In [92]:
import subprocess
from pathlib import Path
from templateflow import api
from nibabel.nifti1 import Nifti1Image
from nilearn import plotting
from nilearn.image import mean_img
from nibabel.orientations import aff2axcodes
In [93]:
def apply_transform(input_img: Path, reference_img: Path, transform: Path, output_img: Path):
"""Apply transform to input image using reference space."""
# Get dimensionality from input image
img = Nifti1Image.load(str(input_img))
ndim = len(img.shape)
if ndim == 4:
input_type = 3 # time-series type
else:
input_type = 0 # scalar type
cmd = [
"antsApplyTransforms",
"-d",
str(3), # dimensionality is 3 regardless
"-e",
str(input_type),
"-i",
str(input_img),
"-r",
str(reference_img),
"-t",
str(transform),
"-o",
str(output_img),
"-n",
"LanczosWindowedSinc",
"--float",
]
print(f"Running command: {' '.join(cmd)}")
subprocess.run(cmd, check=True)
def print_givens(img: Nifti1Image, name: str):
print(f"Image: {name}")
print(f"Shape: {img.shape}")
print(f"Zooms: {img.header.get_zooms()}")
print(f"Orientation: {aff2axcodes(img.affine)}")
In [101]:
# Setup paths
base_dir = Path.home() / "Documents/TEST"
transform_path = base_dir / "V12_to_V11.txt"
# T1w
path_v11_t1w = base_dir / "V11/sub-GRN296_ses-V11_acq-Philips3T3DT1_T1w.nii.gz"
path_v12_t1w = base_dir / "V12/sub-GRN296_ses-V12_acq-Philips3T3DT1_T1w.nii.gz"
path_v12_t1w_registered = path_v12_t1w.parent / path_v12_t1w.name.replace(".nii.gz", "_registered.nii.gz")
img_v11_t1w = Nifti1Image.load(str(path_v11_t1w))
img_v12_t1w = Nifti1Image.load(str(path_v12_t1w))
print_givens(img_v11_t1w, "V11 T1w")
print(img_v11_t1w.affine)
print_givens(img_v12_t1w, "V12 T1w")
print(img_v12_t1w.affine)
print("-" * 100)
# T2w
path_v11_t2w = base_dir / "V11/sub-GRN296_ses-V11_acq-Philips3T3DT2_T2w.nii.gz"
path_v12_t2w = base_dir / "V12/sub-GRN296_ses-V12_acq-Philips3T3DT2_T2w.nii.gz"
path_v12_t2w_registered = path_v12_t2w.parent / path_v12_t2w.name.replace(".nii.gz", "_registered.nii.gz")
img_v11_t2w = Nifti1Image.load(str(path_v11_t2w))
img_v12_t2w = Nifti1Image.load(str(path_v12_t2w))
print_givens(img_v11_t2w, "V11 T2w")
print(img_v11_t2w.affine)
print_givens(img_v12_t2w, "V12 T2w")
print(img_v12_t2w.affine)
print("-" * 100)
# BOLD
path_v11_bold = base_dir / "V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz"
path_v12_bold = base_dir / "V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz"
path_v12_bold_registered = path_v12_bold.parent / path_v12_bold.name.replace(".nii.gz", "_registered.nii.gz")
img_v11_bold = Nifti1Image.load(str(path_v11_bold))
img_v12_bold = Nifti1Image.load(str(path_v12_bold))
print_givens(img_v11_bold, "V11 BOLD")
print(img_v11_bold.affine)
print_givens(img_v12_bold, "V12 BOLD")
print(img_v12_bold.affine)
Image: V11 T1w
Shape: (208, 256, 256)
Zooms: (1.1, 1.1015625, 1.1015625)
Orientation: ('R', 'A', 'S')
[[ 1.09919715e+00 -3.97272855e-02 1.33315139e-02 -1.00281090e+02]
[ 4.18307893e-02 1.05229211e+00 -3.23058039e-01 -5.07127228e+01]
[-1.08275819e-03 3.23331177e-01 1.05304122e+00 -2.41561737e+02]
[ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]
Image: V12 T1w
Shape: (208, 256, 256)
Zooms: (1.1, 1.1015625, 1.1015625)
Orientation: ('R', 'A', 'S')
[[ 1.09916699e+00 3.44870659e-03 4.25405353e-02 -1.25100731e+02]
[ 1.35649145e-02 1.01255357e+00 -4.33579028e-01 -2.85160751e+01]
[-4.04029302e-02 4.33778137e-01 1.01175070e+00 -1.44102097e+02]
[ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]
----------------------------------------------------------------------------------------------------
Image: V11 T2w
Shape: (176, 256, 256)
Zooms: (1.1, 1.1015625, 1.1015625)
Orientation: ('R', 'A', 'S')
[[ 1.09919715e+00 -3.97272855e-02 1.33315139e-02 -8.26938095e+01]
[ 4.18307893e-02 1.05229211e+00 -3.23058039e-01 -5.00434113e+01]
[-1.08275819e-03 3.23331177e-01 1.05304122e+00 -2.41579071e+02]
[ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]
Image: V12 T2w
Shape: (176, 256, 256)
Zooms: (1.1, 1.1015625, 1.1015625)
Orientation: ('R', 'A', 'S')
[[ 1.09916699e+00 3.44870659e-03 4.25405353e-02 -1.07513939e+02]
[ 1.35649145e-02 1.01255357e+00 -4.33579028e-01 -2.82990341e+01]
[-4.04029302e-02 4.33778137e-01 1.01175070e+00 -1.44748520e+02]
[ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]
----------------------------------------------------------------------------------------------------
Image: V11 BOLD
Shape: (64, 64, 42, 200)
Zooms: (3.0, 3.0, 3.5, 2.5000014)
Orientation: ('L', 'A', 'S')
[[-2.99782848e+00 -1.08193457e-01 4.23582494e-02 1.07092514e+02]
[-1.14084661e-01 2.86581683e+00 -1.02645302e+00 -2.20490570e+01]
[ 2.95299338e-03 8.80561531e-01 3.34582973e+00 -1.44069565e+02]
[ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]
Image: V12 BOLD
Shape: (64, 64, 42, 200)
Zooms: (3.0, 3.0, 3.5, 2.5000014)
Orientation: ('L', 'A', 'S')
[[-2.99774766e+00 9.39222239e-03 1.35164261e-01 9.08997879e+01]
[-3.69954631e-02 2.75759292e+00 -1.37761307e+00 -2.62816467e+01]
[ 1.10190526e-01 1.18135321e+00 3.21464062e+00 -3.09833183e+01]
[ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]
In [95]:
# Sanity check, the original t2w images should not be registered; see this via plotting
plotting.plot_img(img_v11_t2w, cmap="gray", title="V11 T2w", cut_coords=(0, 0, 0)).add_overlay(
img_v12_t2w, cmap="Accent", alpha=0.5
)
In [96]:
# T1w
# Apply transform
print("Registering T1w image...")
apply_transform(path_v12_t1w, path_v11_t1w, transform_path, path_v12_t1w_registered)
img_v12_t1w_registered = Nifti1Image.load(str(path_v12_t1w_registered))
print_givens(img_v12_t1w_registered, "V12 T1w registered")
print(img_v12_t1w_registered.affine)
# Plot the registration
plotting.plot_img(img_v11_t1w, cmap="gray", title="V11 T1w", cut_coords=(0, 0, 0)).add_overlay(
img_v12_t1w_registered, cmap="Accent", alpha=0.5
)
Registering T1w image...
Running command: antsApplyTransforms -d 3 -e 0 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_acq-Philips3T3DT1_T1w.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_acq-Philips3T3DT1_T1w.nii.gz -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_acq-Philips3T3DT1_T1w_registered.nii.gz -n LanczosWindowedSinc --float
Image: V12 T1w registered
Shape: (208, 256, 256)
Zooms: (1.1, 1.1015625, 1.1015625)
Orientation: ('R', 'A', 'S')
[[ 1.09920382e+00 -3.97272855e-02 1.33315139e-02 -1.00281090e+02]
[ 4.18310463e-02 1.05229211e+00 -3.23058039e-01 -5.07127228e+01]
[-1.08276482e-03 3.23331177e-01 1.05304122e+00 -2.41561737e+02]
[ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]
In [97]:
# T2w
# Apply transform
print("Registering T2w image...")
apply_transform(path_v12_t2w, path_v11_t2w, transform_path, path_v12_t2w_registered)
img_v12_t2w_registered = Nifti1Image.load(str(path_v12_t2w_registered))
print_givens(img_v12_t2w_registered, "V12 T2w registered")
print(img_v12_t2w_registered.affine)
# Plot the registration
plotting.plot_img(img_v11_t2w, cmap="gray", title="V11 T2w", cut_coords=(0, 0, 0)).add_overlay(
img_v12_t2w_registered, cmap="Accent", alpha=0.5
)
Registering T2w image...
Running command: antsApplyTransforms -d 3 -e 0 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_acq-Philips3T3DT2_T2w.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_acq-Philips3T3DT2_T2w.nii.gz -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_acq-Philips3T3DT2_T2w_registered.nii.gz -n LanczosWindowedSinc --float
Image: V12 T2w registered
Shape: (176, 256, 256)
Zooms: (1.1, 1.1015625, 1.1015625)
Orientation: ('R', 'A', 'S')
[[ 1.09920382e+00 -3.97272855e-02 1.33315139e-02 -8.26938095e+01]
[ 4.18310463e-02 1.05229211e+00 -3.23058039e-01 -5.00434113e+01]
[-1.08276482e-03 3.23331177e-01 1.05304122e+00 -2.41579071e+02]
[ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]
In [98]:
print("Registering BOLD image...")
apply_transform(path_v12_bold, path_v11_bold, transform_path, path_v12_bold_registered)
img_v12_bold_registered = Nifti1Image.load(str(path_v12_bold_registered))
# And finally, check whether the new V12 BOLD image is registered to the V11 BOLD image
plotting.plot_epi(img_v11_bold.slicer[..., 10], cmap="gray", title="V11 BOLD", cut_coords=(0, 0, 0)).add_overlay(
img_v12_bold_registered.slicer[..., 10], cmap="Accent", alpha=0.5
)
Registering BOLD image... Running command: antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold_registered.nii.gz -n LanczosWindowedSinc --float
In [99]:
# Would it work if we applied the transform to each volume of the BOLD image and then concatenated them?
from tempfile import TemporaryDirectory
from subprocess import run
from nilearn.image import concat_imgs, iter_img
with TemporaryDirectory() as temp_dir:
# Instead we will apply the transform to each volume of the BOLD image and then concatenate them
imgs = []
img: Nifti1Image
for ii, img in enumerate(iter_img(img_v12_bold)): # type: ignore
path_temp_img = Path(temp_dir) / f"v12_bold_registered_volume_{ii:03d}.nii.gz"
cmd = [
"antsApplyTransforms",
"-d",
"3",
"-e",
"3",
"-i",
str(path_v12_bold),
"-r",
str(path_v11_bold),
"--time-index",
str(ii),
"-t",
str(transform_path),
"-o",
str(path_temp_img),
]
print(" ".join(cmd))
proc = run(
cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
)
if proc.returncode != 0:
print(proc.stdout.decode())
print(proc.stderr.decode())
raise ValueError(f"Failed to register BOLD image volume {ii}")
imgs.append(Nifti1Image.load(str(path_temp_img)))
img_v12_bold_registered_concatenated = concat_imgs(imgs)
plotting.plot_epi(img_v11_bold.slicer[..., 10], cmap="gray", title="V11 BOLD", cut_coords=(0, 0, 0)).add_overlay(
img_v12_bold_registered_concatenated.slicer[..., 10], cmap="Accent", alpha=0.5
)
antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 0 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_000.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 1 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_001.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 2 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_002.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 3 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_003.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 4 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_004.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 5 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_005.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 6 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_006.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 7 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_007.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 8 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_008.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 9 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_009.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 10 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_010.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 11 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_011.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 12 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_012.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 13 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_013.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 14 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_014.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 15 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_015.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 16 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_016.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 17 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_017.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 18 -t /home/mpasternak/Documents/TEST/V12_to_V11.txt -o /tmp/tmpw_ozslsb/v12_bold_registered_volume_018.nii.gz antsApplyTransforms -d 3 -e 3 -i /home/mpasternak/Documents/TEST/V12/sub-GRN296_ses-V12_task-rest_acq-Philips3T_bold.nii.gz -r /home/mpasternak/Documents/TEST/V11/sub-GRN296_ses-V11_task-rest_acq-Philips3T_bold.nii.gz --time-index 19 -t 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