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<!doctype html>
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<link rel="index" title="Index" href="genindex.html"><link rel="search" title="Search" href="search.html"><link rel="next" title="Setup" href="setup/index.html"><link rel="prev" title="Feature comparison" href="featurecomparison.html">
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<title>Workflow - NaviNIBS documentation</title>
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<p class="caption" role="heading"><span class="caption-text">Usage</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="featurecomparison.html">Feature comparison</a></li>
<li class="toctree-l1 current current-page"><a class="current reference internal" href="#">Workflow</a></li>
<li class="toctree-l1 has-children"><a class="reference internal" href="setup/index.html">Setup</a><input aria-label="Toggle navigation of Setup" class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" role="switch" type="checkbox"/><label for="toctree-checkbox-1"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
<li class="toctree-l2"><a class="reference internal" href="setup/install.html">Installation</a></li>
<li class="toctree-l2"><a class="reference internal" href="setup/setup-ndi.html">NDI tracking setup</a></li>
<li class="toctree-l2"><a class="reference internal" href="setup/setup-optitrack.html">OptiTrack tracking setup</a></li>
<li class="toctree-l2"><a class="reference internal" href="setup/development.html">Development</a></li>
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<li class="toctree-l1 has-children"><a class="reference internal" href="core/index.html">Core features</a><input aria-label="Toggle navigation of Core features" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" role="switch" type="checkbox"/><label for="toctree-checkbox-2"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
<li class="toctree-l2"><a class="reference internal" href="core/SessionManagement.html">Session management</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/ToolConfiguration.html">Tool configuration</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/MRI.html">MRI</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/HeadModel.html">Head model</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/TargetPlanning.html">Target planning</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/SubjectRegistration.html">Subject registration</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/CoilCalibration.html">Coil calibration</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/BasicNavigation.html">Basic navigation</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/TriggeringConfiguration.html">Triggering configuration</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/ElectrodeDigitization.html">Electrode digitization</a></li>
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<li class="toctree-l1"><a class="reference internal" href="datamodel.html">Data model</a></li>
<li class="toctree-l1"><a class="reference internal" href="troubleshooting/index.html">Troubleshooting</a></li>
<li class="toctree-l1"><a class="reference internal" href="citing.html">Citing NaviNIBS</a></li>
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<p class="caption" role="heading"><span class="caption-text">Development</span></p>
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<li class="toctree-l1 has-children"><a class="reference internal" href="source/modules.html">Code</a><input aria-label="Toggle navigation of Code" class="toctree-checkbox" id="toctree-checkbox-4" name="toctree-checkbox-4" role="switch" type="checkbox"/><label for="toctree-checkbox-4"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
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<li class="toctree-l3 has-children"><a class="reference internal" href="source/NaviNIBS.Devices.html">NaviNIBS.Devices package</a><input aria-label="Toggle navigation of NaviNIBS.Devices package" class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" role="switch" type="checkbox"/><label for="toctree-checkbox-6"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
<li class="toctree-l4"><a class="reference internal" href="source/NaviNIBS.Devices.IGTLinkToolPositionsServer.html">NaviNIBS.Devices.IGTLinkToolPositionsServer module</a></li>
<li class="toctree-l4"><a class="reference internal" href="source/NaviNIBS.Devices.ToolPositionsClient.html">NaviNIBS.Devices.ToolPositionsClient module</a></li>
<li class="toctree-l4"><a class="reference internal" href="source/NaviNIBS.Devices.ToolPositionsServer.html">NaviNIBS.Devices.ToolPositionsServer module</a></li>
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<li class="toctree-l3 has-children"><a class="reference internal" href="source/NaviNIBS.Navigator.html">NaviNIBS.Navigator package</a><input aria-label="Toggle navigation of NaviNIBS.Navigator package" class="toctree-checkbox" id="toctree-checkbox-7" name="toctree-checkbox-7" role="switch" type="checkbox"/><label for="toctree-checkbox-7"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
<li class="toctree-l4 has-children"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.html">NaviNIBS.Navigator.GUI package</a><input aria-label="Toggle navigation of NaviNIBS.Navigator.GUI package" class="toctree-checkbox" id="toctree-checkbox-8" name="toctree-checkbox-8" role="switch" type="checkbox"/><label for="toctree-checkbox-8"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
<li class="toctree-l5 has-children"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.CollectionModels.html">NaviNIBS.Navigator.GUI.CollectionModels package</a><input aria-label="Toggle navigation of NaviNIBS.Navigator.GUI.CollectionModels package" class="toctree-checkbox" id="toctree-checkbox-9" name="toctree-checkbox-9" role="switch" type="checkbox"/><label for="toctree-checkbox-9"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.CollectionModels.DigitizedLocationsTableModel.html">NaviNIBS.Navigator.GUI.CollectionModels.DigitizedLocationsTableModel module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.CollectionModels.FiducialsTableModels.html">NaviNIBS.Navigator.GUI.CollectionModels.FiducialsTableModels module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.CollectionModels.HeadPointsTableModel.html">NaviNIBS.Navigator.GUI.CollectionModels.HeadPointsTableModel module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.CollectionModels.HotkeysTableModel.html">NaviNIBS.Navigator.GUI.CollectionModels.HotkeysTableModel module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.CollectionModels.SamplesTableModel.html">NaviNIBS.Navigator.GUI.CollectionModels.SamplesTableModel module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.CollectionModels.TargetsTableModel.html">NaviNIBS.Navigator.GUI.CollectionModels.TargetsTableModel module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.CollectionModels.ToolsTableModel.html">NaviNIBS.Navigator.GUI.CollectionModels.ToolsTableModel module</a></li>
</ul>
</li>
<li class="toctree-l5 has-children"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.EditWindows.html">NaviNIBS.Navigator.GUI.EditWindows package</a><input aria-label="Toggle navigation of NaviNIBS.Navigator.GUI.EditWindows package" class="toctree-checkbox" id="toctree-checkbox-10" name="toctree-checkbox-10" role="switch" type="checkbox"/><label for="toctree-checkbox-10"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.EditWindows.CoilCalibrationWindow.html">NaviNIBS.Navigator.GUI.EditWindows.CoilCalibrationWindow module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.EditWindows.ImportSessionWindow.html">NaviNIBS.Navigator.GUI.EditWindows.ImportSessionWindow module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.EditWindows.PointerCalibrationWindow.html">NaviNIBS.Navigator.GUI.EditWindows.PointerCalibrationWindow module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.EditWindows.ToolCalibrationWindow.html">NaviNIBS.Navigator.GUI.EditWindows.ToolCalibrationWindow module</a></li>
</ul>
</li>
<li class="toctree-l5 has-children"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.html">NaviNIBS.Navigator.GUI.ViewPanels package</a><input aria-label="Toggle navigation of NaviNIBS.Navigator.GUI.ViewPanels package" class="toctree-checkbox" id="toctree-checkbox-11" name="toctree-checkbox-11" role="switch" type="checkbox"/><label for="toctree-checkbox-11"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
<li class="toctree-l6 has-children"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.html">NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel package</a><input aria-label="Toggle navigation of NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel package" class="toctree-checkbox" id="toctree-checkbox-12" name="toctree-checkbox-12" role="switch" type="checkbox"/><label for="toctree-checkbox-12"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
<li class="toctree-l7 has-children"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers.html">NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers package</a><input aria-label="Toggle navigation of NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers package" class="toctree-checkbox" id="toctree-checkbox-13" name="toctree-checkbox-13" role="switch" type="checkbox"/><label for="toctree-checkbox-13"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
<li class="toctree-l8"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers.MeshSurfaceLayer.html">NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers.MeshSurfaceLayer module</a></li>
<li class="toctree-l8"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers.OrientationsLayers.html">NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers.OrientationsLayers module</a></li>
<li class="toctree-l8"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers.PlotLayersGroup.html">NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers.PlotLayersGroup module</a></li>
<li class="toctree-l8"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers.SampleMetadataOrientationsLayer.html">NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers.SampleMetadataOrientationsLayer module</a></li>
<li class="toctree-l8"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers.TargetingAngleErrorLayer.html">NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers.TargetingAngleErrorLayer module</a></li>
<li class="toctree-l8"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers.TargetingCrosshairsLayer.html">NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers.TargetingCrosshairsLayer module</a></li>
<li class="toctree-l8"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers.TargetingErrorLineLayer.html">NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers.TargetingErrorLineLayer module</a></li>
<li class="toctree-l8"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers.TargetingPointLayer.html">NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.ViewLayers.TargetingPointLayer module</a></li>
</ul>
</li>
<li class="toctree-l7"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.NavigatePanel.html">NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.NavigatePanel module</a></li>
<li class="toctree-l7"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.NavigationView.html">NaviNIBS.Navigator.GUI.ViewPanels.NavigatePanel.NavigationView module</a></li>
</ul>
</li>
<li class="toctree-l6 has-children"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.TriggerSettingsPanel.html">NaviNIBS.Navigator.GUI.ViewPanels.TriggerSettingsPanel package</a><input aria-label="Toggle navigation of NaviNIBS.Navigator.GUI.ViewPanels.TriggerSettingsPanel package" class="toctree-checkbox" id="toctree-checkbox-14" name="toctree-checkbox-14" role="switch" type="checkbox"/><label for="toctree-checkbox-14"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
<li class="toctree-l7"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.TriggerSettingsPanel.HotkeyTriggerSourceSettingsWidget.html">NaviNIBS.Navigator.GUI.ViewPanels.TriggerSettingsPanel.HotkeyTriggerSourceSettingsWidget module</a></li>
<li class="toctree-l7"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.TriggerSettingsPanel.LSLTriggerSourceSettingsWidget.html">NaviNIBS.Navigator.GUI.ViewPanels.TriggerSettingsPanel.LSLTriggerSourceSettingsWidget module</a></li>
<li class="toctree-l7"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.TriggerSettingsPanel.TriggerSourceSettingsWidget.html">NaviNIBS.Navigator.GUI.ViewPanels.TriggerSettingsPanel.TriggerSourceSettingsWidget module</a></li>
</ul>
</li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.CameraPanel.html">NaviNIBS.Navigator.GUI.ViewPanels.CameraPanel module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.CoordinateSystemsPanel.html">NaviNIBS.Navigator.GUI.ViewPanels.CoordinateSystemsPanel module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.DigitizeLocationsPanel.html">NaviNIBS.Navigator.GUI.ViewPanels.DigitizeLocationsPanel module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.FiducialsPanel.html">NaviNIBS.Navigator.GUI.ViewPanels.FiducialsPanel module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.HeadModelPanel.html">NaviNIBS.Navigator.GUI.ViewPanels.HeadModelPanel module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.MRIPanel.html">NaviNIBS.Navigator.GUI.ViewPanels.MRIPanel module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.MainViewPanelWithDockWidgets.html">NaviNIBS.Navigator.GUI.ViewPanels.MainViewPanelWithDockWidgets module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.ManageSessionPanel.html">NaviNIBS.Navigator.GUI.ViewPanels.ManageSessionPanel module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.SubjectRegistrationPanel.html">NaviNIBS.Navigator.GUI.ViewPanels.SubjectRegistrationPanel module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.TargetsPanel.html">NaviNIBS.Navigator.GUI.ViewPanels.TargetsPanel module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.ViewPanels.ToolsPanel.html">NaviNIBS.Navigator.GUI.ViewPanels.ToolsPanel module</a></li>
</ul>
</li>
<li class="toctree-l5 has-children"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.Widgets.html">NaviNIBS.Navigator.GUI.Widgets package</a><input aria-label="Toggle navigation of NaviNIBS.Navigator.GUI.Widgets package" class="toctree-checkbox" id="toctree-checkbox-15" name="toctree-checkbox-15" role="switch" type="checkbox"/><label for="toctree-checkbox-15"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.Widgets.CollectionTableWidget.html">NaviNIBS.Navigator.GUI.Widgets.CollectionTableWidget module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.Widgets.EditGridWidget.html">NaviNIBS.Navigator.GUI.Widgets.EditGridWidget module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.Widgets.EditTargetWidget.html">NaviNIBS.Navigator.GUI.Widgets.EditTargetWidget module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.Widgets.MRIViews.html">NaviNIBS.Navigator.GUI.Widgets.MRIViews module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.Widgets.SurfViews.html">NaviNIBS.Navigator.GUI.Widgets.SurfViews module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.Widgets.TrackingStatusWidget.html">NaviNIBS.Navigator.GUI.Widgets.TrackingStatusWidget module</a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.Navigator.GUI.NavigatorGUI.html">NaviNIBS.Navigator.GUI.NavigatorGUI module</a></li>
</ul>
</li>
<li class="toctree-l4 has-children"><a class="reference internal" href="source/NaviNIBS.Navigator.Model.html">NaviNIBS.Navigator.Model package</a><input aria-label="Toggle navigation of NaviNIBS.Navigator.Model package" class="toctree-checkbox" id="toctree-checkbox-16" name="toctree-checkbox-16" role="switch" type="checkbox"/><label for="toctree-checkbox-16"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.Navigator.Model.Addons.html">NaviNIBS.Navigator.Model.Addons module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.Navigator.Model.Calculations.html">NaviNIBS.Navigator.Model.Calculations module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.Navigator.Model.CoordinateSystems.html">NaviNIBS.Navigator.Model.CoordinateSystems module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.Navigator.Model.DigitizedLocations.html">NaviNIBS.Navigator.Model.DigitizedLocations module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.Navigator.Model.DockWidgetLayouts.html">NaviNIBS.Navigator.Model.DockWidgetLayouts module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.Navigator.Model.GenericCollection.html">NaviNIBS.Navigator.Model.GenericCollection module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.Navigator.Model.HeadModel.html">NaviNIBS.Navigator.Model.HeadModel module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.Navigator.Model.MRI.html">NaviNIBS.Navigator.Model.MRI module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.Navigator.Model.MiscSettings.html">NaviNIBS.Navigator.Model.MiscSettings module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.Navigator.Model.Samples.html">NaviNIBS.Navigator.Model.Samples module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.Navigator.Model.Session.html">NaviNIBS.Navigator.Model.Session module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.Navigator.Model.SubjectRegistration.html">NaviNIBS.Navigator.Model.SubjectRegistration module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.Navigator.Model.Targets.html">NaviNIBS.Navigator.Model.Targets module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.Navigator.Model.Tools.html">NaviNIBS.Navigator.Model.Tools module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.Navigator.Model.Triggering.html">NaviNIBS.Navigator.Model.Triggering module</a></li>
</ul>
</li>
<li class="toctree-l4"><a class="reference internal" href="source/NaviNIBS.Navigator.TargetingCoordinator.html">NaviNIBS.Navigator.TargetingCoordinator module</a></li>
</ul>
</li>
<li class="toctree-l3 has-children"><a class="reference internal" href="source/NaviNIBS.util.html">NaviNIBS.util package</a><input aria-label="Toggle navigation of NaviNIBS.util package" class="toctree-checkbox" id="toctree-checkbox-17" name="toctree-checkbox-17" role="switch" type="checkbox"/><label for="toctree-checkbox-17"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
<li class="toctree-l4 has-children"><a class="reference internal" href="source/NaviNIBS.util.GUI.html">NaviNIBS.util.GUI package</a><input aria-label="Toggle navigation of NaviNIBS.util.GUI package" class="toctree-checkbox" id="toctree-checkbox-18" name="toctree-checkbox-18" role="switch" type="checkbox"/><label for="toctree-checkbox-18"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.GUI.Dock.html">NaviNIBS.util.GUI.Dock module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.GUI.ErrorDialog.html">NaviNIBS.util.GUI.ErrorDialog module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.GUI.IconWidget.html">NaviNIBS.util.GUI.IconWidget module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.GUI.Icons.html">NaviNIBS.util.GUI.Icons module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.GUI.QAppWithAsyncioLoop.html">NaviNIBS.util.GUI.QAppWithAsyncioLoop module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.GUI.QCollapsibleSection.html">NaviNIBS.util.GUI.QCollapsibleSection module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.GUI.QDial.html">NaviNIBS.util.GUI.QDial module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.GUI.QFileSelectWidget.html">NaviNIBS.util.GUI.QFileSelectWidget module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.GUI.QFlowLayout.html">NaviNIBS.util.GUI.QFlowLayout module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.GUI.QLineEdit.html">NaviNIBS.util.GUI.QLineEdit module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.GUI.QMouseWheelAdjustmentGuard.html">NaviNIBS.util.GUI.QMouseWheelAdjustmentGuard module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.GUI.QScrollContainer.html">NaviNIBS.util.GUI.QScrollContainer module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.GUI.QTableWidgetDragRows.html">NaviNIBS.util.GUI.QTableWidgetDragRows module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.GUI.QValidators.html">NaviNIBS.util.GUI.QValidators module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.GUI.QWidgetWithCloseSignal.html">NaviNIBS.util.GUI.QWidgetWithCloseSignal module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.GUI.QueuedRedrawMixin.html">NaviNIBS.util.GUI.QueuedRedrawMixin module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.GUI.SpatialTransformWidget.html">NaviNIBS.util.GUI.SpatialTransformWidget module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.GUI.StyleSheets.html">NaviNIBS.util.GUI.StyleSheets module</a></li>
</ul>
</li>
<li class="toctree-l4 has-children"><a class="reference internal" href="source/NaviNIBS.util.lsl.html">NaviNIBS.util.lsl package</a><input aria-label="Toggle navigation of NaviNIBS.util.lsl package" class="toctree-checkbox" id="toctree-checkbox-19" name="toctree-checkbox-19" role="switch" type="checkbox"/><label for="toctree-checkbox-19"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.lsl.LSLStreamResolver.html">NaviNIBS.util.lsl.LSLStreamResolver module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.lsl.LSLStreamSelector.html">NaviNIBS.util.lsl.LSLStreamSelector module</a></li>
</ul>
</li>
<li class="toctree-l4 has-children"><a class="reference internal" href="source/NaviNIBS.util.pyvista.html">NaviNIBS.util.pyvista package</a><input aria-label="Toggle navigation of NaviNIBS.util.pyvista package" class="toctree-checkbox" id="toctree-checkbox-20" name="toctree-checkbox-20" role="switch" type="checkbox"/><label for="toctree-checkbox-20"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
<li class="toctree-l5 has-children"><a class="reference internal" href="source/NaviNIBS.util.pyvista.RemotePlotting.html">NaviNIBS.util.pyvista.RemotePlotting package</a><input aria-label="Toggle navigation of NaviNIBS.util.pyvista.RemotePlotting package" class="toctree-checkbox" id="toctree-checkbox-21" name="toctree-checkbox-21" role="switch" type="checkbox"/><label for="toctree-checkbox-21"><span class="icon"><svg><use href="#svg-arrow-right"></use></svg></span></label><ul>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.util.pyvista.RemotePlotting.RemoteLayeredPlotter.html">NaviNIBS.util.pyvista.RemotePlotting.RemoteLayeredPlotter module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.util.pyvista.RemotePlotting.RemoteLayeredPlotterProxies.html">NaviNIBS.util.pyvista.RemotePlotting.RemoteLayeredPlotterProxies module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.util.pyvista.RemotePlotting.RemotePlotter.html">NaviNIBS.util.pyvista.RemotePlotting.RemotePlotter module</a></li>
<li class="toctree-l6"><a class="reference internal" href="source/NaviNIBS.util.pyvista.RemotePlotting.RemotePlotterProxy.html">NaviNIBS.util.pyvista.RemotePlotting.RemotePlotterProxy module</a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.pyvista.PlotInteraction.html">NaviNIBS.util.pyvista.PlotInteraction module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.pyvista.dataset.html">NaviNIBS.util.pyvista.dataset module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.pyvista.plotting.html">NaviNIBS.util.pyvista.plotting module</a></li>
<li class="toctree-l5"><a class="reference internal" href="source/NaviNIBS.util.pyvista.ticks.html">NaviNIBS.util.pyvista.ticks module</a></li>
</ul>
</li>
<li class="toctree-l4"><a class="reference internal" href="source/NaviNIBS.util.AsyncRunner.html">NaviNIBS.util.AsyncRunner module</a></li>
<li class="toctree-l4"><a class="reference internal" href="source/NaviNIBS.util.Asyncio.html">NaviNIBS.util.Asyncio module</a></li>
<li class="toctree-l4"><a class="reference internal" href="source/NaviNIBS.util.CoilOrientations.html">NaviNIBS.util.CoilOrientations module</a></li>
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<li class="toctree-l4"><a class="reference internal" href="source/NaviNIBS.util.ZMQAsyncioFix.html">NaviNIBS.util.ZMQAsyncioFix module</a></li>
<li class="toctree-l4"><a class="reference internal" href="source/NaviNIBS.util.ZMQConnector.html">NaviNIBS.util.ZMQConnector module</a></li>
<li class="toctree-l4"><a class="reference internal" href="source/NaviNIBS.util.attrs.html">NaviNIBS.util.attrs module</a></li>
<li class="toctree-l4"><a class="reference internal" href="source/NaviNIBS.util.json.html">NaviNIBS.util.json module</a></li>
<li class="toctree-l4"><a class="reference internal" href="source/NaviNIBS.util.logging.html">NaviNIBS.util.logging module</a></li>
<li class="toctree-l4"><a class="reference internal" href="source/NaviNIBS.util.numpy.html">NaviNIBS.util.numpy module</a></li>
<li class="toctree-l4"><a class="reference internal" href="source/NaviNIBS.util.test_attrs.html">NaviNIBS.util.test_attrs module</a></li>
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<li class="toctree-l1"><a class="reference external" href="https://github.com/PrecisionNeuroLab/NaviNIBS">Github</a></li>
<li class="toctree-l1"><a class="reference external" href="https://precisionneuro.stanford.edu">Precision Neurotherapeutics Lab</a></li>
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<section id="workflow">
<h1>Workflow<a class="headerlink" href="#workflow" title="Link to this heading">¶</a></h1>
<section id="first-time-software-setup">
<h2>First-time software setup<a class="headerlink" href="#first-time-software-setup" title="Link to this heading">¶</a></h2>
<ul class="simple">
<li><p><a class="reference internal" href="setup/install.html"><span class="doc">Install</span></a> NaviNIBS.</p></li>
<li><p>Establish communication with pose tracking system (e.g. <a class="reference internal" href="setup/setup-ndi.html"><span class="doc">NDI</span></a>, <a class="reference internal" href="setup/setup-optitrack.html"><span class="doc">OptiTrack</span></a>, or <a class="reference internal" href="addons/simulated-tools.html"><span class="doc">Simulated tools</span></a>).</p></li>
<li><p><a class="reference internal" href="core/ToolConfiguration.html"><span class="doc">Configure tools</span></a>.</p></li>
<li><p><a class="reference internal" href="core/TriggeringConfiguration.html"><span class="doc">Configure triggering</span></a>.</p></li>
<li><p><a class="reference internal" href="core/ElectrodeDigitization.html"><span class="doc">Configure electrode template</span></a> (if applicable).</p></li>
</ul>
</section>
<section id="new-subject-preparation">
<h2>New subject preparation<a class="headerlink" href="#new-subject-preparation" title="Link to this heading">¶</a></h2>
<ul class="simple">
<li><p><a class="reference internal" href="core/MRI.html#mri-acquisition"><span class="std std-ref">Acquire</span></a> a T1-weighted MRI scan, and optionally also a T2-weighted scan.</p></li>
<li><p><a class="reference internal" href="core/HeadModel.html#head-model-generation"><span class="std std-ref">Create a head model</span></a> from the MRI scan.</p></li>
<li><p><a class="reference internal" href="core/SessionManagement.html#creating-a-new-session"><span class="std std-ref">Create a new session</span></a> in NaviNIBS for the subject.</p></li>
<li><p><a class="reference internal" href="core/SessionManagement.html#copying-from-a-template"><span class="std std-ref">Copy settings</span></a> from a template/previous session.</p></li>
<li><p><a class="reference internal" href="core/MRI.html#mri-import"><span class="std std-ref">Import</span></a> MRI data.</p></li>
<li><p><a class="reference internal" href="core/HeadModel.html#head-model-import"><span class="std std-ref">Import</span></a> head model.</p></li>
<li><p><a class="reference internal" href="core/SubjectRegistration.html#fiducial-planning"><span class="std std-ref">Plan fiducial locations</span></a>.</p></li>
<li><p>(Optionally): <a class="reference internal" href="core/TargetPlanning.html"><span class="doc">Plan target(s)</span></a> prior to a session.</p></li>
</ul>
</section>
<section id="new-session-for-a-previous-subject">
<h2>New session for a previous subject<a class="headerlink" href="#new-session-for-a-previous-subject" title="Link to this heading">¶</a></h2>
<ul class="simple">
<li><p><a class="reference internal" href="core/SessionManagement.html#creating-a-new-session"><span class="std std-ref">Create a new session</span></a> in NaviNIBS for the subject.</p></li>
<li><p><a class="reference internal" href="core/SessionManagement.html#copying-from-another-session-in-the-same-subject"><span class="std std-ref">Copy subset</span></a> of settings from previous session</p></li>
</ul>
</section>
<section id="during-a-session">
<h2>During a session<a class="headerlink" href="#during-a-session" title="Link to this heading">¶</a></h2>
<ul class="simple">
<li><p><a class="reference internal" href="core/CoilCalibration.html"><span class="doc">Calibrate coil tracker(s)</span></a></p></li>
<li><p><a class="reference internal" href="core/SubjectRegistration.html#initial-registration"><span class="std std-ref">Register subject</span></a></p></li>
<li><p><a class="reference internal" href="core/BasicNavigation.html"><span class="doc">Basic navigation</span></a></p></li>
<li><p><a class="reference internal" href="core/SubjectRegistration.html#re-registration"><span class="std std-ref">Re-register</span></a> occasionally to correct for subject head tracker shifts.</p></li>
<li><p>(Optionally) <a class="reference internal" href="core/ElectrodeDigitization.html"><span class="doc">digitize electrode locations</span></a>.</p></li>
</ul>
</section>
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<li><a class="reference internal" href="#">Workflow</a><ul>
<li><a class="reference internal" href="#first-time-software-setup">First-time software setup</a></li>
<li><a class="reference internal" href="#new-subject-preparation">New subject preparation</a></li>
<li><a class="reference internal" href="#new-session-for-a-previous-subject">New session for a previous subject</a></li>
<li><a class="reference internal" href="#during-a-session">During a session</a></li>
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