duck-dicom

Reader function

read_dicom

Read DICOM files directly into DuckDB, returning one row per file. Files that can’t be read as DICOM get a NULL entry in the dicom_content column.

Parameters:

Parameter	Type	Description	Required
filepath	VARCHAR	Path to the DICOM file read or glob pattern.	Yes
load_pixel_data	BOOL	Whether to import the pixel data. Default is false.	No

Return schema:

Column Name	Data Type	Description
path	VARCHAR	Path to the DICOM file.
dicom_content	JSON	JSON-rendered contents of the DICOM files.

Examples:

-- read one file
FROM read_dicom('path/to/dicom_file.dcm');

-- use glob pattern
FROM read_dicom('path/to/dicoms/**/*.dcm');

-- import pixel data
FROM read_dicom('path/to/dicom_file.dcm', load_pixel_data=true);

-- extract series description per series instance
SELECT
    dicom_content->'0020000E'->'Value' AS series_instance_uid,
    any_value(dicom_content->'0008103E'->'Value') AS series_description
FROM read_dicom('~/Downloads/slicer_export/**/*.dcm')
GROUP BY 1;

-- extract study description per study instance
SELECT
    dicom_content->'0020000D'->'Value' AS study_instance_uid,
    any_value(dicom_content->'00081030'->'Value') AS study_description
FROM read_dicom('~/Downloads/slicer_export/**/*.dcm')
GROUP BY 1;

The dicom extension also supports reading from cloud object storage through the httpfs extension:

-- configure httpfs and credentials
LOAD httpfs;

CREATE OR REPLACE SECRET my_secret (
    TYPE s3,
    PROVIDER config,
    KEY_ID 'my_key',
    SECRET 'my_secret_key',
    URL_STYLE 'path'
);

-- read one file from an AWS S3 bucket
FROM read_dicom('s3://my-bucket/path/to/dicom_file.dcm');

-- use glob pattern
FROM read_dicom('s3://my-bucket/path/to/dicoms/**/*.dcm');

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