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SNAKE-fMRI Documentation - Home
  • SNAKE (f)MRI Simulator

User Guide

  • Getting Started
  • Extend SNAKE

Explanations

  • How does SNAKE work ?
  • MRD file for simulation

Examples

  • Notes
  • Generate a Phantom and visualize the contrast at different TE values
  • Single anatomical EPI with SNAKE-fMRI
  • Compare Fourier Model and T2* Model for EPI
  • Compare Fourier Model and T2* Model for Stack of Spirals trajectory

References

  • snake.core
    • snake.core.engine
      • snake.core.engine.base
        • BaseAcquisitionEngine
        • MetaEngine
      • snake.core.engine.cartesian
        • EPIAcquisitionEngine
        • EVIAcquisition
      • snake.core.engine.nufft
        • NufftAcquisitionEngine
      • snake.core.engine.utils
        • fft
        • get_contrast_gre
        • get_ideal_phantom
        • get_noise
        • get_phantom_state
    • snake.core.handlers
      • snake.core.handlers.activations
        • snake.core.handlers.activations.activations
        • snake.core.handlers.activations.bold
        • snake.core.handlers.activations.roi
      • snake.core.handlers.base
        • get_handler
        • list_handlers
        • AbstractHandler
        • HandlerList
        • MetaHandler
      • snake.core.handlers.motion
        • snake.core.handlers.motion.image
        • snake.core.handlers.motion.utils
      • snake.core.handlers.noise
        • apply_noise
        • NoiseHandler
      • snake.core.handlers.utils
        • apply_weights
    • snake.core.parallel
      • array_from_shm
      • array_to_shm
      • run_parallel
      • ArrayProps
      • SHM_Wrapper
    • snake.core.phantom
      • snake.core.phantom.data
      • snake.core.phantom.dynamic
        • DynamicData
        • KspaceDynamicData
      • snake.core.phantom.shepp_logan
        • idx_in_ellipse
        • mr_ellipsoid_parameters
        • mr_shepp_logan
      • snake.core.phantom.static
        • serialize_array
        • unserialize_array
        • Phantom
        • PropTissueEnum
        • TissueFile
      • snake.core.phantom.utils
        • resize_tissues
    • snake.core.sampling
      • snake.core.sampling.base
        • BaseSampler
        • MetaSampler
      • snake.core.sampling.factories
        • check_trajectory
        • evi_factory
        • flip2center
        • get_cartesian_mask
        • get_kspace_slice_loc
        • radial_factory
        • rotate_trajectory
        • stack_spiral_factory
        • stacked_epi2d
        • stacked_epi_factory
        • trajectory_generator
        • validate_rng
        • vds_factory
        • AngleRotation
        • VDSorder
        • VDSpdf
      • snake.core.sampling.samplers
        • dir_cos
        • EPI3dAcquisitionSampler
        • EVI3dAcquisitionSampler
        • LoadTrajectorySampler
        • NonCartesianAcquisitionSampler
        • StackOfSpiralSampler
    • snake.core.simulation
      • GreConfig
      • HardwareConfig
      • SimConfig
    • snake.core.smaps
      • get_smaps
  • snake.mrd_utils
    • snake.mrd_utils.loader
      • parse_sim_conf
      • parse_waveform_information
      • read_mrd_header
      • CartesianFrameDataLoader
      • MRDLoader
      • NonCartesianFrameDataLoader
    • snake.mrd_utils.utils
      • b64encode2obj
      • get_waveform_id
      • obj2b64encode
      • serialize_array
      • unserialize_array
      • ACQ
    • snake.mrd_utils.writer
      • add_coil_cov_mrd
      • add_dynamic_mrd
      • add_phantom_mrd
      • add_smaps_mrd
      • get_mrd_header
      • make_base_mrd
  • snake.toolkit
    • snake.toolkit.cli
      • snake.toolkit.cli.acquisition
        • acquisition
        • acquisition_cli
      • snake.toolkit.cli.config
        • cleanup_cuda
        • conf_validator
        • make_hydra_cli
        • snake_handler_resolver
        • snake_sampler_resolver
        • ConfigSNAKE
        • EngineConfig
        • PhantomConfig
        • StatConfig
      • snake.toolkit.cli.main
        • main
        • main_cli
      • snake.toolkit.cli.reconstruction
        • reconstruction
        • reconstruction_cli
    • snake.toolkit.plotting
      • axis3dcut
      • get_axis_properties
      • get_coolgraywarm
      • get_mask_cuts_mask
      • plot_frames_activ
    • snake.toolkit.reconstructors
      • snake.toolkit.reconstructors.base
        • get_reconstructor
        • list_reconstructors
        • BaseReconstructor
        • MetaReconstructor
      • snake.toolkit.reconstructors.fourier
        • fft
        • ifft
      • snake.toolkit.reconstructors.pysap
        • RestartStrategy
        • SequentialReconstructor
        • ZeroFilledReconstructor

Miscellaneous

  • Contributors
  • License
  • Developing SNAKE {#developing-snake}

Related Projects

  • MRI-NUFFT
  • PySAP
  • ModOpt
  • Brainweb-dl
  • Repository
  • Suggest edit
  • Open issue
  • .rst

snake.core

SNAKE-fMRI core package.

snake.mrd_utils

MRD file interfaces for SNAKE.

snake.toolkit

Toolkit for SNAKE.

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Compare Fourier Model and T2* Model for Stack of Spirals trajectory

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By SNAKE-fMRI Contributors

© Copyright 2022, SNAKE-fMRI Contributors.