Apply a transformation to BIDS files

This function orchestrates the process of selecting files from a BIDS project, applying a transformation to each file, and saving the output in a new BIDS derivative directory. It leverages the existing bidser parsing and search infrastructure.

Usage

bids_transform(x, transformer, pipeline_name, ...)

Arguments

x

A bids_project object.

transformer

A function that performs the transformation. It must take two arguments, the input file path and the output directory, and return the output file path. The transformer is responsible for creating the output file.

pipeline_name

The name for the new derivative pipeline.

...

Additional arguments passed to search_files to select files (e.g., subid = "01", task = "rest").

Value

A character vector of paths to the newly created files.

Examples

# \donttest{
tryCatch({
  ds_path <- get_example_bids_dataset("ds001")
  proj <- bids_project(ds_path)

  # Create a simple transformer that adds a description
  add_desc_transformer <- function(infile, outdir) {
    entities <- encode(basename(infile))
    entities$desc <- if (is.null(entities$desc)) "smooth6mm" else 
                     paste(entities$desc, "smooth6mm", sep="")
    
    # Generate new filename
    new_name <- decode_bids_entities(entities)
    outfile <- file.path(outdir, new_name)
    
    # For demo, just copy the file (real transformer would process it)
    file.copy(infile, outfile)
    return(outfile)
  }

  # Apply transformation to functional files for subject 01
  new_files <- bids_transform(proj, add_desc_transformer, "smoothed",
                              subid = "01", suffix = "bold.nii.gz")
  print(length(new_files))

}, error = function(e) {
  message("Example failed: ", e$message)
})
#> No files found matching the selection criteria.
#> [1] 0
# }