crop_to_content_dataset

Crop every NIfTI file in a folder to its minimal foreground box.

crop_to_content_dataset(
    nii_folder: str,
    output_path: str,
    threshold: Optional[float] = None,
    margin: int = 0,
    debug: bool = False
) -> List[str]

Overview

Batch version of crop_to_content: trims blank borders from every .nii.gz file in nii_folder, each with a correct affine. Files that fail to process (including empty volumes) are skipped with a warning.

Parameters

Name	Type	Default	Description
nii_folder	str	required	Folder containing .nii.gz files.
output_path	str	required	Output directory for cropped files.
threshold	float	None	Foreground cutoff. None keeps all non-zero voxels.
margin	int	0	Voxels of padding kept around each box.
debug	bool	False	If True, logs details for each file.

Returns

List[str] – List of output file paths (one per successfully processed file).

Exceptions

Exception	Condition
FileNotFoundError	Folder does not exist or contains no .nii.gz files

Usage Notes

• Per-file boxes: each volume is cropped to its own foreground extent, so output shapes may differ between files.
• Error Handling: files that fail (e.g. empty volumes) are skipped with a warning.
• Progress Display: shows a tqdm progress bar during processing.

Examples

from nidataset.spatial import crop_to_content_dataset

paths = crop_to_content_dataset(
    nii_folder="dataset/scans/",
    output_path="dataset/content/",
    margin=2,
)
print(f"Cropped {len(paths)} volumes")