data-raw/neuroatlas_llm_sheet.md

In bbuchsbaum/neuroatlas: useful atlases/parcellations for neuroimaging analysis

neuroatlas: R package for neuroimaging atlas operations Primary uses: Loading brain templates, accessing standard atlases, manipulating brain parcellations Core capabilities: Template loading, atlas operations, coordinate transformations

Template Loading Functions

get_template(name = "MNI152NLin2009cAsym", desc = "brain", resolution = 1, suffix = "T1w")

Access standardized neuroimaging templates from TemplateFlow

- MNI152NLin2009cAsym (default) - MNI152NLin6Asym - OASIS30ANTs - NKI - WHS

- brain: Brain-extracted template - head: Full head template - mask: Binary brain mask - probseg: Probability maps (GM/WM/CSF)

Load standard MNI template

template <- get_template()

Get 2mm resolution template

template_2mm <- get_template(resolution = 2)

Load brain mask

mask <- get_template_brainmask()

Atlas Operations

Glasser Atlas

get_glasser_atlas(outspace = NULL)

Load Glasser multi-modal cortical parcellation

Schaefer Atlas

get_schaefer_atlas(parcels = c("100","200","300","400","500","600","800","1000"), networks = c("7","17"), resolution = c("1","2"), outspace = NULL)

Load Schaefer cortical parcellation

Surface Atlas

get_schaefer_surfatlas(parcels = "400", networks = "17", surf = c("inflated", "white", "pial"))

Load surface-based Schaefer atlas

Load Glasser atlas

glasser <- get_glasser_atlas()

Load Schaefer atlas with 400 parcels and 17 networks

schaefer <- get_schaefer_atlas(parcels = "400", networks = "17")

Load surface-based atlas

surf_atlas <- get_schaefer_surfatlas(parcels = "400", networks = "17", surf = "inflated")

Utility Functions

Atlas Manipulation

merge_atlases(atlas1, atlas2)

Combine two brain atlases into unified atlas

get_roi(atlas, label = NULL, id = NULL)

Extract specific regions from atlas

Visualization

ggseg_schaefer(atlas, vals, thresh = c(0,0), interactive = TRUE)

Create interactive visualization of Schaefer atlas

plot_glasser(atlas, ...)

Visualize Glasser atlas

Merge two atlases

merged <- merge_atlases(atlas1, atlas2)

Extract ROI

roi <- get_roi(atlas, label = "hippocampus")

Visualize atlas

ggseg_schaefer(atlas, values, thresh = c(-2, 2))

Common Workflows

1. Template-based analysis:

bbuchsbaum/neuroatlas documentation built on Dec. 24, 2024, 4:22 a.m.