Example data used in this document | Accessing group data | Subjects list and demographics | Morphometry data for groups | Automatically masking the medial wall when accessing morphometry data | Faster access to group data | Labels for groups | Labels and masks | Annotations for groups | Aggregating morphometry data | Aggregating group data over entire hemispheres | A single morphometry measure in native space | A single morphometry measure in standard space | Several measures over several hemispheres in native space | Several measures over several hemispheres in standard space | Automatically masking the medial wall when aggregating | Aggregating over atlas regions | Native space | Standard space | Working with atlas data | Creating a label from an atlas region | Mapping one result value to each brain atlas region | Data visualization | Visualizing different types of data | Visualizing annotations (brain parcellations based on an atlas) | Visualizing morphometry data | Visualizing labels | Visualizing arbitrary vertices | Visualizing masks | Visualizing results of region-based analyses | Full control: visualizing vertex colors and color layers | General visualization options | Figure size | Different views | Changing the visualisation surface | Changing the resolution of figures (or other rgloptions) | Changing the resolution of figures with the scimesh backend | Using backgrounds when visualizing data | Saving screenshots and creating GIF movies (and other rglactions) | Example: Creating a GIF animation (movie) | Postprocessing the movies | Drawing colorbars | Plotting a colorbar in the background of a 3D plot | Plotting a colorbar to a separate 2D plot | Exporting publication quality plots | Visualizing groups of subjects

What is scimesh? | Installation | Quick Start | Rendering Features | Render Options Reference | Lighting and Shading | Ambient Lighting | Multi-Light Setups | Specular Highlights | Contrast Adjustment | Camera | Auto-Framing | Manual Camera | Orbiting the Camera | rgl-Compatible Default View | Projection Type | Anti-Aliasing | Wireframe Mode | Screen-Space Ambient Occlusion (SSAO) | Depth Fog | Clip Planes | Semi-Transparent Overlays | Text Labels | Background and Transparency | Working with Meshes | Procedural Geometry | Mesh I/O | Mesh Transforms | Face Colors | Texture Mapping | Mesh Utilities | Bounding Box | Axis Arrows | Lower-Level Rendering | Raw Triangles (no index buffer) | Points | Lines (as Cylinders) | Image Utilities | Colour Bars | Compositing Multiple Images | Image Stacking | Interoperability with Other Packages | rgl / tmesh3d | Rendering an rgl mesh directly | rgl → scimesh (explicit) | scimesh → rgl (inverse) | Matching rgl's Default View | Rvcg, Morpho, fsbrain, and other packages | Examples | FAQ

Why and when to use the scimesh backend | How to switch to the scimesh backend | Example data | Part 1: Different ways to use the export API | A basic export | Custom view angles | A larger grid of views | Forcing a vertical strip instead of a grid | The colorbar | Changing the background color | Transparent background | Part 2: Plotting region-based and vertex-based results | Results: region-based | Results: vertex-based | Part 3: A workflow with manually loaded meshes and data | See it rendered

Audience | Background | Prequisites | Using the functions in your script | Making files from a remote server available locally (on the user computer) | Downloading files in parallel | Storing files in local subdirectories of the package cache | Declarative file manifests | Generating a manifest from a local directory | Accessing a file from the local package cache | Removing files you do not need anymore from the package cache | Manually checking whether a file exists in the package cache | Giving users the option to download extra package data | Interface suggestion | Example implementation of the interface for your package | Limitations and Suggestions

Input data | Q: What kind of input data do I need for fsbrain? | Q: Which file formats are supported? | Q: I want to load a single file that is somewhere on my harddisk, i.e., not within a standard recon-all output directory structure. How can I load it? | Q: Can I use fsbrain to visualize data from SPM12 / CAT12 or other software packages? | What is the best way to visualize data computed in R (or from arbitrary files that do not follow the FreeSurfer recon-all directory layout)? | Can I used fsbrain to visualize surface data from BrainSuite surfaces in DFS format? | Visualization | How can I set the output image resolution? | How can I save high quality figures to PNG images? | Can I save fsbrain figures as vector images (like PDF, EPS, SVG)? | A journal requires me to submit a vector graphics file, what to do? | When visualizing data with outliers and long tails, the colors are not helpful. What to do? | Can I limit the data range, including the min and max values displayed on the color bar? | How can I enforce fixed colorbar settings (i.e., one color should represent the same value) across several images? | How can I change the colormap for the plots? | What are the best colormaps for my data? | I am using a diverging colormap. When plotting the colorbar (legend), the neutral value is not at zero. How to fix it? | The colorbar shows only very few different colors, why is that and how can I change it? | Can I set a custom color for NA values in the plot, like the masked medial wall? | Can I get a color legend when plotting atlas regions from an annotation? I want to know the region names for the colors. | Can I get a color legend when plotting a segmentation/parcellation (different brain regions), based on a color lookup table (like the FreeSurferColorLUT.txt file)? | There is too much whitespace between the different views of the brain. How can I reduce it? | Can I export PNG images with transparent (instead of white) background? | When visualizing data on the inflated surface, the left and right hemisphere overlap and look garbled. How to fix that? | When plotting several views, can I have the subplots arranged in a horizontal strip (rather than 2x2 tiles)? | Various topics | Can I integrate the plots produced by fsbrain into an R Markdown document (the R equivalent of a Python Jupyter notebook)? | Can I use fsbrain to visualize arbitrary triangular meshes in R? | Technical problems | I am getting the error 'invalid value specified for graphical parameter plt', why? | I am getting the error 'Error in squash::cmap, found x values outside map range' | I am getting the warning 'RGL: unable to open X11 display' when loading fsbrain | How can I plot on a machine that does not have X11? | I am trying to plot a very large image with fsbrain, but the output is not as large as expected. Why? | What to do about the error 'lazy-load database is corrupt' when loading fsbrain? | I see no output image after running a vis function, and also get no error message. What to do?

Introduction | Smoothing Per-Vertex Data | Re-Using the Mesh Neighborhood | Creating Sub-Meshes | Working with k-d Trees | Mesh Conversion Utilities | Further Reading

Overview | Prerequisites | Mapping Volume Coordinates to fsaverage Surface | MNI152 coordinates to fsaverage | Colin27 coordinates to fsaverage | Mapping fsaverage Vertices to Volume Coordinates | fsaverage vertices to MNI152 | fsaverage vertices to Colin27 | Combining both hemispheres | Cross-Template Volume-to-Volume Mapping | MNI152 to Colin27 | Colin27 to MNI152 | Projecting Volume Data to the fsaverage Surface | Projecting Surface Data to a Volume | MNI305 to MNI152/Colin27 via Closest Vertex | Linear Method (for Comparison) | Choosing RF-ANTs vs RF-M3Z | Session Info

About the MGH header | Getting access to the header data in MGH or MGZ files | Computing more information from the header | Transformation matrices | Primary slice direction and volume CRS orientation | Check whether the volume is conformed

Background | Reading MGH and MGZ format files | Accessing metadata from the MGH header | A second MGH example | Hint: Further image processing and visualization for volumes | Reading 'curv' format files | Reading morphometry data, no matter the format | Reading morphometry data for a subset of vertices from weight, paint or w files | Reading annotation files | Working with annotation data | Reading surface files (meshes) | Reading arbitrary triangular meshes and converting to rgl mesh3d | Reading labels | Reading color lookup tables (LUT files) | Computing the unique color codes | References | Alternatives, similar and related Packages

Writing 1D morphometry data or other per-vertex information (in MGH, MGZ or curv format) | Writing MGH and MGZ format files with full control over the header | MGH data types | Writing 'curv' format files (morphometry data) | Writing surface format files | Writing label files | Writing color lookup table (LUT) files in ASCII format

About brainloc | Preparation: Getting the data required to run the examples | Using the template subjects from a local FreeSurfer installation | Have the brainloc package download them for you from the internet | Usage Examples Part I: Location information for a vertex or coordinate | Creating a brainparc object | Finding the vertex closest to a query coordinate | Finding the MNI152 and Talairach coordinates for a point or vertex in MNI305 space | Finding the brain atlas region a vertex belongs to, and the distance to all other brain atlas regions from the vertex | Usage Examples Part II: Location information for a cluster

Example data used in this document | Loading volume data | Volume visualization | Basic Lightbox view for raw MRI data | Advanced lightbox view | Raw 3D voxel visualization

Reading WAL files | Preview a WAL texture in R | Writing WAL image files | Exporting to PNG and JPEG | Converting JPG or PNG images to WAL format