Cortical atlases | Stacking all views | Subcortical and tract atlases | Horizontal and vertical | Grid layouts | Picking specific views | Grouping by slice type | Adding view labels | Zooming in on regions of interest | Focus on the regions in your data | Name the focus regions explicitly | Control the margin with zoom_pad | Dropping the grey context | The sf workflow

What's in a brain atlas | Your first brain plot | Arranging views | Showing only certain hemispheres or views | Plotting your own data | Faceting | Highlighting specific regions | Scales and themes | Going further | Finding more atlases

How matching works | A minimal example | Constraining matches with extra columns | Faceting across groups | Troubleshooting | Full control with sf

Reading a single stats file | Reading stats files across subjects | Reading FreeSurfer stats tables | Cleaning label suffixes | Filtering non-region rows

What is a ggseg_atlas? | Anatomy of an atlas | Three atlas types | Core: the region table | Querying an atlas | Extracting render-ready data | Checking and converting

The recipe | What migrate_atlas_files() does | Keeping sf instead | Verifying the result

The manipulation toolkit | Keeping and removing regions | Context regions | Renaming regions | Managing views | Cleaning up geometry | Reordering and gathering | Adding metadata | A full pipeline

Available surfaces | Cortical | Cerebellar | Accessing meshes | Integration with ggseg3d | Mesh structure

What's inside a ggseg_atlas | Cortical pipeline | Subcortical and tract pipelines | Post-processing | System requirements | Tutorials

Parameter hierarchy | Available options | Setting options in R | Verbosity | Cleanup | Skip existing | Geometry parameters | Environment variables | Overriding defaults | Recipes | Development and debugging | Production and CI | Iterating on tolerance

What each pipeline needs | FreeSurfer | ImageMagick | Chrome / Chromium | Parallel processing | Progress bars | Checking your setup

Requirements | Setting up the package repository | Edit DESCRIPTION | Create your atlas | How atlas data is stored | Document your atlas | Getting tests to pass | Multiple atlases in one package | Getting package checks to pass | Adding your package to r-universe | 1. Fork the r-universe repository | 2. Edit packages.json | 3. Submit a pull request | 4. Wait for review | Installing from r-universe | Updating your package

The old system | The current system | Converting old atlases | From a ggseg3d_atlas only | From both 2D and 3D objects | From a 2D ggseg_atlas only | Specifying atlas type | Batch conversion | Post-conversion checklist | Lessons learned from batch conversion | 3D data is not always preserved | Palette entries may not match core rows exactly | Labels with special characters lose sf coverage | Skip ggseg3d tests for atlases without 3D data | Troubleshooting | When to recreate instead

Inspecting an atlas | Removing regions | Keeping regions | Context regions | Labels versus regions | Adding metadata columns | View management | Keeping specific views | Removing views | Reordering views | Removing small regions from views | Gathering views | Adjusting geometry after the fact | Smoothing rough contours | Reducing vertex count | Combining both | Rebuilding the atlas | Putting it together

Finding the binary | The direct route | Wrappers | Parcellate CIFTI data | Compute a correlation matrix | Reduce across maps | Surface curvature | Map a volume to a surface | Math expressions | Getting help | Using wbcmd with ciftiTools | Controlling verbosity

Getting started | Mapping data | Subcortical atlases | Camera and background

Basic Shiny integration | Output sizing | Reactive data | Updating camera and background | Complete example | Performance tips

What a random rotation needs to do | Euler ZYZ rotations | Rodrigues axis-angle rotations | Where Rodrigues has the edge | Geometric transparency | Axis uniformity is explicit | Numerical stability | Idiomatic R | Where Euler has the edge | How much does the difference matter? | Choosing a method | Summary | References

The landscape | Distance-based methods | Variogram matching (burt2020) | Spatial autoregressive model (burt2018) | Moran spectral randomization (moran) | Spin-based methods | Original spin test (alexander_bloch) | Greedy assignment (spin_vasa) | Optimal assignment (spin_hungarian) | Parcel spin methods | Maximum overlap (baum) | Majority vote (cornblath) | Comparing null distributions visually | Using permtest_metric() for custom metrics | Building custom null distributions | Decision guide | References

Vertices to parcels | Parcels back to vertices | The high-level wrappers | Parcel centroids | Average centroid | Surface centroid | Geodesic centroid | Building a parcel-level distance matrix | Parcellation and null models together | Practical considerations | References

Comparing two brain maps | Adding a spatial null model | Visualising the null distribution | Pre-computing null distributions | Working with real brain map files | Accessing the neuromaps atlas collection | Custom metrics with permtest_metric() | Choosing a null model | What comes next | References

Surface meshes | Building a surface graph | Geodesic distances | Partial distance matrices | Euclidean vs geodesic | Vertex areas | Checking the geometry | Format conversions | Annotation to GIFTI | Morphometry to GIFTI | Resampling between coordinate spaces | Putting it together | References

Exploring Freesurfer Output: A Practical Guide | Visualizing Segmented Brain Structures | Analyzing Anatomical Statistics for Brain Structures | Converting and Visualizing Brain Surfaces with mris_convert | Working with Label Files

Understanding Imaging Formats in freesurfer and R | The Freesurfer Reconstruction Pipeline | Converting MRI Images with mri_convert | Correcting for Bias Fields with nu_correct | Brain Extraction with mri_watershed

What's Next? Additional Features and Future Plans | Conclusion

Setting Up Your R Environment for freesurfer | Setting Up Freesurfer Options | Check if Freesurfer is installed | Understanding Freesurfer Output Formats | Understanding how get_fs() fascilitates Freesurfer calls | Why is get_fs() important? | How it works | Example Usage | Organizing Your Freesurfer Analyses

Running the Freesurfer recon-all Pipeline | Restarting the Reconstruction Pipeline | Customizing the Pipeline with recon | Running All Steps (Default) | Customizing Steps | Adding Verbose Output | Running Specific Stages of Reconstruction | Advamced use with the Low-Level reconner Function | Basic Usage | Force Execution | Summary of Functions | Conclusion