def reorient_img(img, out_dir, overwrite=True):
"""
A function to reorient any non-dwi image to RAS+.
Parameters
----------
img : str
File path to a Nifti1Image.
out_dir : str
Path to output directory.
Returns
-------
out_name : str
File path to reoriented Nifti1Image.
"""
from pynets.registration.reg_utils import normalize_xform
# Load image, orient as RAS
orig_img = nib.load(img)
normalized = normalize_xform(nib.as_closest_canonical(orig_img))
# Image may be reoriented
if normalized is not orig_img:
print(f"{'Reorienting '}{img}{' to RAS+...'}")
out_name = (f"{out_dir}/{img.split('/')[-1].split('.nii')[0]}_"
f"reor-RAS.nii{img.split('/')[-1].split('.nii')[1]}")
else:
out_name = (f"{out_dir}/{img.split('/')[-1].split('.nii')[0]}_"
f"noreor-RAS.nii{img.split('/')[-1].split('.nii')[1]}")
if overwrite is False and os.path.isfile(out_name):
pass
else:
normalized.to_filename(out_name)
orig_img.uncache()
normalized.uncache()
del orig_img
return out_name
def reorient_img(img, out_dir):
"""
A function to reorient any non-dwi image to RAS+.
Parameters
----------
img : str
File path to a Nifti1Image.
out_dir : str
Path to output directory.
Returns
-------
out_name : str
File path to reoriented Nifti1Image.
"""
from pynets.registration.reg_utils import normalize_xform
# Load image, orient as RAS
orig_img = nib.load(img)
normalized = normalize_xform(nib.as_closest_canonical(orig_img))
# Image may be reoriented
if normalized is not orig_img:
print("%s%s%s" % ('Reorienting ', img, ' to RAS+...'))
out_name = "%s%s%s%s%s" % (out_dir, '/', img.split('/')[-1].split(
'.nii')[0], '_reor-RAS.nii', img.split('/')[-1].split('.nii')[1])
else:
out_name = "%s%s%s%s%s" % (out_dir, '/', img.split('/')[-1].split(
'.nii')[0], '_noreor-RAS.nii', img.split('/')[-1].split('.nii')[1])
normalized.to_filename(out_name)
orig_img.uncache()
normalized.uncache()
del orig_img
return out_name
def reorient_dwi(dwi_prep, bvecs, out_dir, overwrite=True):
"""
A function to reorient any dwi image and associated bvecs to RAS+.
Parameters
----------
dwi_prep : str
File path to a dwi Nifti1Image.
bvecs : str
File path to corresponding bvecs file.
out_dir : str
Path to output directory.
Returns
-------
out_fname : str
File path to the reoriented dwi Nifti1Image.
out_bvec_fname : str
File path to corresponding reoriented bvecs file.
"""
import os
from pynets.registration.reg_utils import normalize_xform
fname = dwi_prep
bvec_fname = bvecs
out_dir = f"{out_dir}/reg"
if not os.path.isdir(out_dir):
os.makedirs(out_dir)
out_bvec_fname = (
f"{out_dir}/{dwi_prep.split('/')[-1].split('.nii')[0]}_bvecs_reor.bvec"
)
input_img = nib.load(fname)
input_axcodes = nib.aff2axcodes(input_img.affine)
reoriented = nib.as_closest_canonical(input_img)
normalized = normalize_xform(reoriented)
# Is the input image oriented how we want?
new_axcodes = ("R", "A", "S")
if normalized is not input_img:
out_fname = (f"{out_dir}/{dwi_prep.split('/')[-1].split('.nii')[0]}_"
f"reor-RAS.nii{dwi_prep.split('/')[-1].split('.nii')[1]}")
if (overwrite is False and os.path.isfile(out_fname)
and os.path.isfile(out_bvec_fname)):
pass
else:
print(f"Reorienting {dwi_prep} to RAS+...")
# Flip the bvecs
transform_orientation = nib.orientations.ornt_transform(
nib.orientations.axcodes2ornt(input_axcodes),
nib.orientations.axcodes2ornt(new_axcodes),
)
bvec_array = np.loadtxt(bvec_fname)
if bvec_array.shape[0] != 3:
bvec_array = bvec_array.T
if not bvec_array.shape[0] == transform_orientation.shape[0]:
raise ValueError("Unrecognized bvec format")
output_array = np.zeros_like(bvec_array)
for this_axnum, (axnum, flip) in enumerate(transform_orientation):
output_array[this_axnum] = bvec_array[int(axnum)] * float(flip)
np.savetxt(out_bvec_fname, output_array, fmt="%.8f ")
else:
out_fname = (
f"{out_dir}/{dwi_prep.split('/')[-1].split('.nii')[0]}_"
f"noreor-RAS.nii{dwi_prep.split('/')[-1].split('.nii')[1]}")
out_bvec_fname = bvec_fname
if (overwrite is False and os.path.isfile(out_fname)
and os.path.isfile(out_bvec_fname)):
pass
else:
normalized.to_filename(out_fname)
normalized.uncache()
input_img.uncache()
del normalized, input_img
return out_fname, out_bvec_fname
def reorient_dwi(dwi_prep, bvecs, out_dir):
"""
A function to reorient any dwi image and associated bvecs to RAS+.
Parameters
----------
dwi_prep : str
File path to a dwi Nifti1Image.
bvecs : str
File path to corresponding bvecs file.
out_dir : str
Path to output directory.
Returns
-------
out_fname : str
File path to the reoriented dwi Nifti1Image.
out_bvec_fname : str
File path to corresponding reoriented bvecs file.
"""
from pynets.registration.reg_utils import normalize_xform
fname = dwi_prep
bvec_fname = bvecs
out_bvec_fname = "%s%s" % (out_dir, '/bvecs_reor.bvec')
input_img = nib.load(fname)
input_axcodes = nib.aff2axcodes(input_img.affine)
reoriented = nib.as_closest_canonical(input_img)
normalized = normalize_xform(reoriented)
# Is the input image oriented how we want?
new_axcodes = ('R', 'A', 'S')
if normalized is not input_img:
out_fname = "%s%s%s%s%s" % (
out_dir, '/', dwi_prep.split('/')[-1].split('.nii')[0],
'_reor-RAS.nii', dwi_prep.split('/')[-1].split('.nii')[1])
print("%s%s%s" % ('Reorienting ', dwi_prep, ' to RAS+...'))
# Flip the bvecs
transform_orientation = nib.orientations.ornt_transform(
nib.orientations.axcodes2ornt(input_axcodes),
nib.orientations.axcodes2ornt(new_axcodes))
bvec_array = np.loadtxt(bvec_fname)
if bvec_array.shape[0] != 3:
bvec_array = bvec_array.T
if not bvec_array.shape[0] == transform_orientation.shape[0]:
raise ValueError("Unrecognized bvec format")
output_array = np.zeros_like(bvec_array)
for this_axnum, (axnum, flip) in enumerate(transform_orientation):
output_array[this_axnum] = bvec_array[int(axnum)] * float(flip)
np.savetxt(out_bvec_fname, output_array, fmt="%.8f ")
else:
out_fname = "%s%s%s%s%s" % (
out_dir, '/', dwi_prep.split('/')[-1].split('.nii')[0],
'_noreor-RAS.nii', dwi_prep.split('/')[-1].split('.nii')[1])
out_bvec_fname = bvec_fname
normalized.to_filename(out_fname)
normalized.uncache()
input_img.uncache()
del normalized, input_img
return out_fname, out_bvec_fname