
im_labeled_seg = Image('segmentation_labeled.nii')
im_seg = Image('segmentation.nii')
if clean_labels >= 2:
printv(' filling in missing label voxels ...', verbose)
expand_labels(im_labeled_seg)
printv(' removing labeled voxels outside segmentation...', verbose)
crop_labels(im_labeled_seg, im_seg)
printv('Done cleaning.', verbose)
im_labeled_seg.save()
# label discs
printv('\nLabel discs...', verbose)
printv('\nUn-straighten labeled discs...', verbose)
run_proc(
'sct_apply_transfo -i %s -d %s -w %s -o %s -x %s' %
('segmentation_straight_labeled_disc.nii', 'segmentation.nii',
'warp_straight2curve.nii.gz', 'segmentation_labeled_disc.nii',
'label'),
verbose=verbose,
is_sct_binary=True,
)
# come back
os.chdir(curdir)
# Generate output files
path_seg, file_seg, ext_seg = extract_fname(fname_seg)
fname_seg_labeled = os.path.join(path_output,
file_seg + '_labeled' + ext_seg)
printv('\nGenerate output files...', verbose)
generate_output_file(os.path.join(path_tmp, "segmentation_labeled.nii"),
fname_seg_labeled)
generate_output_file(
os.path.join(path_tmp, "segmentation_labeled_disc.nii"),
os.path.join(path_output, file_seg + '_labeled_discs' + ext_seg))
# copy straightening files in case subsequent SCT functions need them
generate_output_file(os.path.join(path_tmp, "warp_curve2straight.nii.gz"),
os.path.join(path_output,
"warp_curve2straight.nii.gz"),
verbose=verbose)
generate_output_file(os.path.join(path_tmp, "warp_straight2curve.nii.gz"),
os.path.join(path_output,
"warp_straight2curve.nii.gz"),
verbose=verbose)
generate_output_file(os.path.join(path_tmp, "straight_ref.nii.gz"),
os.path.join(path_output, "straight_ref.nii.gz"),
verbose=verbose)
# Remove temporary files
if remove_temp_files == 1:
printv('\nRemove temporary files...', verbose)
rmtree(path_tmp)
# Generate QC report
if arguments.qc is not None:
path_qc = os.path.abspath(arguments.qc)
qc_dataset = arguments.qc_dataset
qc_subject = arguments.qc_subject
labeled_seg_file = os.path.join(path_output,
file_seg + '_labeled' + ext_seg)
generate_qc(fname_in,
fname_seg=labeled_seg_file,
args=argv,
path_qc=os.path.abspath(path_qc),
dataset=qc_dataset,
subject=qc_subject,
process='sct_label_vertebrae')
display_viewer_syntax([fname_in, fname_seg_labeled],
colormaps=['', 'subcortical'],
opacities=['1', '0.5'])