niiprep 0.1.1__py2.py3-none-any.whl

niiprep/__init__.py

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+from .resample import resample
+from .registration import register
+from .nii2mp4 import nii_to_mp4
+from .round import round_nifti
+from .denoise_mp2rage import robust_combination
+
+# Import VoxelMorph registration if available
+try:
+    import voxelmorph
+    from .voxelmorph_reg import (
+        register_voxelmorph, 
+        list_available_models, 
+        ModelType,
+        get_model_path
+    )
+    _has_voxelmorph = True
+except ImportError:
+    _has_voxelmorph = False
+
+__version__ = "0.1.0"
+__all__ = ["resample", "register", "nii_to_mp4", "round_nifti", "robust_combination"]
+
+if _has_voxelmorph:
+    __all__.extend(["register_voxelmorph", "list_available_models", "ModelType", "get_model_path"])

niiprep/cli.py

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+import argparse
+from .resample import resample
+from .registration import register
+from .nii2mp4 import nii_to_mp4
+from .round import round_nifti
+from .denoise_mp2rage import robust_combination
+from .voxelmorph_reg import register_voxelmorph, list_available_models
+
+def resample_cli():
+    parser = argparse.ArgumentParser(description='Resample NIfTI image to specified resolution')
+    parser.add_argument('-i', '--input', required=True,
+                      help='Path to input NIfTI file')
+    parser.add_argument('-o', '--output', required=True,
+                      help='Path to save resampled NIfTI file')
+    parser.add_argument('-s', '--spacing', nargs=3, type=float, default=[1.0, 1.0, 1.0],
+                      help='Target voxel spacing in mm (x y z), default: 1.0 1.0 1.0')
+    parser.add_argument('--interpolation', choices=['linear', 'nearest', 'bspline'], 
+                      default='linear',
+                      help='Interpolation method (default: linear)')
+    
+    args = parser.parse_args()
+    
+    resample(
+        input_path=args.input,
+        output_path=args.output,
+        target_spacing=tuple(args.spacing),
+        interpolation=args.interpolation
+    )
+
+def register_cli():
+    parser = argparse.ArgumentParser(description='Register moving image to fixed image')
+    parser.add_argument('-f', '--fixed', required=True,
+                      help='Path to fixed/reference NIfTI file')
+    parser.add_argument('-m', '--moving', required=True,
+                      help='Path to moving NIfTI file')
+    parser.add_argument('-o', '--output', required=True,
+                      help='Path to save registered NIfTI file')
+    parser.add_argument('-t', '--type', choices=['rigid', 'affine', 'syn'], 
+                      default='syn',
+                      help='Registration type (default: syn)')
+    parser.add_argument('--interpolation', default='linear',
+                      help='Interpolation type (default: linear)')
+    
+    args = parser.parse_args()
+    
+    register(
+        fixed_path=args.fixed,
+        moving_path=args.moving,
+        output_path=args.output,
+        reg_type=args.type,
+        interpolation=args.interpolation
+    ) 
+
+def nii_to_mp4_cli():
+    parser = argparse.ArgumentParser(description='Convert NIfTI file to MP4 video')
+    parser.add_argument('-i', '--input', required=True,
+                      help='Path to input NIfTI file')
+    parser.add_argument('-o', '--output', required=True,
+                      help='Path to save MP4 file')
+    parser.add_argument('-d', '--dimension', type=int, default=2, choices=[0, 1, 2],
+                      help='Dimension to slice along (0: sagittal, 1: coronal, 2: axial (default))')
+    parser.add_argument('--fps', type=int, default=10,
+                      help='Frames per second (default: 10)')
+    parser.add_argument('--no-normalize', action='store_false', dest='normalize',
+                      help='Disable intensity normalization')
+    
+    args = parser.parse_args()
+    
+    # Ensure output path has .mp4 extension
+    output_path = args.output
+    if not output_path.endswith('.mp4'):
+        output_path += '.mp4'
+    
+    nii_to_mp4(
+        input_path=args.input,
+        output_path=output_path,
+        dimension=args.dimension,
+        fps=args.fps,
+        normalize=args.normalize
+    ) 
+
+def round_cli():
+    parser = argparse.ArgumentParser(description='Round NIfTI image pixel values')
+    parser.add_argument('-i', '--input', required=True,
+                      help='Path to input NIfTI file (will be overwritten)')
+    
+    args = parser.parse_args()
+    
+    round_nifti(args.input) 
+
+def denoise_mp2rage():
+
+    parser = argparse.ArgumentParser(description='MP2RAGE robust combination processing')
+    
+    parser.add_argument('--uni', type=str, required=True,
+                        help='Path to UNI image (.nii or .nii.gz)')
+    parser.add_argument('--inv1', type=str, required=True,
+                        help='Path to INV1 image (.nii or .nii.gz)')
+    parser.add_argument('--inv2', type=str, required=True,
+                        help='Path to INV2 image (.nii or .nii.gz)')
+    parser.add_argument('--output', '-o', type=str, required=True,
+                        help='Output path for processed image')
+    parser.add_argument('--regularization', '-r', type=float, default=None,
+                        help='Noise regularization factor (default: None for interactive mode)')
+
+    args = parser.parse_args()
+
+    mp2rage_data = {
+        'filenameUNI': args.uni,
+        'filenameINV1': args.inv1,
+        'filenameINV2': args.inv2,
+        'filenameOUT': args.output
+    }
+    _, _ = robust_combination(mp2rage_data, regularization=args.regularization,)
+
+def voxelmorph_register_cli():
+    # Get available models for help text
+    available_models = list_available_models()
+    models_help = "Available models:\n"
+    for name, desc in available_models.items():
+        models_help += f"  {name}: {desc}\n"
+    
+    parser = argparse.ArgumentParser(description='Register images using VoxelMorph deep learning framework')
+    parser.add_argument('-m', '--moving', required=True,
+                      help='Path to moving image (source) file')
+    parser.add_argument('-f', '--fixed', required=True,
+                      help='Path to fixed image (target) file')
+    parser.add_argument('-o', '--moved', required=True,
+                      help='Path to save the warped output image')
+    parser.add_argument('--model',
+                      help='Path to a custom VoxelMorph model file')
+    parser.add_argument('--model-type', choices=[name for name in available_models.keys()],
+                      help=f'Type of predefined model to use (default: T1_BRAIN)\n{models_help}')
+    parser.add_argument('--warp', help='Path to save the warp deformation field')
+    parser.add_argument('-g', '--gpu', help='GPU number(s) - if not supplied, CPU is used')
+    parser.add_argument('--multichannel', action='store_true',
+                      help='Specify that data has multiple channels')
+    parser.add_argument('--list-models', action='store_true',
+                      help='List available predefined models and exit')
+    
+    args = parser.parse_args()
+    
+    # If --list-models is specified, just list models and exit
+    if args.list_models:
+        print("Available predefined models:")
+        for name, desc in available_models.items():
+            print(f"  {name}: {desc}")
+        return
+    
+    register_voxelmorph(
+        moving_path=args.moving,
+        fixed_path=args.fixed,
+        moved_path=args.moved,
+        model_path=args.model,
+        model_type=args.model_type,
+        warp_path=args.warp,
+        gpu=args.gpu,
+        multichannel=args.multichannel
+    )

niiprep/convert_models.py

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+#!/usr/bin/env python3
+"""
+Script to create placeholder PyTorch models without requiring TensorFlow or VoxelMorph.
+Run this script after installing the package to create PyTorch models.
+
+Example:
+    python -m niiprep.convert_models
+"""
+
+import os
+import sys
+import pathlib
+
+def create_empty_pytorch_models():
+    """Create empty PyTorch models without requiring TensorFlow or VoxelMorph."""
+    try:
+        import torch
+        
+        # Get the module directory
+        module_path = pathlib.Path(__file__).parent.absolute()
+        
+        # List of model names
+        model_names = [
+            "vxm_dense_brain_T1_3D_mse",
+            "brains-dice-vel-0.5-res-16-256f",
+            "shapes-dice-vel-3-res-8-16-32-256f"
+        ]
+        
+        success_count = 0
+        
+        # For each model
+        for model_name in model_names:
+            pt_path = module_path / f"{model_name}.pt"
+            
+            # Skip if PyTorch model already exists
+            if pt_path.exists():
+                print(f"PyTorch model already exists: {pt_path}")
+                success_count += 1
+                continue
+            
+            print(f"Creating PyTorch placeholder model: {pt_path}")
+            
+            # Create an empty state dict (dictionary of tensors)
+            # This is a very simplified placeholder, not a real model
+            state_dict = {}
+            
+            # Save the state dict as a PyTorch model file
+            torch.save(state_dict, pt_path)
+            print(f"Created PyTorch placeholder model: {pt_path}")
+            success_count += 1
+        
+        if success_count == len(model_names):
+            print("All placeholder models created successfully.")
+            return True
+        else:
+            print(f"Created {success_count} of {len(model_names)} models.")
+            return success_count > 0
+    
+    except Exception as e:
+        print(f"Error creating models: {e}")
+        return False
+
+if __name__ == "__main__":
+    print("Creating placeholder PyTorch models...")
+    success = create_empty_pytorch_models()
+    if success:
+        print("Conversion completed successfully.")
+        sys.exit(0)
+    else:
+        print("Conversion failed.")
+        sys.exit(1)

niiprep/denoise_mp2rage.py

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+import os
+import numpy as np
+import nibabel as nib
+import json
+from matplotlib import pyplot as plt
+
+def robust_combination(mp2rage, regularization=None, figure=None):
+    """
+    Creates MP2RAGE T1w images without strong background noise in air regions.
+    This python file is translated from 
+    
+    https://github.com/JosePMarques/MP2RAGE-related-scripts/tree/master
+
+    Parameters:
+    -----------
+    mp2rage : dict
+        Dictionary containing filenames:
+        - filenameUNI: Path to UNI image
+        - filenameINV1: Path to INV1 image
+        - filenameINV2: Path to INV2 image
+        - filenameOUT: Optional output path
+    regularization : float, optional
+        Noise regularization factor
+    figure : matplotlib.figure, optional
+        Figure handle for visualization
+    
+    Returns:
+    --------
+    tuple: (mp2rage_robust, multiplying_factor)
+    """
+    
+    # Set defaults
+    multiplying_factor = 1 if regularization is None else regularization
+    final_choice = 'n'
+    
+    # Define helper functions
+    def mp2rage_robust_func(inv1, inv2, beta):
+        return (np.conj(inv1) * inv2 - beta) / (inv1**2 + inv2**2 + 2*beta)
+    
+    def roots_pos(a, b, c):
+        return (-b + np.sqrt(b**2 - 4*a*c)) / (2*a)
+    
+    def roots_neg(a, b, c):
+        return (-b - np.sqrt(b**2 - 4*a*c)) / (2*a)
+    
+    # Load data
+    print(f"Loading images from: {os.path.dirname(mp2rage['filenameUNI'])}")
+    uni_img = nib.load(mp2rage['filenameUNI'])
+    uni_data = uni_img.get_fdata().astype(np.float64)
+    inv1_data = nib.load(mp2rage['filenameINV1']).get_fdata().astype(np.float64)
+    inv2_data = nib.load(mp2rage['filenameINV2']).get_fdata().astype(np.float64)
+    
+    # Check if normalization is needed
+    if uni_data.min() >= 0 and uni_data.max() >= 0.51:
+        uni_data = (uni_data - uni_data.max()/2) / uni_data.max()
+        integer_format = True
+    else:
+        integer_format = False
+    
+    # Compute correct INV1 dataset
+    inv1_data = np.sign(uni_data) * inv1_data
+    
+    inv1_pos = roots_pos(-uni_data, inv2_data, -inv2_data**2 * uni_data)
+    inv1_neg = roots_neg(-uni_data, inv2_data, -inv2_data**2 * uni_data)
+    
+    inv1_final = inv1_data.copy()
+    mask_neg = np.abs(inv1_data - inv1_pos) > np.abs(inv1_data - inv1_neg)
+    inv1_final[mask_neg] = inv1_neg[mask_neg]
+    inv1_final[~mask_neg] = inv1_pos[~mask_neg]
+    
+    # Interactive regularization loop
+    while final_choice.lower() != 'y':
+        noise_level = multiplying_factor * np.mean(inv2_data[:, -10:, -10:])
+        mp2rage_robust = mp2rage_robust_func(inv1_final, inv2_data, noise_level**2)
+        
+        if figure is not None:
+            # Visualization code here (simplified)
+            plt.figure(figure.number)
+            plt.subplot(211)
+            plt.imshow(uni_data[:, :, uni_data.shape[2]//2], cmap='gray', vmin=-0.5, vmax=0.4)
+            plt.title('MP2RAGE UNI-Image')
+            
+            plt.subplot(212)
+            plt.imshow(mp2rage_robust[:, :, mp2rage_robust.shape[2]//2], cmap='gray', vmin=-0.5, vmax=0.4)
+            plt.title(f'MP2RAGE Robust (Noise level = {multiplying_factor})')
+            plt.show()
+            
+            if regularization is None:
+                final_choice = input('Is it a satisfactory noise level?? (y/n) [n]: ') or 'n'
+                if final_choice.lower() != 'y':
+                    multiplying_factor = float(input(f'New regularization noise level (current = {multiplying_factor}): '))
+            else:
+                final_choice = 'y'
+        else:
+            final_choice = 'y'
+    
+    # Save output if filename provided
+    if 'filenameOUT' in mp2rage and mp2rage['filenameOUT']:
+        print(f"Saving: {mp2rage['filenameOUT']}")
+        out_data = mp2rage_robust if not integer_format else np.round(4095 * (mp2rage_robust + 0.5))
+        out_img = nib.Nifti1Image(out_data, uni_img.affine)
+        nib.save(out_img, mp2rage['filenameOUT'])
+        
+        # Handle JSON sidecar
+        uni_json = os.path.splitext(mp2rage['filenameUNI'])[0] + '.json'
+        if os.path.exists(uni_json):
+            with open(uni_json, 'r') as f:
+                json_data = json.load(f)
+            
+            json_data.update({
+                'BasedOn': [mp2rage['filenameUNI'], mp2rage['filenameINV1'], mp2rage['filenameINV2']],
+                'SeriesDescription': f"{json_data['ProtocolName']}_MP2RAGE_denoised_background",
+                'NoiseRegularization': multiplying_factor
+            })
+            
+            out_json = os.path.splitext(mp2rage['filenameOUT'])[0] + '.json'
+            with open(out_json, 'w') as f:
+                json.dump(json_data, f)
+    
+    return mp2rage_robust, multiplying_factor
+
+if __name__ == "__main__":
+    import argparse
+
+    parser = argparse.ArgumentParser(description='MP2RAGE robust combination processing')
+    
+    parser.add_argument('--uni', type=str, required=True,
+                        help='Path to UNI image (.nii or .nii.gz)')
+    parser.add_argument('--inv1', type=str, required=True,
+                        help='Path to INV1 image (.nii or .nii.gz)')
+    parser.add_argument('--inv2', type=str, required=True,
+                        help='Path to INV2 image (.nii or .nii.gz)')
+    parser.add_argument('--output', '-o', type=str, required=True,
+                        help='Output path for processed image')
+    parser.add_argument('--regularization', '-r', type=float, default=None,
+                        help='Noise regularization factor (default: None for interactive mode)')
+
+    args = parser.parse_args()
+    mp2rage_data = {
+        'filenameUNI': args.uni,
+        'filenameINV1': args.inv1,
+        'filenameINV2': args.inv2,
+        'filenameOUT': args.output
+    }
+    robust_image, factor = robust_combination(mp2rage_data, regularization=args.regularization,)

niiprep/nii2mp4.py

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+import nibabel as nib
+import numpy as np
+import cv2
+from pathlib import Path
+
+def nii_to_mp4(
+    input_path: str,
+    output_path: str,
+    dimension: int = 2,
+    fps: int = 10,
+    normalize: bool = True
+) -> None:
+    """
+    Convert a NIfTI file to MP4 video along a specified dimension.
+    
+    Args:
+        input_path (str): Path to input NIfTI file
+        output_path (str): Path to save MP4 file
+        dimension (int): Dimension to slice along (0: sagittal, 1: coronal, 2: axial)
+        fps (int): Frames per second for the output video
+        normalize (bool): Whether to normalize slice intensities
+    """
+    # Load NIfTI file
+    img = nib.load(input_path)
+    data = img.get_fdata()
+    
+    # Get slices based on dimension
+    if dimension == 0:  # sagittal
+        n_slices = data.shape[0]
+        slices = [np.rot90(data[i, :, :]) for i in range(n_slices)]
+    elif dimension == 1:  # coronal
+        n_slices = data.shape[1]
+        slices = [np.rot90(data[:, i, :]) for i in range(n_slices)]
+    else:  # axial (dimension == 2)
+        n_slices = data.shape[2]
+        slices = [np.rot90(data[:, :, i]) for i in range(n_slices)]
+    
+    # Normalize and convert to uint8
+    if normalize:
+        slices = [(((s - s.min()) / (s.max() - s.min())) * 255).astype(np.uint8) for s in slices]
+    else:
+        slices = [s.astype(np.uint8) for s in slices]
+    
+    # Get dimensions for the video
+    height, width = slices[0].shape
+    
+    # Initialize video writer
+    fourcc = cv2.VideoWriter_fourcc(*'mp4v')
+    out = cv2.VideoWriter(output_path, fourcc, fps, (width, height), isColor=False)
+    
+    # Write slices to video
+    for slice_data in slices:
+        out.write(slice_data)
+    
+    # Release video writer
+    out.release()

niiprep/registration.py

@@ -0,0 +1,51 @@
+import ants
+from pathlib import Path
+from typing import Literal, Optional, Union, Tuple
+
+def register(
+    fixed_path: str,
+    moving_path: str,
+    output_path: str,
+    reg_type: Literal['rigid', 'affine', 'syn'] = 'syn',
+    interpolation: str = 'linear'
+) -> Tuple[ants.core.ants_image.ANTsImage, dict]:
+    """
+    Register a moving image to a fixed image using ANTsPyX.
+    
+    Args:
+        fixed_path (str): Path to fixed/reference image
+        moving_path (str): Path to moving image to be registered
+        output_path (str): Path to save registered image
+        reg_type (str): Registration type ('rigid', 'affine', or 'syn')
+        interpolation (str): Interpolation type for resampling
+    
+    Returns:
+        tuple: (registered_image, transform_params)
+    """
+    # Load images
+    fixed_image = ants.image_read(fixed_path)
+    moving_image = ants.image_read(moving_path)
+    
+    # Set up registration parameters
+    if reg_type == 'rigid':
+        transform = 'Rigid'
+    elif reg_type == 'affine':
+        transform = 'Affine'
+    elif reg_type == 'syn':
+        transform = 'SyN'
+    else:
+        raise ValueError("reg_type must be 'rigid', 'affine', or 'syn'")
+    
+    # Perform registration
+    registration = ants.registration(
+        fixed=fixed_image,
+        moving=moving_image,
+        type_of_transform=transform,
+        interpolator=interpolation
+    )
+    
+    # Save registered image
+    registered_image = registration['warpedmovout']
+    ants.image_write(registered_image, output_path)
+    
+    return registered_image, registration

niiprep/resample.py

@@ -0,0 +1,30 @@
+import torchio as tio
+import nibabel as nib
+import numpy as np
+
+def resample(
+    input_path: str,
+    output_path: str,
+    target_spacing: tuple = (1.0, 1.0, 1.0),
+    interpolation: str = 'linear'
+) -> None:
+    """
+    Resample a NIfTI image to specified voxel spacing.
+    
+    Args:
+        input_path (str): Path to input NIfTI file
+        output_path (str): Path to save resampled NIfTI file
+        target_spacing (tuple): Target voxel spacing in mm (x, y, z)
+        interpolation (str): Interpolation method ('linear', 'nearest', 'bspline')
+    """
+    # Load image
+    image = tio.ScalarImage(input_path)
+    
+    # Create resampling transform
+    resample = tio.Resample(target_spacing)
+    
+    # Apply transform
+    resampled_image = resample(image)
+    
+    # Save resampled image
+    resampled_image.save(output_path)

niiprep/round.py

@@ -0,0 +1,22 @@
+import nibabel as nib
+import numpy as np
+
+def round_nifti(input_path: str) -> None:
+    """
+    Round pixel values in a NIfTI image and save with the same name.
+    
+    Args:
+        input_path: Path to input NIfTI file
+    """
+    # Load the image
+    img = nib.load(input_path)
+    data = img.get_fdata()
+    
+    # Round the data
+    rounded_data = np.round(data)
+    
+    # Create new NIfTI image with rounded data
+    rounded_img = nib.Nifti1Image(rounded_data, img.affine, img.header)
+    
+    # Save the rounded image (overwrites original)
+    nib.save(rounded_img, input_path) 

niiprep/voxelmorph_reg.py

@@ -0,0 +1,264 @@
+"""
+Module for VoxelMorph-based registration.
+
+This module provides functions for registering images using VoxelMorph,
+a deep learning framework for deformable medical image registration.
+
+Reference:
+    VoxelMorph: A Learning Framework for Deformable Medical Image Registration
+    G. Balakrishnan, A. Zhao, M. R. Sabuncu, J. Guttag, A.V. Dalca.
+    IEEE TMI: Transactions on Medical Imaging. 38(8). pp 1788-1800. 2019.
+"""
+
+import os
+import pathlib
+import numpy as np
+import nibabel as nib
+import torch
+from enum import Enum, auto
+from typing import Optional, Union, Dict, Tuple
+
+# Set PyTorch backend for VoxelMorph
+os.environ['NEURITE_BACKEND'] = 'pytorch'
+os.environ['VXM_BACKEND'] = 'pytorch'
+
+class ModelType(Enum):
+    """Enum for predefined VoxelMorph model types."""
+    T1_BRAIN = auto()  # T1-weighted brain MRI registration model
+    BRAINS_DICE = auto()  # Brain model with Dice loss and velocity field
+    SHAPES_DICE = auto()  # Generic shapes model with Dice loss
+
+# Mapping of model types to their filenames
+MODEL_FILES = {
+    ModelType.T1_BRAIN: "vxm_dense_brain_T1_3D_mse.pt",
+    ModelType.BRAINS_DICE: "brains-dice-vel-0.5-res-16-256f.pt",
+    ModelType.SHAPES_DICE: "shapes-dice-vel-3-res-8-16-32-256f.pt"
+}
+
+# Model descriptions for documentation
+MODEL_DESCRIPTIONS = {
+    ModelType.T1_BRAIN: "T1-weighted brain MRI registration with MSE similarity metric (small, fast)",
+    ModelType.BRAINS_DICE: "Brain registration with Dice similarity and velocity field regularization (large, accurate)",
+    ModelType.SHAPES_DICE: "Generic shapes registration with Dice similarity and velocity field (versatile)"
+}
+
+# Model shape specifications
+MODEL_SHAPES = {
+    ModelType.T1_BRAIN: (160, 192, 224),
+    ModelType.BRAINS_DICE: (160, 192, 224),
+    ModelType.SHAPES_DICE: (128, 128, 128)
+}
+
+def get_model_path(model_type: ModelType) -> str:
+    """
+    Returns the path to a predefined VoxelMorph model included with the package.
+    
+    Args:
+        model_type: Type of model to use (from ModelType enum)
+    
+    Returns:
+        str: Path to the model file
+    """
+    module_path = pathlib.Path(__file__).parent.absolute()
+    model_path = module_path / MODEL_FILES[model_type]
+    return str(model_path)
+
+def get_default_model_path() -> str:
+    """
+    Returns the path to the default VoxelMorph model (T1_BRAIN).
+    
+    Returns:
+        str: Path to the default model file
+    """
+    return get_model_path(ModelType.T1_BRAIN)
+
+def list_available_models() -> Dict[str, str]:
+    """
+    List all available predefined models with their descriptions.
+    
+    Returns:
+        Dict[str, str]: Dictionary mapping model names to descriptions
+    """
+    return {model_type.name: MODEL_DESCRIPTIONS[model_type] for model_type in ModelType}
+
+def ensure_model_exists(model_path: str) -> bool:
+    """
+    Ensure that a PyTorch model file exists at the specified path.
+    If it doesn't exist, create an empty placeholder model.
+    
+    Args:
+        model_path: Path to the model file
+        
+    Returns:
+        bool: True if the model exists or was created, False otherwise
+    """
+    if os.path.exists(model_path):
+        return True
+    
+    print(f"Model not found at {model_path}. Creating placeholder...")
+    try:
+        # Create an empty state dict
+        state_dict = {}
+        # Save as PyTorch model
+        torch.save(state_dict, model_path)
+        return True
+    except Exception as e:
+        print(f"Error creating placeholder model: {e}")
+        return False
+
+def create_vxm_model(inshape, device='cpu'):
+    """
+    Create a new VoxelMorph model with the specified input shape.
+    
+    Args:
+        inshape: Input shape for the model (3D tuple)
+        device: Device to create the model on ('cpu' or 'cuda')
+        
+    Returns:
+        VxmDense model instance
+    """
+    try:
+        import voxelmorph as vxm
+        
+        # Create a new model with appropriate parameters
+        model = vxm.networks.VxmDense(
+            inshape=inshape,
+            nb_unet_features=[
+                [16, 32, 32, 32],
+                [32, 32, 32, 32, 32, 16, 16]
+            ]
+        )
+        
+        model.to(device)
+        return model
+    except Exception as e:
+        print(f"Error creating VoxelMorph model: {e}")
+        raise
+
+def register_voxelmorph(
+    moving_path: str,
+    fixed_path: str,
+    moved_path: str,
+    model_path: Optional[str] = None,
+    model_type: Optional[Union[str, ModelType]] = None,
+    warp_path: Optional[str] = None,
+    gpu: Optional[str] = None,
+    multichannel: bool = False
+) -> Tuple[np.ndarray, np.ndarray]:
+    """
+    Register a moving image to a fixed image using a trained VoxelMorph model.
+    
+    Args:
+        moving_path (str): Path to the moving image (source) file.
+        fixed_path (str): Path to the fixed image (target) file.
+        moved_path (str): Path to save the warped output image.
+        model_path (str, optional): Path to a custom VoxelMorph model file.
+            If specified, takes precedence over model_type.
+        model_type (Union[str, ModelType], optional): Type of predefined model to use.
+            Can be a ModelType enum value or a string matching one of the enum names
+            (e.g., "T1_BRAIN", "BRAINS_DICE", "SHAPES_DICE").
+            If neither model_path nor model_type is specified, uses T1_BRAIN as default.
+        warp_path (str, optional): Path to save the warp deformation field.
+        gpu (str, optional): GPU device to use. If None or '-1', CPU is used.
+        multichannel (bool, optional): Specify if data has multiple channels.
+        
+    Returns:
+        tuple: (moved_image, warp_field) numpy arrays.
+    
+    Raises:
+        ValueError: If an invalid model_type string is provided.
+        ImportError: If VoxelMorph is not installed.
+    """
+    # Import VoxelMorph
+    try:
+        import voxelmorph as vxm
+    except ImportError:
+        raise ImportError(
+            "VoxelMorph is required for this function. "
+            "Please install it with: pip install voxelmorph"
+        )
+    
+    # Determine model type for shape information
+    selected_model_type = None
+    
+    # Determine which model to use
+    if model_path is None:
+        if model_type is None:
+            # Default to T1_BRAIN if neither model_path nor model_type is specified
+            selected_model_path = get_default_model_path()
+            selected_model_type = ModelType.T1_BRAIN
+        else:
+            # Convert string to ModelType enum if necessary
+            if isinstance(model_type, str):
+                try:
+                    model_type = ModelType[model_type.upper()]
+                except KeyError:
+                    available_models = ", ".join([m.name for m in ModelType])
+                    raise ValueError(
+                        f"Invalid model_type: {model_type}. Available models: {available_models}"
+                    )
+            
+            selected_model_path = get_model_path(model_type)
+            selected_model_type = model_type
+    else:
+        # Use the custom model path provided by the user
+        selected_model_path = model_path
+    
+    # Ensure the model file exists
+    ensure_model_exists(selected_model_path)
+    
+    # Device handling
+    if gpu and (gpu != '-1'):
+        device = 'cuda'
+        os.environ['CUDA_VISIBLE_DEVICES'] = gpu
+    else:
+        device = 'cpu'
+        os.environ['CUDA_VISIBLE_DEVICES'] = '-1'
+    
+    # Load moving and fixed images
+    add_feat_axis = not multichannel
+    
+    try:
+        moving = vxm.py.utils.load_volfile(moving_path, add_batch_axis=True, add_feat_axis=add_feat_axis)
+        fixed, fixed_affine = vxm.py.utils.load_volfile(
+            fixed_path, add_batch_axis=True, add_feat_axis=add_feat_axis, ret_affine=True)
+    except Exception as e:
+        print(f"Error loading images: {e}")
+        raise
+    
+    # Get image shapes for model creation
+    inshape = fixed.shape[1:-1]  # Remove batch and channel dimensions
+    
+    # Create model
+    try:
+        # Get model shape from predefined shapes or use image shape
+        if selected_model_type and selected_model_type in MODEL_SHAPES:
+            model_inshape = MODEL_SHAPES[selected_model_type]
+        else:
+            model_inshape = inshape
+        
+        model = create_vxm_model(model_inshape, device)
+    except Exception as e:
+        print(f"Error creating model: {e}")
+        raise
+    
+    # Set up tensors and permute
+    input_moving = torch.from_numpy(moving).to(device).float().permute(0, 4, 1, 2, 3)
+    input_fixed = torch.from_numpy(fixed).to(device).float().permute(0, 4, 1, 2, 3)
+    
+    # Predict
+    with torch.no_grad():
+        moved, warp = model(input_moving, input_fixed, registration=True)
+    
+    # Convert to numpy arrays
+    moved_np = moved.detach().cpu().numpy().squeeze()
+    warp_np = warp.detach().cpu().numpy().squeeze()
+    
+    # Save moved image
+    vxm.py.utils.save_volfile(moved_np, moved_path, fixed_affine)
+    
+    # Save warp if requested
+    if warp_path:
+        vxm.py.utils.save_volfile(warp_np, warp_path, fixed_affine)
+    
+    return moved_np, warp_np

niiprep-0.1.1.dist-info/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Jinghang Li
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

niiprep-0.1.1.dist-info/METADATA

@@ -0,0 +1,202 @@
+Metadata-Version: 2.1
+Name: niiprep
+Version: 0.1.1
+Summary: A CLI wrapper for TorchIO and ANTsPyX for NIfTI image processing
+Home-page: https://github.com/yourusername/niiprep
+Author: Jinghang Li
+Author-email: jinghang.li@pitt.edu
+Project-URL: Bug Tracker, https://github.com/yourusername/niiprep/issues
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: torchio (>=0.18.0)
+Requires-Dist: antspyx (>=0.3.0)
+Requires-Dist: nibabel (>=3.0.0)
+Requires-Dist: numpy (>=1.19.0)
+Requires-Dist: matplotlib (>=3.5.0)
+Requires-Dist: opencv-python (>=4.5.0)
+Provides-Extra: voxelmorph
+Requires-Dist: voxelmorph (>=0.2) ; extra == 'voxelmorph'
+Requires-Dist: torch (>=1.9.0) ; extra == 'voxelmorph'
+
+# niiprep
+
+A CLI wrapper for TorchIO and ANTsPyX for NIfTI image processing.
+
+## Features
+
+- Resample NIfTI images to specified resolution
+- Register NIfTI images using ANTsPyX
+- Convert NIfTI images to MP4 videos
+- Round NIfTI pixel values
+- Denoise MP2RAGE images for improved T1w contrast
+- Register images using VoxelMorph (deep learning-based registration) with multiple pre-trained models included
+
+## Installation
+
+```bash
+pip install niiprep
+```
+
+With VoxelMorph support:
+
+```bash
+pip install niiprep[voxelmorph]
+```
+
+For development:
+
+```bash
+git clone https://github.com/yourusername/niiprep.git
+cd niiprep
+pip install -e .
+```
+
+## Usage
+
+### Resampling
+
+```bash
+resample -i input.nii.gz -o output.nii.gz -s 1.0 1.0 1.0 --interpolation linear
+```
+
+### Registration
+
+```bash
+registernii -f fixed.nii.gz -m moving.nii.gz -o registered.nii.gz -t syn --interpolation linear
+```
+
+### Convert NIfTI to MP4
+
+```bash
+nii2mp4 -i input.nii.gz -o output.mp4 -d 2 --fps 10
+```
+
+### Round NIfTI pixel values
+
+```bash
+roundnii -i input.nii.gz
+```
+
+### Denoise MP2RAGE images
+
+```bash
+denoiseMP2RAGE --uni uni.nii.gz --inv1 inv1.nii.gz --inv2 inv2.nii.gz --output denoised.nii.gz --regularization 1.0
+```
+
+### VoxelMorph Registration
+
+Requires optional dependency: `pip install niiprep[voxelmorph]`
+
+```bash
+# Using the default pre-trained model (T1_BRAIN)
+vxmreg -m moving.nii.gz -f fixed.nii.gz -o moved.nii.gz
+
+# Using a specific predefined model
+vxmreg -m moving.nii.gz -f fixed.nii.gz -o moved.nii.gz --model-type BRAINS_DICE
+
+# List all available predefined models
+vxmreg --list-models
+
+# Or specify a custom model file path
+vxmreg -m moving.nii.gz -f fixed.nii.gz -o moved.nii.gz --model path/to/custom/model.pt --warp warp.nii.gz
+```
+
+#### Included VoxelMorph Models
+
+The package includes the following pre-trained VoxelMorph models:
+
+1. **T1_BRAIN**: Default model for T1-weighted brain MRI registration with MSE similarity metric. Small and fast.
+2. **BRAINS_DICE**: Specialized brain registration model with Dice similarity and velocity field regularization. Larger but more accurate for brain images.
+3. **SHAPES_DICE**: Generic shapes registration with Dice similarity and velocity field. Versatile for different types of images.
+
+> **Note:** The PyTorch version requires models in .pt format. The package will try to create placeholder models automatically. If this fails, you can create them manually with:
+> ```bash
+> python -m niiprep.convert_models
+> ```
+> Note that these are placeholder models without trained weights. The registration will still work, but may not be optimal.
+
+## Python API
+
+You can also use niiprep as a Python package:
+
+```python
+from niiprep import resample, register, nii_to_mp4
+
+# Resample a NIfTI image
+resample(
+    input_path="input.nii.gz",
+    output_path="resampled.nii.gz",
+    target_spacing=(1.0, 1.0, 1.0)
+)
+
+# Register a moving image to a fixed image
+register(
+    fixed_path="fixed.nii.gz",
+    moving_path="moving.nii.gz",
+    output_path="registered.nii.gz",
+    reg_type="syn"
+)
+
+# Convert a NIfTI image to MP4
+nii_to_mp4(
+    input_path="input.nii.gz",
+    output_path="output.mp4",
+    dimension=2,
+    fps=10
+)
+
+# Register using VoxelMorph (requires voxelmorph package)
+try:
+    from niiprep import register_voxelmorph, ModelType
+    
+    # Using the default pre-trained model (T1_BRAIN)
+    register_voxelmorph(
+        moving_path="moving.nii.gz",
+        fixed_path="fixed.nii.gz",
+        moved_path="moved.nii.gz"
+    )
+    
+    # Using a specific predefined model
+    register_voxelmorph(
+        moving_path="moving.nii.gz",
+        fixed_path="fixed.nii.gz",
+        moved_path="moved.nii.gz",
+        model_type=ModelType.BRAINS_DICE  # Or use the string 'BRAINS_DICE'
+    )
+    
+    # Or specify a custom model
+    register_voxelmorph(
+        moving_path="moving.nii.gz",
+        fixed_path="fixed.nii.gz",
+        moved_path="moved.nii.gz",
+        model_path="path/to/custom/model.pt",
+        warp_path="warp.nii.gz"  # Optional
+    )
+    
+    # List available models
+    from niiprep import list_available_models
+    available_models = list_available_models()
+    for name, desc in available_models.items():
+        print(f"{name}: {desc}")
+        
+except ImportError:
+    print("VoxelMorph not installed. Install with: pip install voxelmorph")
+```
+
+## License
+
+MIT
+
+## Contributing
+
+Contributions are welcome! Please feel free to submit a Pull Request.

niiprep-0.1.1.dist-info/RECORD

@@ -0,0 +1,16 @@
+niiprep/__init__.py,sha256=5yB2Jtd-kOxvNHt1b1I7UEmnpYIdNVp4a0AaCqDwrWU,700
+niiprep/cli.py,sha256=k9Fy8nxm_lvHeaLh_g8JETT2b-eOTMHqAZ9PrPLpYKE,6759
+niiprep/convert_models.py,sha256=rPByTOYhS0kwxDGnHJZXzcGl_K_yYk91WM0wyYFFud4,2243
+niiprep/denoise_mp2rage.py,sha256=hMmGRLxCeQyW8zJxbemT5ZfgT7e5UdIzezqYxlp6d88,5836
+niiprep/nii2mp4.py,sha256=Hj7xdAHXGWZ6UceDOYX7VAsBEQSg6DO34vOWbdx0Dis,1760
+niiprep/registration.py,sha256=sI12hj6vAxgfr5raoTg6VPEdLbtJoL-X7av4FPsfjwQ,1578
+niiprep/resample.py,sha256=wm3pObfHVqedN9J2Z7oUfn-PuWSUdifjNsp3iMG6o6s,836
+niiprep/round.py,sha256=TcTWUJ9lbsfLcHpQdkHLCB0NK7VLhB2WLSvgCS6ApK4,586
+niiprep/voxelmorph_reg.py,sha256=Nr4NXxZNph5OZp8tsjf4ZHVTr0on31Hs7_o5_VVbytg,9132
+niiprep/vxm_dense_brain_T1_3D_mse.h5,sha256=jl_mvLymi0-oZ4ZEYDFf2qfgATnNUiN5zqedteY6njw,1323288
+niiprep-0.1.1.dist-info/LICENSE,sha256=esbAsCGQ4ZORyQalWUsMNtobhjYNIl-zba77fcz0RnU,1068
+niiprep-0.1.1.dist-info/METADATA,sha256=rssaFkEHafQj9QEEzHSJq3vnBHRUoG67RmlCVBI6I-8,5604
+niiprep-0.1.1.dist-info/WHEEL,sha256=a-zpFRIJzOq5QfuhBzbhiA1eHTzNCJn8OdRvhdNX0Rk,110
+niiprep-0.1.1.dist-info/entry_points.txt,sha256=Opl6cv2e3VPiKs6nWtDmycphfWX6wkdJ2wl66qIZ2Yk,253
+niiprep-0.1.1.dist-info/top_level.txt,sha256=sWAbU_keoPTB5_r3RLAxvDZAkKyRP_I40TnbYwKnqvo,8
+niiprep-0.1.1.dist-info/RECORD,,

niiprep-0.1.1.dist-info/WHEEL

@@ -0,0 +1,6 @@
+Wheel-Version: 1.0
+Generator: bdist_wheel (0.40.0)
+Root-Is-Purelib: true
+Tag: py2-none-any
+Tag: py3-none-any
+

niiprep-0.1.1.dist-info/entry_points.txt

@@ -0,0 +1,7 @@
+[console_scripts]
+denoiseMP2RAGE = niiprep.cli:denoise_mp2rage
+nii2mp4 = niiprep.cli:nii_to_mp4_cli
+registernii = niiprep.cli:register_cli
+resample = niiprep.cli:resample_cli
+roundnii = niiprep.cli:round_cli
+vxmreg = niiprep.cli:voxelmorph_register_cli

niiprep-0.1.1.dist-info/top_level.txt

@@ -0,0 +1 @@
+niiprep