dcm2dir 0.1.0

Dicom Organizer: Organize DICOM files into a structured output folder.

dcm2dir

Dicom Organizer recursively scans a given root folder for DICOM files, extracts relevant metadata, and organizes the files into a structured output folder.# DICOM Organizer

Description

This Python script recursively scans a given root folder for DICOM files, extracts relevant metadata, and organizes the files into a structured output folder. The folder structure is customizable using placeholders for different DICOM tags. Additionally, a CSV report is generated with details of all processed DICOM series.

Features

• Recursively scans and organizes DICOM files.
• Supports customizable folder structures.
• Utilizes multi-threading for faster processing.
• Generates a CSV report listing all series metadata.
• Handles missing DICOM tags gracefully.

Installation

Ensure you have Python installed, then install the required dependencies:

pip install pydicom tqdm

Usage

Run the script with the following command-line arguments:

python dcm2dir.py -i <input_folder> -o <output_folder> [-r <csv_report>] [-f <folder_structure>]

Arguments:

• -i, --input (required): Path to the root folder containing DICOM files.
• -o, --output (required): Path to the destination folder where organized files will be stored.
• -r, --report (optional): Path to save the generated CSV report.
• -f, --folder-structure (optional): Custom folder structure using placeholders. See "Folder Structure" section.

Example Usage:

python dcm2dir.py -i ./dicoms -o ./organized -r report.csv -f "%i/%x_%t/%s_%d"

Folder Structure:

The folder structure can be customized using placeholders for different DICOM tags. The following placeholders are available:

• %a: Antenna (coil) name
• %b: Basename
• %c: Comments
• %d: Description
• %e: Echo number
• %f: Folder name
• %g: Accession number
• %i: ID of patient
• %j: SeriesInstanceUID
• %k: StudyInstanceUID
• %m: Manufacturer
• %n: Name of patient
• %o: MediaObjectInstanceUID
• %p: Protocol
• %r: Instance number
• %s: Series number
• %t: Exam date
• %u: Acquisition number
• %v: Vendor
• %x: Study ID
• %z: Sequence name

If -f is not provided, the default structure is used:

"-f %i/%x_%t/%s_%d"

which correspond to:

- <PatientID>
    - <StudyID>_<ExamDate>
        -<SeriesNumber>_<SeriesDescription>

Output

The script organizes DICOM files into the specified output folder following the given structure. A CSV report is saved, containing the following columns:

• SubjectID
• ExamDate
• ExamID
• SeriesID
• SeriesDescription

Notes

• Non-alphanumeric characters in metadata are replaced with underscores.
• If a DICOM tag is missing, a default placeholder na is used.
• The script uses multi-threading for better performance.

License

This project is open-source and available under the MIT License.