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FastSurfer
FastSurfer
  • User Guide
    • Introduction to FastSurfer
    • Quick Start
    • Installation
    • Examples
    • FastSurfer Flags
    • Output files
    • Modules
      • Corpus Callosum Pipeline
    • Docker Support
    • Singularity Support
    • Running FastSurfer as MacOS package
    • Manual Edits
    • Longitudinal Processing
    • Security Policy
    • FastSurfer License
  • Scripts
    • LONG: long_fastsurfer.sh
    • BATCH: brun_fastsurfer.sh
    • SLURM: srun_fastsurfer.sh
    • Advanced scripts
      • FastSurferCNN: run_prediction.py
      • CerebNet: run_prediction.py
      • HypVINN: run_prediction.py
      • CorpusCallosum: fastsurfer_cc.py
      • CorpusCallosum: cc_visualization.py
      • Surface pipeline: recon-surf.sh
      • FastSurferCNN: segstats.py
      • recon_surf: long_compat_segmentHA.py
    • FastSurfer Utilities
      • FastSurferCNN: download_checkpoints.py
      • FastSurferCNN: generate_hdf5.py
      • FastSurferCNN: run_model.py
  • Contributor Guide
    • git hook setup / CD
    • Code of Conduct
    • Contribution Guide
  • 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.lta
      • FastSurferCNN.utils.mapper
      • FastSurferCNN.utils.meters
      • FastSurferCNN.utils.metrics
      • FastSurferCNN.utils.misc
      • FastSurferCNN.utils.parallel
      • FastSurferCNN.utils.parser_defaults
      • FastSurferCNN.utils.run_tools
    • 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.misc
    • CorpusCallosum
      • CorpusCallosum.fastsurfer_cc
      • CorpusCallosum.cc_visualization
      • CorpusCallosum.paint_cc_into_pred
    • CorpusCallosum.data
      • CorpusCallosum.data.constants
      • CorpusCallosum.data.fsaverage_cc_template
      • CorpusCallosum.data.read_write
    • CorpusCallosum.localization
      • CorpusCallosum.localization.inference
    • CorpusCallosum.segmentation
      • CorpusCallosum.segmentation.inference
      • CorpusCallosum.segmentation.segmentation_postprocessing
    • CorpusCallosum.shape
      • CorpusCallosum.shape.postprocessing
      • CorpusCallosum.shape.mesh
      • CorpusCallosum.shape.metrics
      • CorpusCallosum.shape.thickness
      • CorpusCallosum.shape.subsegment_contour
      • CorpusCallosum.shape.endpoint_heuristic
      • CorpusCallosum.shape.contour
    • CorpusCallosum.transforms
      • CorpusCallosum.transforms.localization
      • CorpusCallosum.transforms.segmentation
    • CorpusCallosum.utils
      • CorpusCallosum.utils.checkpoint
      • CorpusCallosum.utils.mapping_helpers
      • CorpusCallosum.utils.types
      • CorpusCallosum.utils.visualization
    • 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.map_surf_label
      • recon_surf.N4_bias_correct
      • 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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Advanced scriptsΒΆ

  • FastSurferCNN: run_prediction.py
  • CerebNet: run_prediction.py
  • HypVINN: run_prediction.py
  • CorpusCallosum: fastsurfer_cc.py
  • CorpusCallosum: cc_visualization.py
  • Surface pipeline: recon-surf.sh
  • FastSurferCNN: segstats.py
  • recon_surf: long_compat_segmentHA.py
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FastSurferCNN: run_prediction.py
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SLURM: srun_fastsurfer.sh
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