Function reference • bstr

All functions
`BstrColormap-class` `BstrColormap`	An S4 class for representing colormaps
`BstrData-class` `BstrData`	S4 class for storing data for statistical analysis
`BstrModel-class` `BstrModel`	S4 class for representing the statistical model
`BstrOutput-class` `BstrOutput`	S4 class for saving results of statistical analysis
`BstrRmdOutput`	R6 super class for Rmd output functionality
`BstrRmdRoiOutput`	R6 derived class for Rmd ROI output functionality
`BstrRmdVolumeOutput`	R6 derived class for Rmd surface output functionality
`anova_vec()`	A vectorized version of analysis of variance (ANOVA).
`bs_BIDS_diffusion_file_string()`	Generate the BIDS designated diffusion surface file
`bs_BIDS_volume_jacobian_file_string()`	Generate the designated BIDS compatible (T1w) tensor-based morphometry file
`bs_analysis_type_to_readable_string`	Mapping of analysis_type to readable string
`bs_atlas_files`	List of atlas files used in BrainSuite
`bs_atlas_files_suffix`	List of suffixes for atlas files used in BrainSuite
`bs_binary_files`	List of binaries used in BrainSuite analysis
`bs_diffusion_file_string()`	Generate the designated diffusion surface file
`bs_file_formats`	List of file formats used in BrainSuite
`bs_model_type_to_readable_string`	Mapping of model_type to readable string
`bs_stat_overlays`	List of statistical and other overlay types used in BrainSuite
`bs_stat_overlays_mapping_to_label`	Mapping of stat overlays to label strings
`bs_surface_file_string()`	Generate the designated cortical surface file
`bs_volume_jacobian_file_string()`	Generate the designated tensor-based morphometry file
`bstr`	bstr: BrainSuite Statistics toolbox
`bstr_anova()`	Perform analysis of variance (ANOVA) for brain imaging data.
`bstr_corr()`	Test for Correlation between a variable `corr_var` and a brain imaging phenotype.
`bstr_lm()`	Linear regression for brain imaging data.
`bstr_lmer()`	Linear mixed-effects model for brain imaging data.
`bstr_load_roi_data()`	Load ROI data from subjects (BIDS compatible)
`bstr_p_adjust()`	Adjust p-values for multiple comparisons testing
`bstr_roi_anova()`	This function performs the ANOVA analysis for ROIs
`bstr_roi_lmer_anova()`	This function performs the ANOVA Linear Mixed Effects analysis for ROIs
`bstr_ttest()`	T-test for for brain imaging phenotypes
`check_file_exists()`	Check if file exists
`check_files()`	Check that subject directory and demographics files exist
`check_modelspec_validity()`	Check that modelspec.ini file is valid
`check_multiple_files_exists()`	Check if multiple files exists all at once
`check_tbm_atlas_and_mask()`	Check and return the maskfile and the atlas file
`colorbar()`	Generates the components of a colorbar for an individual voxelcoordinate and overlay
`coord2ind()`	Convert a 3D coordinate from an image to a linear vector index Equivalent to sub2ind from MATLAB(R) Does not perform error checking for bounds
`copy_dba_data()`	Package diffusion data for reproducible statistical analysis.
`copy_roi_data()`	Package ROI data for reproducible statistical analysis.
`copy_sba_data()`	Package cortical surface data for reproducible statistical analysis.
`copy_tbm_data()`	Package tensor-based morphometry data for reproducible statistical analysis.
`corr_vec()`	Vectorized correlation between a variable and brain imaging data.
`delete_and_recreate_dir()`	Delete and recreate directory
`file_copy()`	Copy files from the inputted source to the inputted destination
`get_brainsuite_atlas_id_from_logfile()`	Read the BrainSuite atlas identifier from the svreg log file.
`get_brainsuite_atlas_path_from_logfile()`	Read the BrainSuite atlas path from the svreg log file.
`get_brainsuite_install_path()`	Retrieve BrainSuite installation path
`get_brainsuite_logfilename()`	Gets the BraisSuite svreg.log file's filepath
`get_brainsuite_logfilename_for_all_subjects()`	Get the svreg log file for each subject
`get_brainsuite_path_from_bstr_ini()`	Retrieve BrainSuite installation path from bstr.ini
`get_brainsute_custom_volume_atlas_prefix()`	Read the BrainSuite atlas prefix from the atlas
`get_bs_file_list()`	Stops analysis if desired type of analysis is not a valid analysis type
`get_bstr_ini_path()`	Retrieve bstr.ini path in the package
`get_color_palette()`	Get a color palette (Hex color code list) for a colormap
`get_custom_dba_atlas_and_mask()`	Get the diffusion custom atlas and mask
`get_custom_sba_atlas_and_mask()`	Check that cortical surface atlas exists
`get_custom_tbm_atlas_and_mask()`	Get the custom tensor based morphometry atlas and mask
`get_dba_atlas()`	Get the BrainSuite tensor based morphometry atlas
`get_dba_atlas_and_mask()`	Get the diffusion atlas and mask
`get_dba_file_list()`	Returns a list of the diffusion files for all subjects
`get_dba_mask()`	Get the BrainSuite tensor based morphometry mask
`get_labeldesc_path()`	Retrieve label description path in the package
`get_logpvalue_colormap()`	Get log pvalue colormap
`get_logpvalue_colors()`	Get log pvalue colors, generate lut, and calculate min/max values
`get_render_image_filename()`	Returns the filename for the designated image
`get_roi_file_list()`	Returns a list of all ROI files for all subjects
`get_roi_name()`	Get the ROI name from the ROI label
`get_roi_specs()`	Get the ROI modelspec.ini file
`get_roi_tag()`	Get the ROI tag from the ROI label
`get_sba_atlas()`	Get the desired cortical surface atlas
`get_sba_atlas_files()`	Get the cortical surface modelspec.ini file
`get_sba_file_list()`	Returns a list of the cortical surface files for all subjects
`get_tbm_atlas()`	Get the BrainSuite tensor based morphometry atlas
`get_tbm_atlas_and_mask()`	Get the tensor based morphometry atlas and mask
`get_tbm_atlas_files()`	Get the tensor-based morphometry modelspec.ini file
`get_tbm_file_list()`	Returns a list of the tensor-based files for all subjects
`get_tbm_mask()`	Get the BrainSuite tensor based morphometry mask
`get_tvalue_colors()`	Get tvalue colors, generate lut, and calculate min/max values
`get_voxelcoord()`	Get voxel coordinates of all significant clusters (up to number of clusters)
`ind2coord()`	Convert a linear array index to a 3D coordinate in an image Equivalent to ind2sub from MATLAB(R) Does not perform error checking for bounds
`is_brainsute_installed()`	Check if BrainSuite is installed.
`is_valid_brainsute_install_path()`	Check if a given BrainSuite path is valid
`lm_vec()`	Vectorized linear regression for brain imaging phenotypes.
`lmer_vec()`	Vectorized linear mixed-effects regression for brain imaging phenotypes.
`load_bstr_data()`	Load data for statistical analysis.
`load_bstr_data_from_filelist()`	Load data for statistical analysis from a filelist
`load_data()`	A generic function to load data for statistical analysis.
`load_dba_data()`	Load diffusion data for statistical analysis.
`load_roi_data()`	Load ROI data for statistical analysis.
`load_sba_data()`	Load cortical surface data for statistical analysis.
`load_sba_data_from_filelist()`	Load cortical surface data for statistical analysis.
`load_tbm_data()`	Load tensor-based morphometry data for statistical analysis.
`load_tbm_data_from_filelist()`	Load TBM data from file list for statistical analysis.
`log10_transform()`	log10 transform
`package_data()`	Package data for reproducible statistical analysis.
`parse_lm()`	Returns an error if necessary elements are missing in the model
`parse_model()`	Returns a list denoting which elements are present in the model
`read_demographics()`	Reads the demographics from an inputted csv file
`read_label_desc()`	#' Read BrainSuite label description file #' @export read_label_desc_xml2 <- function() label_desc_filename <- system.file("extdata", "brainsuite_labeldescriptions_14May2014.xml", package = 'bstr') x1 <- xml2::read_xml(label_desc_filename) labels <-xml2::xml_find_all(x1, './/label') return (data.frame(roiid = xml2::xml_attr(labels, 'id'), roiname = xml2::xml_attr(labels, 'fullname'))) Read BrainSuite label description file
`read_modelspec()`	Read modelspec.ini file
`read_roi_data_for_all_subjects()`	Reads the BrainSuite ROI data file saved for each subject and returns the filenames
`read_roistats_txt()`	Read ROI stats file
`readdfs()`	Read dfs file
`readdfsattributes()`	Read dfs file attributes only
`roi_types`	List ofROI types
`save_BrainSuiteLUT()`	Saves and writes the lut for BrainSuite use
`save_bstr_color_files()`	Save the color LUT and ini colormap images
`save_bstr_out()`	Save the statistical analysis output
`save_bstr_out_nifti_image()`	Save the nifti image to the output file
`save_bstr_out_surface()`	Save the surface output to the given ouput directory
`save_bstr_rds()`	Save the measure to the output directory
`save_colorbar()`	Creates the display of a colorbar for an individual voxelcoordinate and overlay
`save_colormap_to_ini()`	Saves the colormap values for min and max to an ini file
`save_out()`	Generic save function for `BstrOutput`
`save_vol_stats_out()`	Save the volume statistics
`set_brainsuite_path_in_bstr_ini()`	Set BrainSuite installation path in bstr.ini
`setup()`	Setup script for bstr
`sign_tvalues()`	This function calculates the sign of t values. Differently from the sign() function, sign_tvalues(0) = 1
`ttest_vec()`	Vectorized t-test for for brain imaging phenotypes
`writedfs()`	Write dfs file

Reference

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