def test_align():
"""
Test align functionality
"""
import pkg_resources
# Linear registration
base_dir = os.path.abspath(
pkg_resources.resource_filename("pynets", "../data/examples"))
anat_dir = f"{base_dir}/003/anat"
inp = f"{anat_dir}/sub-003_T1w_brain.nii.gz"
ref = pkg_resources.resource_filename(
"pynets", f"templates/MNI152_T1_brain_"
f"2mm.nii.gz")
out = f"{anat_dir}/highres2standard.nii.gz"
xfm_out = f"{anat_dir}/highres2standard.mat"
utils.align(inp,
ref,
xfm=xfm_out,
out=out,
dof=12,
searchrad=True,
bins=256,
interp=None,
cost="mutualinfo",
sch=None,
wmseg=None,
init=None)
highres2standard_linear = nib.load(out)
assert highres2standard_linear is not None
def RegisterParcellation2MNIFunc_align(uatlas, template, template_mask,
t1w_brain, t1w2mni_xfm,
aligned_atlas_t1w, aligned_atlas_mni,
t1w2mni_warp, simple):
"""
A function to perform atlas alignment from T1w atlas --> MNI.
"""
import time
from pynets.registration import utils as regutils
from nilearn.image import resample_to_img
atlas_img = nib.load(uatlas)
t1w_brain_img = nib.load(t1w_brain)
uatlas_res_template = resample_to_img(atlas_img,
t1w_brain_img,
interpolation="nearest")
uatlas_res_template = nib.Nifti1Image(
np.asarray(uatlas_res_template.dataobj).astype('uint16'),
affine=uatlas_res_template.affine,
header=uatlas_res_template.header,
)
nib.save(uatlas_res_template, aligned_atlas_t1w)
if simple is False:
try:
regutils.apply_warp(
template,
aligned_atlas_t1w,
aligned_atlas_mni,
warp=t1w2mni_warp,
interp="nn",
sup=True,
)
time.sleep(0.5)
except BaseException:
print("Warning: Atlas is not in correct dimensions, or input is "
"low quality,\nusing linear template registration.")
regutils.align(
aligned_atlas_t1w,
template,
init=t1w2mni_xfm,
out=aligned_atlas_mni,
dof=6,
searchrad=True,
interp="nearestneighbour",
cost="mutualinfo",
)
time.sleep(0.5)
else:
regutils.align(
aligned_atlas_t1w,
template,
init=t1w2mni_xfm,
out=aligned_atlas_mni,
dof=6,
searchrad=True,
interp="nearestneighbour",
cost="mutualinfo",
)
time.sleep(0.5)
return aligned_atlas_mni
def tissue2dwi_align(self):
"""
A function to perform alignment of ventricle ROI's from MNI
space --> dwi and CSF from T1w space --> dwi. First generates and
performs dwi space alignment of avoidance/waypoint masks for
tractography. First creates ventricle ROI. Then creates transforms
from stock MNI template to dwi space. For this to succeed, must first
have called both t1w2dwi_align.
"""
import sys
import time
import os.path as op
import pkg_resources
from pynets.core.utils import load_runconfig
from nilearn.image import resample_to_img
from nipype.utils.filemanip import fname_presuffix, copyfile
from pynets.core.nodemaker import three_to_four_parcellation
from nilearn.image import math_img, index_img
hardcoded_params = load_runconfig()
tiss_class = hardcoded_params['tracking']["tissue_classifier"][0]
fa_template_path = pkg_resources.resource_filename(
"pynets", f"templates/standard/FA_{self.vox_size}.nii.gz")
if sys.platform.startswith('win') is False:
try:
fa_template_img = nib.load(fa_template_path)
except indexed_gzip.ZranError as e:
print(
e, f"\nCannot load FA template. Do you have git-lfs "
f"installed?")
else:
try:
fa_template_img = nib.load(fa_template_path)
except ImportError as e:
print(e, f"\nCannot load FA template. Do you have git-lfs ")
mni_template_img = nib.load(self.input_mni_brain)
if not np.allclose(fa_template_img.affine, mni_template_img.affine) \
or not \
np.allclose(fa_template_img.shape, mni_template_img.shape):
fa_template_img_res = resample_to_img(fa_template_img,
mni_template_img)
nib.save(fa_template_img_res, self.fa_template_res)
else:
self.fa_template_res = fname_presuffix(fa_template_path,
suffix="_tmp",
newpath=op.dirname(
self.reg_path_img))
copyfile(fa_template_path,
self.fa_template_res,
copy=True,
use_hardlink=False)
# Register Lateral Ventricles and Corpus Callosum rois to t1w
resample_to_img(nib.load(self.mni_atlas),
nib.load(self.input_mni_brain),
interpolation='nearest').to_filename(self.mni_roi_ref)
roi_parcels = three_to_four_parcellation(self.mni_roi_ref)
ventricle_roi = math_img("img1 + img2",
img1=index_img(roi_parcels, 2),
img2=index_img(roi_parcels, 13))
self.mni_vent_loc = fname_presuffix(self.mni_vent_loc,
suffix="_tmp",
newpath=op.dirname(
self.reg_path_img))
ventricle_roi.to_filename(self.mni_vent_loc)
del roi_parcels, ventricle_roi
# Create transform from the HarvardOxford atlas in MNI to T1w.
# This will be used to transform the ventricles to dwi space.
regutils.align(
self.mni_roi_ref,
self.input_mni_brain,
xfm=self.xfm_roi2mni_init,
init=None,
bins=None,
dof=6,
cost="mutualinfo",
searchrad=True,
interp="spline",
out=None,
)
# Create transform to align roi to mni and T1w using flirt
regutils.applyxfm(
self.input_mni_brain,
self.mni_vent_loc,
self.xfm_roi2mni_init,
self.vent_mask_mni,
)
time.sleep(0.5)
if self.simple is False:
# Apply warp resulting from the inverse MNI->T1w created earlier
regutils.apply_warp(
self.t1w_brain,
self.vent_mask_mni,
self.vent_mask_t1w,
warp=self.mni2t1w_warp,
interp="nn",
sup=True,
)
time.sleep(0.5)
if sys.platform.startswith('win') is False:
try:
nib.load(self.corpuscallosum)
except indexed_gzip.ZranError as e:
print(
e, f"\nCannot load Corpus Callosum ROI. "
f"Do you have git-lfs installed?")
else:
try:
nib.load(self.corpuscallosum)
except ImportError as e:
print(
e, f"\nCannot load Corpus Callosum ROI. "
f"Do you have git-lfs installed?")
regutils.apply_warp(
self.t1w_brain,
self.corpuscallosum,
self.corpuscallosum_mask_t1w,
warp=self.mni2t1w_warp,
interp="nn",
sup=True,
)
else:
regutils.applyxfm(self.vent_mask_mni, self.t1w_brain,
self.mni2t1_xfm, self.vent_mask_t1w)
time.sleep(0.5)
regutils.applyxfm(
self.corpuscallosum,
self.t1w_brain,
self.mni2t1_xfm,
self.corpuscallosum_mask_t1w,
)
time.sleep(0.5)
# Applyxfm to map FA template image to T1w space
regutils.applyxfm(self.t1w_brain, self.fa_template_res,
self.mni2t1_xfm, self.fa_template_t1w)
time.sleep(0.5)
# Applyxfm tissue maps to dwi space
if self.t1w_brain_mask is not None:
regutils.applyxfm(
self.ap_path,
self.t1w_brain_mask,
self.t1wtissue2dwi_xfm,
self.t1w_brain_mask_in_dwi,
)
time.sleep(0.5)
regutils.applyxfm(self.ap_path, self.vent_mask_t1w,
self.t1wtissue2dwi_xfm, self.vent_mask_dwi)
time.sleep(0.5)
regutils.applyxfm(self.ap_path, self.csf_mask, self.t1wtissue2dwi_xfm,
self.csf_mask_dwi)
time.sleep(0.5)
regutils.applyxfm(self.ap_path, self.gm_mask, self.t1wtissue2dwi_xfm,
self.gm_in_dwi)
time.sleep(0.5)
regutils.applyxfm(self.ap_path, self.wm_mask, self.t1wtissue2dwi_xfm,
self.wm_in_dwi)
time.sleep(0.5)
regutils.applyxfm(
self.ap_path,
self.corpuscallosum_mask_t1w,
self.t1wtissue2dwi_xfm,
self.corpuscallosum_dwi,
)
time.sleep(0.5)
csf_thr = 0.95
wm_thr = 0.05
gm_thr = 0.05
# Threshold WM to binary in dwi space
nib.save(math_img(f"img > {wm_thr}", img=nib.load(self.wm_in_dwi)),
self.wm_in_dwi_bin)
# Threshold GM to binary in dwi space
nib.save(math_img(f"img > {gm_thr}", img=nib.load(self.gm_in_dwi)),
self.gm_in_dwi_bin)
# Threshold CSF to binary in dwi space
nib.save(math_img(f"img > {csf_thr}", img=nib.load(self.csf_mask_dwi)),
self.csf_mask_dwi_bin)
# Threshold WM to binary in dwi space
self.wm_in_dwi = regutils.apply_mask_to_image(self.wm_in_dwi,
self.wm_in_dwi_bin,
self.wm_in_dwi)
# Threshold GM to binary in dwi space
self.gm_in_dwi = regutils.apply_mask_to_image(self.gm_in_dwi,
self.gm_in_dwi_bin,
self.gm_in_dwi)
# Threshold CSF to binary in dwi space
self.csf_mask = regutils.apply_mask_to_image(self.csf_mask_dwi,
self.csf_mask_dwi_bin,
self.csf_mask_dwi)
# Create ventricular CSF mask
print("Creating Ventricular CSF mask...")
math_img("(img1 + img2) > 0.0001",
img1=nib.load(self.csf_mask_dwi),
img2=nib.load(self.vent_mask_dwi)).to_filename(
self.vent_csf_in_dwi)
print("Creating Corpus Callosum mask...")
math_img("(img1*img2 - img3) > 0.0001",
img1=nib.load(self.corpuscallosum_dwi),
img2=nib.load(self.wm_in_dwi_bin),
img3=nib.load(self.vent_csf_in_dwi)).to_filename(
self.corpuscallosum_dwi)
# Create GM-WM interface image
math_img("((img1*img2 + img3)*img4) > 0.0001",
img1=nib.load(self.gm_in_dwi_bin),
img2=nib.load(self.wm_in_dwi_bin),
img3=nib.load(self.corpuscallosum_dwi),
img4=nib.load(self.B0_mask)).to_filename(
self.wm_gm_int_in_dwi)
return
def t1w2dwi_align(self):
"""
A function to perform alignment from T1w_MNI --> DWI. Uses a local
optimization cost function to get the two images close, and then uses
bbr to obtain a good alignment of brain boundaries.
Assumes input dwi is already preprocessed and brain extracted.
"""
import time
self.ap_path = regutils.apply_mask_to_image(self.ap_path, self.B0_mask,
self.ap_path)
self.fa_path = regutils.apply_mask_to_image(self.fa_path, self.B0_mask,
self.fa_path)
# Align T1w-->DWI
regutils.align(
self.ap_path,
self.t1w_brain,
xfm=self.t1w2dwi_xfm,
bins=None,
interp="spline",
dof=6,
cost="mutualinfo",
out=None,
searchrad=True,
sch=None,
)
time.sleep(0.5)
self.dwi2t1w_xfm = regutils.invert_xfm(self.t1w2dwi_xfm,
self.dwi2t1w_xfm)
time.sleep(0.5)
if self.simple is False:
# Flirt bbr
try:
print("Learning a Boundary-Based Mapping from T1w-->DWI ...")
regutils.align(
self.fa_path,
self.t1w_brain,
wmseg=self.wm_edge,
xfm=self.dwi2t1w_bbr_xfm,
init=self.dwi2t1w_xfm,
bins=256,
dof=7,
searchrad=True,
interp="spline",
out=None,
cost="bbr",
sch="${FSLDIR}/etc/flirtsch/bbr.sch",
)
time.sleep(0.5)
self.t1w2dwi_bbr_xfm = regutils.invert_xfm(
self.dwi2t1w_bbr_xfm, self.t1w2dwi_bbr_xfm)
time.sleep(0.5)
# Apply the alignment
regutils.align(
self.t1w_brain,
self.ap_path,
init=self.t1w2dwi_bbr_xfm,
xfm=self.t1wtissue2dwi_xfm,
bins=None,
interp="spline",
dof=6,
cost="mutualinfo",
out=self.t1w2dwi,
searchrad=True,
sch=None,
)
time.sleep(0.5)
except BaseException:
# Apply the alignment
regutils.align(
self.t1w_brain,
self.ap_path,
init=self.t1w2dwi_xfm,
xfm=self.t1wtissue2dwi_xfm,
bins=None,
interp="spline",
dof=6,
cost="mutualinfo",
out=self.t1w2dwi,
searchrad=True,
sch=None,
)
time.sleep(0.5)
else:
# Apply the alignment
regutils.align(
self.t1w_brain,
self.ap_path,
init=self.t1w2dwi_xfm,
xfm=self.t1wtissue2dwi_xfm,
bins=None,
interp="spline",
dof=6,
cost="mutualinfo",
out=self.t1w2dwi,
searchrad=True,
sch=None,
)
time.sleep(0.5)
self.t1w2dwi = regutils.apply_mask_to_image(self.t1w2dwi, self.B0_mask,
self.t1w2dwi)
return
def t1w2mni_align(self):
"""
A function to perform alignment from T1w --> MNI template.
"""
import time
# Create linear transform/ initializer T1w-->MNI
regutils.align(
self.t1w_brain,
self.input_mni_brain,
xfm=self.t12mni_xfm_init,
bins=None,
interp="spline",
out=None,
dof=12,
cost="mutualinfo",
searchrad=True,
)
time.sleep(0.5)
# Attempt non-linear registration of T1 to MNI template
if self.simple is False:
try:
print(f"Learning a non-linear mapping from T1w --> "
f"{self.template_name} ...")
# Use FNIRT to nonlinearly align T1 to MNI template
regutils.align_nonlinear(
self.t1w_brain,
self.input_mni,
xfm=self.t12mni_xfm_init,
out=self.t1_aligned_mni,
warp=self.warp_t1w2mni,
ref_mask=self.input_mni_mask,
)
time.sleep(0.5)
# Get warp from MNI -> T1
regutils.inverse_warp(self.t1w_brain, self.mni2t1w_warp,
self.warp_t1w2mni)
time.sleep(0.5)
# Get mat from MNI -> T1
self.mni2t1_xfm = regutils.invert_xfm(self.t12mni_xfm_init,
self.mni2t1_xfm)
time.sleep(0.5)
except BaseException:
# Falling back to linear registration
regutils.align(
self.t1w_brain,
self.input_mni_brain,
xfm=self.mni2t1_xfm,
init=self.t12mni_xfm_init,
bins=None,
dof=12,
cost="mutualinfo",
searchrad=True,
interp="spline",
out=self.t1_aligned_mni,
sch=None,
)
time.sleep(0.5)
# Get mat from MNI -> T1
self.mni2t1_xfm = regutils.invert_xfm(self.t12mni_xfm,
self.mni2t1_xfm)
time.sleep(0.5)
else:
# Falling back to linear registration
regutils.align(
self.t1w_brain,
self.input_mni_brain,
xfm=self.t12mni_xfm,
init=self.t12mni_xfm_init,
bins=None,
dof=12,
cost="mutualinfo",
searchrad=True,
interp="spline",
out=self.t1_aligned_mni,
sch=None,
)
time.sleep(0.5)
# Get mat from MNI -> T1
self.t12mni_xfm = regutils.invert_xfm(self.mni2t1_xfm,
self.t12mni_xfm)
time.sleep(0.5)
def tissue2dwi_align(self):
"""
A function to perform alignment of ventricle ROI's from MNI
space --> dwi and CSF from T1w space --> dwi. First generates and
performs dwi space alignment of avoidance/waypoint masks for
tractography. First creates ventricle ROI. Then creates transforms
from stock MNI template to dwi space. For this to succeed, must first
have called both t1w2dwi_align.
"""
import sys
import time
import os.path as op
import pkg_resources
from pynets.core.utils import load_runconfig
from nilearn.image import resample_to_img
hardcoded_params = load_runconfig()
tiss_class = hardcoded_params['tracking']["tissue_classifier"][0]
fa_template_path = pkg_resources.resource_filename(
"pynets", f"templates/FA_{self.vox_size}.nii.gz")
if sys.platform.startswith('win') is False:
try:
fa_template_img = nib.load(fa_template_path)
except indexed_gzip.ZranError as e:
print(
e, f"\nCannot load FA template. Do you have git-lfs "
f"installed?")
else:
try:
fa_template_img = nib.load(fa_template_path)
except ImportError as e:
print(e, f"\nCannot load FA template. Do you have git-lfs ")
mni_template_img = nib.load(self.input_mni_brain)
fa_template_img_res = resample_to_img(fa_template_img,
mni_template_img)
nib.save(fa_template_img_res, self.fa_template_res)
# Register Lateral Ventricles and Corpus Callosum rois to t1w
if not op.isfile(self.mni_atlas):
raise FileNotFoundError("FSL atlas for ventricle reference not"
" found!")
# Create transform to MNI atlas to T1w using flirt. This will be use to
# transform the ventricles to dwi space.
regutils.align(
self.mni_atlas,
self.input_mni_brain,
xfm=self.xfm_roi2mni_init,
init=None,
bins=None,
dof=6,
cost="mutualinfo",
searchrad=True,
interp="spline",
out=None,
)
time.sleep(0.5)
if sys.platform.startswith('win') is False:
try:
nib.load(self.mni_vent_loc)
except indexed_gzip.ZranError as e:
print(
e, f"\nCannot load ventricle ROI. Do you have git-lfs "
f"installed?")
else:
try:
nib.load(self.mni_vent_loc)
except ImportError as e:
print(
e, f"\nCannot load ventricle ROI. Do you have git-lfs "
f"installed?")
# Create transform to align roi to mni and T1w using flirt
regutils.applyxfm(
self.input_mni_brain,
self.mni_vent_loc,
self.xfm_roi2mni_init,
self.vent_mask_mni,
)
time.sleep(0.5)
if self.simple is False:
# Apply warp resulting from the inverse MNI->T1w created earlier
regutils.apply_warp(
self.t1w_brain,
self.vent_mask_mni,
self.vent_mask_t1w,
warp=self.mni2t1w_warp,
interp="nn",
sup=True,
)
time.sleep(0.5)
if sys.platform.startswith('win') is False:
try:
nib.load(self.corpuscallosum)
except indexed_gzip.ZranError as e:
print(
e, f"\nCannot load Corpus Callosum ROI. "
f"Do you have git-lfs installed?")
else:
try:
nib.load(self.corpuscallosum)
except ImportError as e:
print(
e, f"\nCannot load Corpus Callosum ROI. "
f"Do you have git-lfs installed?")
regutils.apply_warp(
self.t1w_brain,
self.corpuscallosum,
self.corpuscallosum_mask_t1w,
warp=self.mni2t1w_warp,
interp="nn",
sup=True,
)
else:
regutils.applyxfm(self.vent_mask_mni, self.t1w_brain,
self.mni2t1_xfm, self.vent_mask_t1w)
time.sleep(0.5)
regutils.applyxfm(
self.corpuscallosum,
self.t1w_brain,
self.mni2t1_xfm,
self.corpuscallosum_mask_t1w,
)
time.sleep(0.5)
# Applyxfm to map FA template image to T1w space
regutils.applyxfm(self.t1w_brain, self.fa_template_res,
self.mni2t1_xfm, self.fa_template_t1w)
time.sleep(0.5)
# Applyxfm tissue maps to dwi space
if self.t1w_brain_mask is not None:
regutils.applyxfm(
self.ap_path,
self.t1w_brain_mask,
self.t1wtissue2dwi_xfm,
self.t1w_brain_mask_in_dwi,
)
time.sleep(0.5)
regutils.applyxfm(self.ap_path, self.vent_mask_t1w,
self.t1wtissue2dwi_xfm, self.vent_mask_dwi)
time.sleep(0.5)
regutils.applyxfm(self.ap_path, self.csf_mask, self.t1wtissue2dwi_xfm,
self.csf_mask_dwi)
time.sleep(0.5)
regutils.applyxfm(self.ap_path, self.gm_mask, self.t1wtissue2dwi_xfm,
self.gm_in_dwi)
time.sleep(0.5)
regutils.applyxfm(self.ap_path, self.wm_mask, self.t1wtissue2dwi_xfm,
self.wm_in_dwi)
time.sleep(0.5)
regutils.applyxfm(
self.ap_path,
self.corpuscallosum_mask_t1w,
self.t1wtissue2dwi_xfm,
self.corpuscallosum_dwi,
)
time.sleep(0.5)
if tiss_class == 'wb' or tiss_class == 'cmc':
csf_thr = 0.50
wm_thr = 0.15
gm_thr = 0.10
else:
csf_thr = 0.99
wm_thr = 0.10
gm_thr = 0.075
# Threshold WM to binary in dwi space
thr_img = nib.load(self.wm_in_dwi)
thr_img = math_img(f"img > {wm_thr}", img=thr_img)
nib.save(thr_img, self.wm_in_dwi_bin)
# Threshold GM to binary in dwi space
thr_img = nib.load(self.gm_in_dwi)
thr_img = math_img(f"img > {gm_thr}", img=thr_img)
nib.save(thr_img, self.gm_in_dwi_bin)
# Threshold CSF to binary in dwi space
thr_img = nib.load(self.csf_mask_dwi)
thr_img = math_img(f"img > {csf_thr}", img=thr_img)
nib.save(thr_img, self.csf_mask_dwi_bin)
# Threshold WM to binary in dwi space
self.wm_in_dwi = regutils.apply_mask_to_image(self.wm_in_dwi,
self.wm_in_dwi_bin,
self.wm_in_dwi)
time.sleep(0.5)
# Threshold GM to binary in dwi space
self.gm_in_dwi = regutils.apply_mask_to_image(self.gm_in_dwi,
self.gm_in_dwi_bin,
self.gm_in_dwi)
time.sleep(0.5)
# Threshold CSF to binary in dwi space
self.csf_mask = regutils.apply_mask_to_image(self.csf_mask_dwi,
self.csf_mask_dwi_bin,
self.csf_mask_dwi)
time.sleep(0.5)
# Create ventricular CSF mask
print("Creating Ventricular CSF mask...")
os.system(f"fslmaths {self.vent_mask_dwi} -kernel sphere 10 -ero "
f"-bin {self.vent_mask_dwi}")
time.sleep(1)
os.system(f"fslmaths {self.csf_mask_dwi} -add {self.vent_mask_dwi} "
f"-bin {self.vent_csf_in_dwi}")
time.sleep(1)
print("Creating Corpus Callosum mask...")
os.system(
f"fslmaths {self.corpuscallosum_dwi} -mas {self.wm_in_dwi_bin} "
f"-sub {self.vent_csf_in_dwi} "
f"-bin {self.corpuscallosum_dwi}")
time.sleep(1)
# Create gm-wm interface image
os.system(f"fslmaths {self.gm_in_dwi_bin} -mul {self.wm_in_dwi_bin} "
f"-add {self.corpuscallosum_dwi} "
f"-mas {self.B0_mask} -bin {self.wm_gm_int_in_dwi}")
time.sleep(1)
return
