Bidsify command
The lacuna bidsify command converts a directory of NIfTI mask files to BIDS format.
Synopsis
lacuna bidsify <input_dir> <output_dir> --space <SPACE> [options]
Description
Converts loose NIfTI mask files into a BIDS-compliant dataset structure. Input filenames become subject IDs (special characters are removed). For example: patient_001.nii.gz becomes sub-patient001/.
Arguments
Required arguments
| Argument |
Description |
input_dir |
Directory containing NIfTI mask files (.nii or .nii.gz) |
output_dir |
Output directory for BIDS dataset |
--space, -s |
Coordinate space of the masks: MNI152NLin6Asym or MNI152NLin2009cAsym |
Optional BIDS entities
| Option |
Description |
--session LABEL, -ses LABEL |
Session label (e.g., 01, baseline). Creates ses-<label> subdirectory. |
--label NAME, -l NAME |
Label for the mask entity (e.g., lesion, tumor) |
Other options
| Option |
Description |
-v, --verbose |
Print progress messages |
Examples
# Basic conversion
lacuna bidsify /raw/masks /bids --space MNI152NLin6Asym
# With session and label
lacuna bidsify /raw /bids --space MNI152NLin6Asym --session 01 --label lesion
# Different MNI space
lacuna bidsify ./masks ./bids_masks --space MNI152NLin2009cAsym
See Also