def gen_tissue(self):
"""
A function to segment and threshold tissue types from T1w.
"""
# Segment the t1w brain into probability maps
maps = regutils.segment_t1w(self.t1w_brain, self.map_path)
self.wm_mask = maps['wm_prob']
self.gm_mask = maps['gm_prob']
self.csf_mask = maps['csf_prob']
self.t1w_brain = regutils.check_orient_and_dims(self.t1w_brain, self.vox_size)
self.wm_mask = regutils.check_orient_and_dims(self.wm_mask, self.vox_size)
self.gm_mask = regutils.check_orient_and_dims(self.gm_mask, self.vox_size)
self.csf_mask = regutils.check_orient_and_dims(self.csf_mask, self.vox_size)
# Threshold WM to binary in dwi space
t_img = load_img(self.wm_mask)
mask = math_img('img > 0.2', img=t_img)
mask.to_filename(self.wm_mask_thr)
# Threshold T1w brain to binary in anat space
t_img = load_img(self.t1w_brain)
mask = math_img('img > 0.0', img=t_img)
mask.to_filename(self.t1w_brain_mask)
# Extract wm edge
os.system("fslmaths {} -edge -bin -mas {} {}".format(self.wm_mask_thr, self.wm_mask_thr, self.wm_edge))
return
def gen_tissue(
self, wm_mask_existing, gm_mask_existing, csf_mask_existing, overwrite
):
"""
A function to segment and threshold tissue types from T1w.
"""
import time
import shutil
# Segment the t1w brain into probability maps
if (
wm_mask_existing is not None
and gm_mask_existing is not None
and csf_mask_existing is not None
and overwrite is False
):
print("Existing segmentations detected...")
wm_mask = regutils.check_orient_and_dims(
wm_mask_existing, self.basedir_path, self.vox_size,
overwrite=False)
gm_mask = regutils.check_orient_and_dims(
gm_mask_existing, self.basedir_path, self.vox_size,
overwrite=False)
csf_mask = regutils.check_orient_and_dims(
csf_mask_existing, self.basedir_path, self.vox_size,
overwrite=False)
else:
try:
maps = regutils.segment_t1w(self.t1w_brain, self.map_name)
time.sleep(0.5)
wm_mask = maps["wm_prob"]
gm_mask = maps["gm_prob"]
csf_mask = maps["csf_prob"]
except RuntimeError as e:
import sys
print(e,
"Segmentation failed. Does the input anatomical image "
"still contained skull?"
)
sys.exit(1)
# Threshold WM to binary in dwi space
t_img = nib.load(wm_mask)
mask = math_img("img > 0.20", img=t_img)
mask.to_filename(self.wm_mask_thr)
# Extract wm edge
self.wm_edge = regutils.get_wm_contour(wm_mask, self.wm_mask_thr,
self.wm_edge)
time.sleep(0.5)
shutil.copyfile(wm_mask, self.wm_mask)
shutil.copyfile(gm_mask, self.gm_mask)
shutil.copyfile(csf_mask, self.csf_mask)
return
def test_segment_t1w():
"""
Test segment_t1w functionality
"""
base_dir = str(Path(__file__).parent/"examples")
anat_dir = f"{base_dir}/003/anat"
t1w = f"{anat_dir}/sub-003_T1w.nii.gz"
basename = f"{anat_dir}/test_segment_t1w"
out = reg_utils.segment_t1w(t1w, basename, opts='')
print(out)
assert out is not None
def gen_tissue(self, wm_mask_existing, gm_mask_existing, overwrite):
"""
A function to segment and threshold tissue types from T1w.
"""
# Segment the t1w brain into probability maps
if (wm_mask_existing is not None and gm_mask_existing is not None
and overwrite is False):
print("Existing segmentations detected...")
gm_mask = regutils.check_orient_and_dims(gm_mask_existing,
self.basedir_path,
self.vox_size,
overwrite=False)
wm_mask = regutils.check_orient_and_dims(wm_mask_existing,
self.basedir_path,
self.vox_size,
overwrite=False)
else:
try:
maps = regutils.segment_t1w(self.t1w_brain, self.map_name)
gm_mask = maps["gm_prob"]
wm_mask = maps["wm_prob"]
except RuntimeError:
print(
"Segmentation failed. Does the input anatomical image still contained skull?"
)
# Threshold GM to binary in func space
t_img = nib.load(gm_mask)
mask = math_img("img > 0.02", img=t_img)
mask.to_filename(self.gm_mask_thr)
os.system(
f"fslmaths {gm_mask} -mas {self.gm_mask_thr} {self.gm_mask} 2>/dev/null"
)
# Threshold WM to binary in dwi space
t_img = nib.load(wm_mask)
mask = math_img("img > 0.50", img=t_img)
mask.to_filename(self.wm_mask_thr)
# Extract wm edge
os.system(
f"fslmaths {wm_mask} -edge -bin -mas {self.wm_mask_thr} {self.wm_edge} 2>/dev/null"
)
return
def gen_tissue(self):
"""
A function to segment and threshold tissue types from T1w.
"""
# Segment the t1w brain into probability maps
maps = regutils.segment_t1w(self.t1w_brain, self.map_path)
self.gm_mask = maps['gm_prob']
self.t1w_brain = regutils.check_orient_and_dims(self.t1w_brain, self.vox_size)
self.gm_mask = regutils.check_orient_and_dims(self.gm_mask, self.vox_size)
# Threshold WM to binary in dwi space
t_img = load_img(self.gm_mask)
mask = math_img('img > 0.1', img=t_img)
mask.to_filename(self.gm_mask_thr)
# Threshold T1w brain to binary in anat space
t_img = load_img(self.t1w_brain)
mask = math_img('img > 0.0', img=t_img)
mask.to_filename(self.t1w_brain_mask)
return
def gen_tissue(self):
# Segment the t1w brain into probability maps
self.maps = mgru.segment_t1w(self.t1w_brain, self.map_path)
self.wm_mask = self.maps['wm_prob']
self.gm_mask = self.maps['gm_prob']
self.csf_mask = self.maps['csf_prob']
self.t1w_brain = utils.match_target_vox_res(self.t1w_brain,
self.vox_size,
self.anat_path,
sens='anat')
self.wm_mask = utils.match_target_vox_res(self.wm_mask,
self.vox_size,
self.anat_path,
sens='anat')
self.gm_mask = utils.match_target_vox_res(self.gm_mask,
self.vox_size,
self.anat_path,
sens='anat')
self.csf_mask = utils.match_target_vox_res(self.csf_mask,
self.vox_size,
self.anat_path,
sens='anat')
# Threshold WM to binary in dwi space
self.t_img = load_img(self.wm_mask)
self.mask = math_img('img > 0.2', img=self.t_img)
self.mask.to_filename(self.wm_mask_thr)
# Threshold T1w brain to binary in anat space
self.t_img = load_img(self.t1w_brain)
self.mask = math_img('img > 0.0', img=self.t_img)
self.mask.to_filename(self.t1w_brain_mask)
# Extract wm edge
cmd = 'fslmaths ' + self.wm_mask_thr + ' -edge -bin -mas ' + self.wm_mask_thr + ' ' + self.wm_edge
os.system(cmd)
return
