RFT_vertex_analysis: Vertex-wise analysis with random field theory cluster correction

Description

Fits a linear or linear mixed model with the cortical or hippocampal surface data as the predicted outcome, and returns cluster-thresholded (Random field theory) t-stat map selected contrast.

Usage

RFT_vertex_analysis(
  model,
  contrast,
  random,
  formula,
  formula_dataset,
  inverse = FALSE,
  surf_data,
  p = 0.05,
  atlas = 1,
  smooth_FWHM,
  VWR_check = TRUE
)

Value

A list object containing the cluster level results, unthresholded t-stat map, thresholded t-stat map, positive, negative and bidirectional cluster maps, and a FDR-corrected p-value map.

Arguments

model

An N X P data.frame object containing N rows for each subject and P columns for each predictor included in the model. This data.frame should not include the random effects variable.

contrast

A N x 1 numeric vector or object containing the values of the predictor of interest. Its length should equal the number of subjects in model (and can be a single column from model). The cluster-thresholded t-stat maps will be estimated only for this predictor.

random

A N x 1 numeric vector or object containing the values of the random variable (optional). Its length should be equal to the number of subjects in model (it should NOT be inside the model data.frame).

formula

An optional string or formula object describing the predictors to be fitted against the surface data, replacing the model, contrast, or random arguments. If this argument is used, the formula_dataset argument must also be provided.

The dependent variable (DV) is not needed, and the formula will start with ~. The DV will be the surface data value by default, but it can be swapped with contrast as IV via the "inverse" argument.
The first independent variable in the formula will always be interpreted as the contrast of interest for which to estimate cluster-thresholded t-stat maps.
Only one random regressor can be given and must be indicated as '(1|variable_name)'.

formula_dataset

An optional data.frame object containing the independent variables to be used with the formula (the IV names in the formula must match their column names in the dataset).

inverse

A boolean object stating whether to set the surface data as predictor of the contrast variable, instead of as dependent variable (default is FALSE). Other covariates in the model remain independent variables. This makes modelling slower.

surf_data

A N x V matrix object containing the surface data (N row for each subject, V for each vertex), in fsaverage5 (20484 vertices), fsaverage6 (81924 vertices), fslr32k (64984 vertices) or hippocampal (14524 vertices) space. See also Hipvextract(), SURFvextract() or FSLRvextract output formats. Alternatively, a string object containing the path to the surface object (.rds file) outputted by extraction functions may be given.

p

A numeric object specifying the p-value to threshold the results (Default is 0.05)

atlas

A numeric integer object corresponding to the atlas of interest. 1=Desikan, 2=Destrieux-148, 3=Glasser-360, 4=Schaefer-100, 5=Schaefer-200, 6=Schaefer-400. Set to 1 by default. This argument is ignored for hippocampal surfaces. For applicable SubCortexMesh surfaces, 1=default base ROI, 2=anatomical atlas.

smooth_FWHM

A numeric vector object specifying the desired smoothing width in mm. It should not be specified if the surf_data has been smoothed previously with smooth_surf(), because this result in surf_data being smoothed twice.

VWR_check

A boolean object specifying whether to check and validate system requirements. Default is TRUE.

Details

The function imports and adapts the 'BrainStat' Python library.

By default, false discovery rate correction is used together with the Random field theory (RFT) cluster correction. To look at data without any form of cluster correction, users can simply refer to the outputted 'tstat_map'.

Output definitions:

nverts: number of vertices in the cluster
P: p-value of the cluster
X, Y and Z: MNI coordinates of the vertex with the highest t-statistic in the cluster.
tstat: t statistic of the vertex with the highest t-statistic in the cluster
region: the region this highest -statistic vertex is located in, as determined/labelled by the selected atlas

Examples

Run this code

demodata = readRDS(system.file('demo_data/SPRENG_behdata_site1.rds', 
package = 'VertexWiseR'))[1:100,]
CTv = readRDS(file = url(paste0("https://github.com",
"/CogBrainHealthLab/VertexWiseR/blob/main/inst/demo_data/",
"SPRENG_CTv_site1.rds?raw=TRUE")))[1:100,] 

vertexwise_model=RFT_vertex_analysis(model=demodata[,c("sex","age")], 
contrast=demodata[,"age"], surf_data = CTv, atlas=1,p = 0.05, 
VWR_check=FALSE)

#Description of the output:
#vertexwise_model$cluster_level_results

#Formula alternative:
#formula= as.formula("~ age + sex")
#vertexwise_model=RFT_vertex_analysis(formula=formula, 
#formula_dataset=demodata, surf_data = CTv, atlas=1, p = 0.05, 
#VWR_check=FALSE)