cv-dicom-12bit-pixel-correction

Overview

Some DICOM files store pixel data as 12-bit unsigned integers (BitsStored=12, PixelRepresentation=0) but report a RescaleIntercept near 0 instead of -1024. This causes pixel values to wrap around at 4096, producing artifacts. Detecting and correcting this before HU conversion prevents corrupted images from entering the training pipeline.

Quick Start

import pydicom
import numpy as np

def correct_dcm(dcm):
    x = dcm.pixel_array + 1000
    px_mode = 4096
    x[x >= px_mode] = x[x >= px_mode] - px_mode
    dcm.PixelData = x.tobytes()
    dcm.RescaleIntercept = -1000

def safe_pixel_array(dcm):
    if (dcm.BitsStored == 12
        and dcm.PixelRepresentation == 0
        and int(dcm.RescaleIntercept) > -100):
        correct_dcm(dcm)
    return dcm.pixel_array * dcm.RescaleSlope + dcm.RescaleIntercept

Workflow

1. Check DICOM metadata: BitsStored, PixelRepresentation, RescaleIntercept
2. If 12-bit unsigned with suspiciously high intercept (> -100), apply correction
3. Shift pixels by +1000, wrap values >= 4096 back by subtracting 4096
4. Update RescaleIntercept to -1000 and rewrite PixelData
5. Proceed with normal HU conversion using corrected values

Key Decisions

• Detection condition: BitsStored==12 AND PixelRepresentation==0 AND RescaleIntercept > -100. This catches the specific encoder bug without affecting normal files.
• Shift value: +1000 followed by modulo 4096 unwraps the overflow. The new intercept (-1000) produces correct HU values.
• In-place vs copy: Modifying dcm.PixelData in-place is faster but mutates the object. Clone first if you need the original.

References

• RSNA InceptionV3 Keras