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BrainDeer 2.0.0a1 — Developer Docs
BrainDeer 2.0.0a1 — Developer Docs

Foundations

  • Architecture overview
  • Contributing

Extending

  • Plugin development
  • Subsystems in detail
    • Warp engine (warp/)
    • Rendering (rendering/)
    • Infrastructure: I/O & BIDS

Reference

  • API map by layer

Project

  • Architecture decision records (ADRs)
  • API Reference
    • brain_deer
      • brain_deer.app
        • brain_deer.app.cli
        • brain_deer.app.launch
        • brain_deer.app.startup
      • brain_deer.application
        • brain_deer.application.brain_deer_api
        • brain_deer.application.ports
          • brain_deer.application.ports.viewer
      • brain_deer.commands
        • brain_deer.commands.advisor
        • brain_deer.commands.analysis
        • brain_deer.commands.atlas_browser
        • brain_deer.commands.blender
        • brain_deer.commands.definitions
        • brain_deer.commands.leaddbs
        • brain_deer.commands.montage
        • brain_deer.commands.nl_intent
        • brain_deer.commands.preferences
        • brain_deer.commands.registry
        • brain_deer.commands.session
        • brain_deer.commands.warpdrive
      • brain_deer.domain
      • brain_deer.export
        • brain_deer.export.screenshot_export
      • brain_deer.infrastructure
        • brain_deer.infrastructure.bids
          • brain_deer.infrastructure.bids.datalad
          • brain_deer.infrastructure.bids.derivatives
          • brain_deer.infrastructure.bids.entities
          • brain_deer.infrastructure.bids.import_convert
          • brain_deer.infrastructure.bids.integrations
          • brain_deer.infrastructure.bids.layout
          • brain_deer.infrastructure.bids.loader
          • brain_deer.infrastructure.bids.mapper
          • brain_deer.infrastructure.bids.qc_batch
          • brain_deer.infrastructure.bids.rawimages
          • brain_deer.infrastructure.bids.session
          • brain_deer.infrastructure.bids.sidecar
          • brain_deer.infrastructure.bids.subject_switch
          • brain_deer.infrastructure.bids.swap
          • brain_deer.infrastructure.bids.tractometry
          • brain_deer.infrastructure.bids.validate
        • brain_deer.infrastructure.io
          • brain_deer.infrastructure.io.dicom
          • brain_deer.infrastructure.io.mesh
          • brain_deer.infrastructure.io.nifti
          • brain_deer.infrastructure.io.volume_proxy
        • brain_deer.infrastructure.orientation
      • brain_deer.plugin_api
        • brain_deer.plugin_api.v1
      • brain_deer.plugins
        • brain_deer.plugins.braindeer_ai
          • brain_deer.plugins.braindeer_ai.agent
          • brain_deer.plugins.braindeer_ai.dev_context
          • brain_deer.plugins.braindeer_ai.plugin
          • brain_deer.plugins.braindeer_ai.prompts
          • brain_deer.plugins.braindeer_ai.scaffold
        • brain_deer.plugins.laminosaurus
          • brain_deer.plugins.laminosaurus.analysis
          • brain_deer.plugins.laminosaurus.plugin
          • brain_deer.plugins.laminosaurus.widget
        • brain_deer.plugins.leaddbs_atlas_widget
        • brain_deer.plugins.leaddbs_space_paths
        • brain_deer.plugins.leaddbs_stimulation_manager
          • brain_deer.plugins.leaddbs_stimulation_manager.plugin
          • brain_deer.plugins.leaddbs_stimulation_manager.widget
        • brain_deer.plugins.roi_studio
          • brain_deer.plugins.roi_studio.plugin
          • brain_deer.plugins.roi_studio.widget
        • brain_deer.plugins.vr_stream
          • brain_deer.plugins.vr_stream.plugin
        • brain_deer.plugins.warpdrive
          • brain_deer.plugins.warpdrive.geometry
          • brain_deer.plugins.warpdrive.overlay2d
          • brain_deer.plugins.warpdrive.overlay3d
          • brain_deer.plugins.warpdrive.plugin
          • brain_deer.plugins.warpdrive.snap
          • brain_deer.plugins.warpdrive.style
          • brain_deer.plugins.warpdrive.tools
            • brain_deer.plugins.warpdrive.tools.base
            • brain_deer.plugins.warpdrive.tools.draw
            • brain_deer.plugins.warpdrive.tools.point_to_point
            • brain_deer.plugins.warpdrive.tools.shrink_expand
            • brain_deer.plugins.warpdrive.tools.smudge
          • brain_deer.plugins.warpdrive.widget
      • brain_deer.plugins_host
        • brain_deer.plugins_host.companion_registry
        • brain_deer.plugins_host.plugin_manager
      • brain_deer.presentation
        • brain_deer.presentation.colormap_registry
        • brain_deer.presentation.qt
          • brain_deer.presentation.qt.app_menu
          • brain_deer.presentation.qt.bids_import_dialog
          • brain_deer.presentation.qt.bids_mapping_dialog
          • brain_deer.presentation.qt.bids_panel
          • brain_deer.presentation.qt.bottom_panel
          • brain_deer.presentation.qt.colormap_editor
          • brain_deer.presentation.qt.command_palette
          • brain_deer.presentation.qt.invisible_splitter
          • brain_deer.presentation.qt.left_panel
          • brain_deer.presentation.qt.main_window
          • brain_deer.presentation.qt.panel_auto_hide_pin
          • brain_deer.presentation.qt.perfect_layout
          • brain_deer.presentation.qt.preferences_window
          • brain_deer.presentation.qt.projection_links
          • brain_deer.presentation.qt.right_panel
          • brain_deer.presentation.qt.scene_3d_controls
          • brain_deer.presentation.qt.scene_rig_controls
          • brain_deer.presentation.qt.sims_mode
          • brain_deer.presentation.qt.surface_studio_panel
          • brain_deer.presentation.qt.viewer_panel
        • brain_deer.presentation.typography
      • brain_deer.surface
        • brain_deer.surface.atlas
        • brain_deer.surface.connectome
        • brain_deer.surface.figures
        • brain_deer.surface.meshes
        • brain_deer.surface.plotting
        • brain_deer.surface.projection
        • brain_deer.surface.resources
        • brain_deer.surface.scene_model
        • brain_deer.surface.subcortical
        • brain_deer.surface.tracts
      • brain_deer.tools
        • brain_deer.tools.roi_measurement
      • brain_deer.utils
        • brain_deer.utils.fa_dec
        • brain_deer.utils.load_timing
      • brain_deer.warp
        • brain_deer.warp.apply
        • brain_deer.warp.corrections
        • brain_deer.warp.field
        • brain_deer.warp.io
        • brain_deer.warp.modifiable
        • brain_deer.warp.rbf
        • brain_deer.warp.session
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brain_deer.plugins.warpdrive¶

WarpDrive plugin — interactive manual refinement of a nonlinear normalization.

Submodules¶

  • brain_deer.plugins.warpdrive.geometry
  • brain_deer.plugins.warpdrive.overlay2d
  • brain_deer.plugins.warpdrive.overlay3d
  • brain_deer.plugins.warpdrive.plugin
  • brain_deer.plugins.warpdrive.snap
  • brain_deer.plugins.warpdrive.style
  • brain_deer.plugins.warpdrive.tools
  • brain_deer.plugins.warpdrive.widget
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brain_deer.plugins.warpdrive.geometry
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  • brain_deer.plugins.warpdrive
    • Submodules