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FastSurfer
FastSurfer
  • User Guide
    • Introduction to FastSurfer
    • Quick Start
    • Installation
    • Examples
    • FastSurfer Flags
    • Output files
    • Docker Support
    • Singularity Support
    • Manual Edits
    • Longitudinal Processing
    • Security Policy
    • Contributor Covenant Code of Conduct
    • Contributing to FastSurfer
    • FastSurfer License
  • Scripts
    • BATCH: brun_fastsurfer.sh
    • SLURM: srun_fastsurfer.sh
    • Advanced scripts
      • FastSurferCNN: run_prediction.py
      • CerebNet: run_prediction.py
      • HypVINN: run_prediction.py
      • Surface pipeline: recon-surf.sh
      • FastSurferCNN: segstats.py
    • FastSurfer Utilities
      • FastSurferCNN: download_checkpoints.py
      • FastSurferCNN: generate_hdf5.py
      • FastSurferCNN: run_model.py
  • FastSurfer API
    • FastSurferCNN
      • FastSurferCNN.download_checkpoints
      • FastSurferCNN.generate_hdf5
      • FastSurferCNN.inference
      • FastSurferCNN.quick_qc
      • FastSurferCNN.reduce_to_aseg
      • FastSurferCNN.run_prediction
      • FastSurferCNN.segstats
      • FastSurferCNN.version
    • FastSurferCNN.data_loader
      • FastSurferCNN.data_loader.augmentation
      • FastSurferCNN.data_loader.conform
      • FastSurferCNN.data_loader.data_utils
      • FastSurferCNN.data_loader.dataset
      • FastSurferCNN.data_loader.loader
    • FastSurferCNN.models
      • FastSurferCNN.models.interpolation_layer
      • FastSurferCNN.models.losses
      • FastSurferCNN.models.networks
      • FastSurferCNN.models.sub_module
    • FastSurferCNN.utils
      • FastSurferCNN.utils.arg_types
      • FastSurferCNN.utils.checkpoint
      • FastSurferCNN.utils.common
      • FastSurferCNN.utils.load_config
      • FastSurferCNN.utils.logging
      • FastSurferCNN.utils.lr_scheduler
      • FastSurferCNN.utils.mapper
      • FastSurferCNN.utils.meters
      • FastSurferCNN.utils.metrics
      • FastSurferCNN.utils.misc
      • FastSurferCNN.utils.parser_defaults
      • FastSurferCNN.utils.run_tools
      • FastSurferCNN.utils.threads
    • CerebNet
      • CerebNet.apply_warp
      • CerebNet.inference
      • CerebNet.run_prediction
    • CerebNet.dataloader
      • CerebNet.data_loader.augmentation
      • CerebNet.data_loader.data_utils
      • CerebNet.data_loader.dataset
      • CerebNet.data_loader.loader
    • CerebNet.datasets
      • CerebNet.datasets.generate_hdf5
      • CerebNet.datasets.load_data
      • CerebNet.datasets.utils
      • CerebNet.datasets.wm_merge_clean
    • CerebNet_models
      • CerebNet.models.networks
      • CerebNet.models.sub_module
    • CerebNet.utils
      • CerebNet.utils.checkpoint
      • CerebNet.utils.load_config
      • CerebNet.utils.lr_scheduler
      • CerebNet.utils.meters
      • CerebNet.utils.metrics
      • CerebNet.utils.misc
    • HypVINN
      • HypVINN.inference
      • HypVINN.run_prediction
    • HypVINN.data_loader
      • HypVINN.data_loader.data_utils
      • HypVINN.data_loader.dataset
    • HypVINN.models
      • HypVINN.models.networks
    • HypVINN.utils
    • recon_surf
      • recon_surf.align_points
      • recon_surf.align_seg
      • recon_surf.create_annotation
      • recon_surf.fs_balabels
      • recon_surf.lta
      • recon_surf.map_surf_label
      • recon_surf.N4_bias_correct
      • recon_surf.paint_cc_into_pred
      • recon_surf.rewrite_oriented_surface
      • recon_surf.rewrite_mc_surface
      • recon_surf.rotate_sphere
      • recon_surf.sample_parc
      • recon_surf.smooth_aparc
      • recon_surf.spherically_project_wrapper
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ScriptsΒΆ

  • BATCH: brun_fastsurfer.sh
    • Usage
    • Subject Lists
    • Parallelization with brun_fastsurfer.sh
    • Questions
  • SLURM: srun_fastsurfer.sh
    • Usage
    • Debugging SLURM runs
  • Advanced scripts
    • FastSurferCNN: run_prediction.py
    • CerebNet: run_prediction.py
    • HypVINN: run_prediction.py
    • Surface pipeline: recon-surf.sh
    • FastSurferCNN: segstats.py
  • FastSurfer Utilities
    • FastSurferCNN: download_checkpoints.py
    • FastSurferCNN: generate_hdf5.py
    • FastSurferCNN: run_model.py
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