MR Images to PDF — Troubleshooting Common Conversion Issues

MR Images to PDF — Troubleshooting Common Conversion IssuesConverting MR (magnetic resonance) images to PDF is a common task for radiologists, clinicians, researchers, and patients who need to share, archive, or print scans. While the process is often straightforward, several issues can arise: poor image quality, large file sizes, missing metadata, incompatible file formats (DICOM vs. common image types), page orientation problems, and privacy concerns. This article walks through common problems, explains their causes, and gives practical step-by-step fixes and best practices to ensure reliable, secure, and high-quality MR-to-PDF conversions.

---

1. Understand the source: DICOM vs. standard image formats

Most MR scanners save images in DICOM (Digital Imaging and Communications in Medicine) format. DICOM files contain both image pixel data and extensive metadata (patient ID, study date, image orientation, slice location, acquisition parameters). Converting directly from DICOM to PDF is different from converting a standard image (JPEG, PNG, TIFF).

• If you start with DICOM, use a DICOM-aware tool to preserve metadata and ensure correct image orientation and window/level settings.
• If you have exported images as JPEG/PNG, you may already have windowing applied, but metadata is often lost and image quality may be altered by compression.

---

2. Common issues and fixes

Issue: Low image quality or poor contrast in the PDF

Causes:

• Incorrect window/level settings during export
• Over-compression when saving as JPEG before PDF conversion
• Downscaling during PDF creation

Fixes:

• Export directly from the PACS/viewer using a DICOM-to-PDF option when available; these usually capture the correct windowing.
• Adjust window/level in the viewer to the optimal setting before export.
• Export as lossless images (PNG or TIFF) or use direct DICOM-to-PDF conversion to avoid JPEG artifacts.
• Set high resolution (300–600 DPI) for the PDF if intended for printing; 150–300 DPI is usually sufficient for on-screen viewing.

Issue: Huge PDF file size

Causes:

• Multiple high-resolution slices embedded as separate images
• Using lossless TIFFs or embedding full DICOM images without compression
• Including unnecessary sequences or repeated images

Fixes:

• Choose appropriate image resolution and JPEG compression level (e.g., JPEG quality 80–90% balances size and quality).
• Remove redundant slices; include only representative series or key images.
• Use PDF tools that support image downsampling and compression during export.
• Combine images into a single PDF instead of embedding each DICOM as a full object where possible.

Issue: Missing or incorrect patient/study metadata

Causes:

• Converting exported JPEG/PNG images loses DICOM metadata.
• Some converters strip metadata for privacy by default.

Fixes:

• Use DICOM-aware converters to embed metadata into PDF as text or annotations if needed.
• For sharing, intentionally remove or redact personal data; use DICOM anonymizers or redact within the PDF.
• Verify header fields (patient name, DOB, study date) before finalizing — some viewers allow selecting which fields to include.

Issue: Orientation, slice ordering, or alignment incorrect

Causes:

• Viewer and converter use different orientation conventions.
• Slices exported out of acquisition order.
• Multiplanar reconstructions saved without preserving orientation tags.

Fixes:

• Use the PACS/viewer “Export to PDF” or “Print” function, which typically preserves orientation and ordering.
• Confirm slice order in the viewer before export; export full series instead of individual screenshots.
• Use tools that read DICOM tags (Image Position (Patient), Image Orientation (Patient)) to maintain correct placement.

Issue: Invisible overlays, annotations, or burned-in text

Causes:

• Overlays may be stored as separate layers in DICOM and not flattened during export.
• Some viewers render annotations on-screen but don’t include them in exported images.

Fixes:

• Enable burned-in annotations if you need the annotations visible in the PDF, or export both annotated and clean versions.
• Use the viewer’s export settings to include overlays/annotations, or use screenshot-to-PDF only when annotations are visible on screen and must be captured.
• For reporting, prefer embedding structured reports or separate annotation layers in the PDF if supported.

Issue: Multi-series or multi-study organization is lost

Causes:

• Simple image-to-PDF converters merge images without preserving series boundaries or study headers.
• File naming alone may not convey grouping.

Fixes:

• Use a converter that groups images by Series Description, Study Instance UID, or accession numbers and inserts headings in the PDF.
• Manually build a PDF with a table of contents and section headings for each series/study.
• Export each series as a separate PDF, then combine maintaining bookmarks.

Issue: Security and PHI leakage

Causes:

• DICOM metadata contains identifiable patient information.
• Sharing PDFs without anonymization can expose PHI.

Fixes:

• Use DICOM anonymization tools to strip or replace identifying tags before conversion.
• If metadata is needed for clinical reasons, restrict access and use secure transfer methods (encrypted email, secure file transfer).
• When sharing a PDF publicly or outside care teams, remove or redact patient identifiers and consider adding institutional headers instead.

---

3. Recommended tools and workflows

Short workflows for common needs:

• Quick clinical export (report + key images):

  1. In PACS viewer, set window/level and select key images.
  2. Use “Export to PDF” or “Print to PDF”—enable annotations/report inclusion as needed.
  3. Check metadata and redact if sharing externally.

• Research or archive (full series, metadata preserved):

  1. Use a DICOM-to-PDF tool that preserves tags (e.g., specialized DICOM tool or command-line utilities).
  2. Export lossless or minimal-compression images and embed study/series headers.
  3. Compress PDF wisely, and archive with checksums.

• Batch conversion:

  1. Use scripts or utilities (dcm2jpg/dcmj2pnm + imagemagick + ghostscript, or a dedicated DICOM toolkit) to convert series in bulk.
  2. Maintain naming and folder structure that mirrors Study/Series UIDs.
  3. Create combined PDFs with bookmarks per series.

Common tools:

• PACS viewer built-in PDF export (most reliable for orientation/metadata)
• OsiriX / Horos (macOS) — good UI and export options
• RadiAnt DICOM Viewer — fast exports on Windows
• dcm4che, pydicom, dicom2pdf scripts — for programmatic control
• ImageMagick + Ghostscript — for image processing and PDF creation (use cautiously; ensure DICOM tags handled separately)

---

4. Tips for maintaining diagnostic quality

• Preserve original pixel data when possible; avoid lossy JPEG for primary diagnostic images.
• Use consistent window/level settings and document them.
• For printed reports, 300 DPI and lossless or high-quality JPEG is recommended.
• Validate converted PDFs against original images to ensure no critical detail is lost.

---

5. Troubleshooting checklist

1. Verify source format (DICOM vs. exported images).
2. Confirm window/level and annotations are set how you want them.
3. Choose a conversion path that preserves required metadata.
4. Select resolution/compression balancing size vs. quality.
5. Check orientation and slice order in the output.
6. Redact or anonymize PHI before external sharing.
7. Test the PDF on multiple viewers to ensure portability.

---

6. Example: command-line batch conversion (concept)

Use pydicom to read DICOM, Pillow to save PNG, and ImageMagick/ghostscript to create PDF. (This is a conceptual outline — adapt to your environment.)

1. Read DICOM and apply window/level with pydicom + numpy.
2. Save slices as PNG/TIFF at desired resolution.
3. Use ImageMagick: convert -density 300 *.png output.pdf
4. Optionally compress PDF with ghostscript: gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/ebook -dNOPAUSE -dQUIET -dBATCH -sOutputFile=out_compressed.pdf output.pdf

---

7. Final notes

Converting MR images to PDF requires attention to image quality, metadata, ordering, and privacy. Choosing DICOM-aware tools and setting the correct export options will prevent most issues. For programmatic or bulk workflows, use libraries that understand DICOM tags and image pixel handling, and always validate output visually before clinical use.