This function creates an fMRI dataset object specifically from H5 files using the fmristore package. Each scan is stored as an H5 file that loads to an H5NeuroVec object.
Usage
fmri_h5_dataset(
h5_files,
mask_source,
TR,
run_length,
event_table = data.frame(),
base_path = ".",
censor = NULL,
preload = FALSE,
mask_dataset = "data/elements",
data_dataset = "data"
)Arguments
- h5_files
A vector of one or more file paths to H5 files containing the fMRI data.
- mask_source
File path to H5 mask file, regular mask file, or in-memory NeuroVol object.
- TR
The repetition time in seconds of the scan-to-scan interval.
- run_length
A vector of one or more integers indicating the number of scans in each run.
- event_table
A data.frame containing the event onsets and experimental variables. Default is an empty data.frame.
- base_path
The file path to be prepended to relative file names. Default is "." (current directory).
- censor
A binary vector indicating which scans to remove. Default is NULL.
- preload
Read H5NeuroVec objects eagerly rather than on first access. Default is FALSE.
- mask_dataset
Character string specifying the dataset path within H5 file for mask (default: "data/elements").
- data_dataset
Character string specifying the dataset path within H5 files for data (default: "data").
Value
An fMRI dataset object of class c("fmri_file_dataset", "volumetric_dataset", "fmri_dataset", "list").
Examples
if (FALSE) { # \dontrun{
# Create an fMRI dataset with H5NeuroVec files (standard fmristore format)
dset <- fmri_h5_dataset(
h5_files = c("scan1.h5", "scan2.h5", "scan3.h5"),
mask_source = "mask.h5",
TR = 2,
run_length = c(150, 150, 150)
)
# Create an fMRI dataset with H5 files and NIfTI mask
dset <- fmri_h5_dataset(
h5_files = "single_scan.h5",
mask_source = "mask.nii",
TR = 2,
run_length = 300
)
# Custom dataset paths (if using non-standard H5 structure)
dset <- fmri_h5_dataset(
h5_files = "custom_scan.h5",
mask_source = "custom_mask.h5",
TR = 2,
run_length = 200,
data_dataset = "my_data_path",
mask_dataset = "my_mask_path"
)
} # }