def fix_roi_values_freesurferLUT(roi_image, white_matter_file, csf_file,
prob_thresh):
from coma.helpers import wm_labels_only, csf_labels_only, prepare_for_uint8
_, name, _ = split_filename(roi_image)
white_matter_default = 2
csf_default = 3
# Get regions labelled white and csf
wm_label_file = op.abspath(name + "_WM.nii.gz")
wm_only = wm_labels_only(roi_image, out_filename=wm_label_file)
wm_label_image = nb.load(wm_only)
wm_labels = wm_label_image.get_data()
csf_label_file = op.abspath(name + "_CSF.nii.gz")
csf_only = csf_labels_only(roi_image, out_filename=csf_label_file)
csf_label_image = nb.load(csf_only)
csf_labels = csf_label_image.get_data()
wm_image = nb.load(white_matter_file)
wm_data = wm_image.get_data()
csf_image = nb.load(csf_file)
csf_data = csf_image.get_data()
image = nb.load(roi_image)
data = image.get_data()
assert (data.shape == wm_data.shape == csf_data.shape)
data[np.where(wm_labels > 0)] = white_matter_default
data[np.where(csf_labels > 0)] = csf_default
# Be careful with the brackets here. & takes priority over comparisons
data[np.where((wm_data > prob_thresh)
& (data == 0))] = white_matter_default
data[np.where((csf_data > prob_thresh) & (data == 0))] = csf_default
wm_labels[np.where(data == white_matter_default)] = 1
wm_labels[np.where(data == csf_default)] = 0
wm_labels[np.where(data == 0)] = 0
wm_labels = wm_labels.astype(np.uint8)
new_wm_label_image = nb.Nifti1Image(dataobj=wm_labels,
affine=wm_image.get_affine(),
header=wm_image.get_header())
new_wm_label_image.set_data_dtype(np.uint8)
_, name, _ = split_filename(white_matter_file)
wm_label_file = op.abspath(name + "_fixedWM.nii.gz")
nb.save(new_wm_label_image, wm_label_file)
csf_data[np.where(data != csf_default)] = 0
csf_data[np.where(csf_labels > 0)] = 1
csf_data = csf_data.astype(np.uint8)
csf_label_image = nb.Nifti1Image(dataobj=csf_data,
affine=csf_image.get_affine(),
header=csf_image.get_header())
csf_label_image.set_data_dtype(np.uint8)
_, name, _ = split_filename(csf_file)
csf_label_file = op.abspath(name + "_fixedCSF.nii.gz")
nb.save(csf_label_image, csf_label_file)
hdr = image.get_header()
data_uint8, remap_dict = prepare_for_uint8(data, ignore=range(0, 3))
data_uint8 = data_uint8.astype(np.uint8)
data_uint8[np.where(data == csf_default)] = csf_default
data_uint8[np.where(data == white_matter_default)] = white_matter_default
fixed = nb.Nifti1Image(dataobj=data_uint8,
affine=image.get_affine(),
header=hdr)
_, name, _ = split_filename(roi_image)
fixed.set_data_dtype(np.uint8)
fixed_roi_image = op.abspath(name + "_fixedROIs.nii.gz")
nb.save(fixed, fixed_roi_image)
return fixed_roi_image, wm_label_file, csf_label_file, remap_dict
def fix_roi_values_freesurferLUT(roi_image, white_matter_file, csf_file, prob_thresh):
from coma.helpers import wm_labels_only, csf_labels_only, prepare_for_uint8
_, name, _ = split_filename(roi_image)
white_matter_default = 2
csf_default = 3
# Get regions labelled white and csf
wm_label_file = op.abspath(name + "_WM.nii.gz")
wm_only = wm_labels_only(roi_image, out_filename=wm_label_file)
wm_label_image = nb.load(wm_only)
wm_labels = wm_label_image.get_data()
csf_label_file = op.abspath(name + "_CSF.nii.gz")
csf_only = csf_labels_only(roi_image, out_filename=csf_label_file)
csf_label_image = nb.load(csf_only)
csf_labels = csf_label_image.get_data()
wm_image = nb.load(white_matter_file)
wm_data = wm_image.get_data()
csf_image = nb.load(csf_file)
csf_data = csf_image.get_data()
image = nb.load(roi_image)
data = image.get_data()
assert(data.shape == wm_data.shape == csf_data.shape)
data[np.where(wm_labels > 0)] = white_matter_default
data[np.where(csf_labels > 0)] = csf_default
# Be careful with the brackets here. & takes priority over comparisons
data[np.where((wm_data > prob_thresh) & (data == 0))] = white_matter_default
data[np.where((csf_data > prob_thresh) & (data == 0))] = csf_default
wm_labels[np.where(data == white_matter_default)] = 1
wm_labels[np.where(data == csf_default)] = 0
wm_labels[np.where(data == 0)] = 0
wm_labels = wm_labels.astype(np.uint8)
new_wm_label_image = nb.Nifti1Image(
dataobj=wm_labels, affine=wm_image.get_affine(), header=wm_image.get_header())
new_wm_label_image.set_data_dtype(np.uint8)
_, name, _ = split_filename(white_matter_file)
wm_label_file = op.abspath(name + "_fixedWM.nii.gz")
nb.save(new_wm_label_image, wm_label_file)
csf_data[np.where(data != csf_default)] = 0
csf_data[np.where(csf_labels > 0)] = 1
csf_data = csf_data.astype(np.uint8)
csf_label_image = nb.Nifti1Image(
dataobj=csf_data, affine=csf_image.get_affine(), header=csf_image.get_header())
csf_label_image.set_data_dtype(np.uint8)
_, name, _ = split_filename(csf_file)
csf_label_file = op.abspath(name + "_fixedCSF.nii.gz")
nb.save(csf_label_image, csf_label_file)
hdr = image.get_header()
data_uint8, remap_dict = prepare_for_uint8(data, ignore=range(0, 3))
data_uint8 = data_uint8.astype(np.uint8)
data_uint8[np.where(data == csf_default)] = csf_default
data_uint8[np.where(data == white_matter_default)] = white_matter_default
fixed = nb.Nifti1Image(
dataobj=data_uint8, affine=image.get_affine(), header=hdr)
_, name, _ = split_filename(roi_image)
fixed.set_data_dtype(np.uint8)
fixed_roi_image = op.abspath(name + "_fixedROIs.nii.gz")
nb.save(fixed, fixed_roi_image)
return fixed_roi_image, wm_label_file, csf_label_file, remap_dict
def fix_roi_values_noLUT(roi_image, gm_file, white_matter_file, csf_file,
prob_thresh):
from coma.helpers import prepare_for_uint8
_, name, _ = split_filename(roi_image)
white_matter_default = 2
csf_default = 3
gm_image = nb.load(gm_file)
gm_data = gm_image.get_data()
wm_image = nb.load(white_matter_file)
wm_data = wm_image.get_data()
csf_image = nb.load(csf_file)
csf_data = csf_image.get_data()
image = nb.load(roi_image)
data = image.get_data()
assert (data.shape == gm_data.shape == wm_data.shape == csf_data.shape)
data_uint8, remap_dict = prepare_for_uint8(data, ignore=[0])
data_uint8 = data_uint8.astype(np.uint8)
data_uint8[np.where(data_uint8 == csf_default)] = csf_default
data_uint8[np.where(
data_uint8 == white_matter_default)] = white_matter_default
# Be careful with the brackets here. & takes priority over comparisons
data_uint8[np.where((wm_data > prob_thresh)
& (data_uint8 == 0))] = white_matter_default
data_uint8[np.where((csf_data > prob_thresh)
& (data_uint8 == 0))] = csf_default
wm_data[np.where(data_uint8 == white_matter_default)] = 1
wm_data[np.where(data_uint8 == csf_default)] = 0
wm_data[np.where(data_uint8 == 0)] = 0
wm_data = wm_data.astype(np.uint8)
new_wm_label_image = nb.Nifti1Image(dataobj=wm_data,
affine=wm_image.get_affine(),
header=wm_image.get_header())
new_wm_label_image.set_data_dtype(np.uint8)
_, name, _ = split_filename(white_matter_file)
wm_label_file = op.abspath(name + "_fixedWM.nii.gz")
nb.save(new_wm_label_image, wm_label_file)
csf_data[np.where(data_uint8 != csf_default)] = 0
csf_data = csf_data.astype(np.uint8)
csf_label_image = nb.Nifti1Image(dataobj=csf_data,
affine=csf_image.get_affine(),
header=csf_image.get_header())
csf_label_image.set_data_dtype(np.uint8)
_, name, _ = split_filename(csf_file)
csf_label_file = op.abspath(name + "_fixedCSF.nii.gz")
nb.save(csf_label_image, csf_label_file)
hdr = image.get_header()
unlabelled = np.where((gm_data > prob_thresh) & (data_uint8 == 0))[0]
# Create extra ROI if there are extra GM regions in the GM mask
if len(unlabelled) > 0:
highestlabel = np.max(data_uint8)
assert (highestlabel != 255)
data_uint8[np.where((gm_data > 0)
& (data_uint8 == 0))] = highestlabel + 1
fixed = nb.Nifti1Image(dataobj=data_uint8,
affine=image.get_affine(),
header=hdr)
_, name, _ = split_filename(roi_image)
fixed.set_data_dtype(np.uint8)
fixed_roi_image = op.abspath(name + "_fixedROIs.nii.gz")
nb.save(fixed, fixed_roi_image)
return fixed_roi_image, wm_label_file, csf_label_file, remap_dict
def fix_roi_values_noLUT(roi_image, gm_file, white_matter_file, csf_file, prob_thresh):
from coma.helpers import prepare_for_uint8
_, name, _ = split_filename(roi_image)
white_matter_default = 2
csf_default = 3
gm_image = nb.load(gm_file)
gm_data = gm_image.get_data()
wm_image = nb.load(white_matter_file)
wm_data = wm_image.get_data()
csf_image = nb.load(csf_file)
csf_data = csf_image.get_data()
image = nb.load(roi_image)
data = image.get_data()
assert(data.shape == gm_data.shape == wm_data.shape == csf_data.shape)
data_uint8, remap_dict = prepare_for_uint8(data, ignore=[0])
data_uint8 = data_uint8.astype(np.uint8)
data_uint8[np.where(data_uint8 == csf_default)] = csf_default
data_uint8[np.where(data_uint8 == white_matter_default)] = white_matter_default
# Be careful with the brackets here. & takes priority over comparisons
data_uint8[np.where((wm_data > prob_thresh) & (data_uint8 == 0))] = white_matter_default
data_uint8[np.where((csf_data > prob_thresh) & (data_uint8 == 0))] = csf_default
wm_data[np.where(data_uint8 == white_matter_default)] = 1
wm_data[np.where(data_uint8 == csf_default)] = 0
wm_data[np.where(data_uint8 == 0)] = 0
wm_data = wm_data.astype(np.uint8)
new_wm_label_image = nb.Nifti1Image(
dataobj=wm_data, affine=wm_image.get_affine(), header=wm_image.get_header())
new_wm_label_image.set_data_dtype(np.uint8)
_, name, _ = split_filename(white_matter_file)
wm_label_file = op.abspath(name + "_fixedWM.nii.gz")
nb.save(new_wm_label_image, wm_label_file)
csf_data[np.where(data_uint8 != csf_default)] = 0
csf_data = csf_data.astype(np.uint8)
csf_label_image = nb.Nifti1Image(
dataobj=csf_data, affine=csf_image.get_affine(), header=csf_image.get_header())
csf_label_image.set_data_dtype(np.uint8)
_, name, _ = split_filename(csf_file)
csf_label_file = op.abspath(name + "_fixedCSF.nii.gz")
nb.save(csf_label_image, csf_label_file)
hdr = image.get_header()
unlabelled = np.where((gm_data > prob_thresh) & (data_uint8 == 0))[0]
# Create extra ROI if there are extra GM regions in the GM mask
if len(unlabelled) > 0:
highestlabel = np.max(data_uint8)
assert(highestlabel != 255)
data_uint8[np.where((gm_data > 0) & (data_uint8 == 0))] = highestlabel + 1
fixed = nb.Nifti1Image(
dataobj=data_uint8, affine=image.get_affine(), header=hdr)
_, name, _ = split_filename(roi_image)
fixed.set_data_dtype(np.uint8)
fixed_roi_image = op.abspath(name + "_fixedROIs.nii.gz")
nb.save(fixed, fixed_roi_image)
return fixed_roi_image, wm_label_file, csf_label_file, remap_dict
