utils/dicom

DICOM Tools

Inspect a DICOM study, convert it to NIfTI, PNG or MP4, and validate DICOM objects.

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Overview

What it does

DICOM Tools are the file utilities behind every MedRun upload, available as runs of their own. They answer the practical questions that come before and after any analysis: what is on this CD, which series belong together, can this object be opened elsewhere, and is this DICOM file well formed.

Three tools make up the model. Inspect, the default, reads files, zips or a DICOMDIR and returns a manifest of studies, series and instances. Convert turns DICOM into analysis and viewing formats and back. Validate checks a DICOM object against the standard and lists what is wrong with it.

Intended use

Technical support for anyone moving imaging data between systems: checking a patient CD before reading it, preparing NIfTI volumes and label maps for training and analysis, producing MP4 previews of cine loops, and checking that a segmentation or structured report is accepted by a PACS before it is sent. These tools do not interpret images.

Who it is for

Radiographers, PACS administrators, imaging researchers and data scientists, and developers who integrate MedRun into their own systems and need to see a study the way MedRun sees it.

Inputs and protocol

Accepted input

DICOM: Part 10 files, multi-frame objects, zips, and CD or DVD exports with a DICOMDIR.
Derived objects: Segmentation (SEG), RT Structure Set (RTSTRUCT) and Structured Report (SR) objects for conversion or validation.
Other formats for conversion: NIfTI-1/2, NRRD and MHA volumes, MP4 and AVI cine exports, PNG, JPEG and HEIC images, and PDF.

Compressed pixel data in JPEG, JPEG-LS, JPEG 2000 and HTJ2K transfer syntaxes is decoded; MONOCHROME1 images are inverted and rescale slope and intercept applied before conversion.

What inspect reads

Item	Why
Study and Series Instance UIDs	Groups instances into studies and series
Byte-identical and repeated SOP instances	Duplicates on CD exports are listed and skipped
Transfer syntax and multi-frame layout	Shows how each object is encoded
Spacing, orientation, frame rate and calibration	The geometry and timing that models depend on
Burned-in annotation attribute, free-text fields and private tags	Shows which files carry text in the pixels or vendor-specific data elements

Optional context

For conversion, the target format (for example NIfTI with BIDS sidecars, PNG or MP4) is chosen in options.

Outputs and standards

The result

Each tool returns its own result. The default run returns the inspection manifest.

Tool	Content
Inspect (default)	Study manifest: studies, series, instances, duplicates, transfer syntaxes, multi-frame details, geometry and timing
Convert	DICOM to NIfTI, NRRD, PNG or MP4; SEG and RTSTRUCT to and from NIfTI label maps; transfer-syntax transcoding; cine to MP4 preview
Validate	Validation report: missing Type 1 and Type 2 attributes, wrong value representations, invalid UIDs, SEG and SR template errors

Standards

Manifest: DICOM JSON model (PS3.18), the same representation DICOMweb uses.
Conversion targets: NIfTI-1/2 with BIDS 1.11 sidecars; DICOM Segmentation Storage and Label Map Segmentation Storage; RTSTRUCT; MP4 (H.264).
Validation rules: IOD module tables of PS3.3 (Type 1, 2 and 3 attributes) and SR template constraints of PS3.16.
Interchange: DICOMweb QIDO-RS, WADO-RS and STOW-RS (PS3.18).

Related tools

utils/dicom/inspect: study manifest of any upload; the default run of this model.
utils/dicom/convert: format conversion of images, cine loops and segmentations.
utils/dicom/validate: validation report for a DICOM object, uploaded or produced by MedRun.

Files are read as uploaded, and nothing in the source files is changed.