Creates a group dataset from NIfTI files containing effect sizes and their standard errors or variances. Supports various input configurations including beta/SE pairs, beta/variance pairs, or t-statistics with degrees of freedom.
Usage
group_data_from_nifti(
beta_paths = NULL,
se_paths = NULL,
var_paths = NULL,
t_paths = NULL,
df = NULL,
subjects = NULL,
covariates = NULL,
mask = NULL,
target_space = NULL,
validate = TRUE
)Arguments
- beta_paths
Character vector of paths to beta/effect size NIfTI files
- se_paths
Character vector of paths to standard error NIfTI files
- var_paths
Character vector of paths to variance NIfTI files (alternative to se_paths)
- t_paths
Character vector of paths to t-statistic NIfTI files
- df
Degrees of freedom (scalar or vector). Required if using t_paths.
- subjects
Character vector of subject identifiers. If NULL, extracted from file paths.
- covariates
Data frame of subject-level covariates (optional)
- mask
Path to mask NIfTI file or mask object (optional but recommended)
- target_space
Path to template NIfTI for spatial alignment checking
- validate
Logical. Validate that all files exist and have matching dimensions (default: TRUE)
Examples
if (FALSE) { # \dontrun{
# From FSL FEAT output (COPE and VARCOPE files)
gd <- group_data_from_nifti(
beta_paths = Sys.glob("feat_output/sub-*/cope1.nii.gz"),
var_paths = Sys.glob("feat_output/sub-*/varcope1.nii.gz"),
subjects = sprintf("sub-%02d", 1:20),
mask = "group_mask.nii.gz"
)
# From SPM contrast images
gd <- group_data_from_nifti(
beta_paths = Sys.glob("SPM/sub*/con_0001.nii"),
se_paths = Sys.glob("SPM/sub*/se_0001.nii"),
mask = "SPM/mask.nii"
)
# From t-statistics only (for Stouffer's Z combination)
gd <- group_data_from_nifti(
t_paths = Sys.glob("stats/sub-*/tstat1.nii.gz"),
df = 100, # Or vector of per-subject df
mask = "group_mask.nii.gz"
)
} # }