Transcoding of DICOM files ¶

Contents

Transcoding of DICOM files

General information ¶

DICOM transcoding refers to the process of changing the transfer syntax of some DICOM instance.

Transcoding can be used to compress DICOM images, which is useful to reduce the required storage area or to optimize the network bandwidth for exchanges between sites. Conversely, transcoding can be used to decompress DICOM images, which is needed as many DICOM viewers or specialized analysis software do not provide support for compressed transfer syntaxes.

Support for transcoding was introduced in Orthanc 1.7.0.

Motivation for transcoding ¶

Let’s consider the following basic workflow, in which some imaging workstation must access a medical image that originates from a PACS and that is served through an Orthanc proxy:

This is quite a common situation, e.g. in university hospitals where researchers must access medical images without having authorization to log in the clinical PACS. It is also common if the main PACS restricts the number of workstations that can directly be connected to it, or if Orthanc acts as gateway through Internet.

The problem is that the software running on workstations might not be able to display some DICOM transfer syntaxes. This is especially true in research software, that is often limited to uncompressed transfer syntaxes. For instance, let’s consider the following scenario where a workstation wants to access an image from the PACS:

A typical PACS system will decide, when requested to export an image using DICOM C-Store, to compress the image in order to reduce the network bandwidth and the storage requirements. Orthanc is fine with it: As a vendor neutral archive, Orthanc can basically receive/store/transmit any DICOM transfer syntax. Unfortunately, this might not be the case of the target workstation, that is often limited to some selected transfer syntaxes. As a consequence, the workstation will complain about not being to use the DICOM file (in the situation depicted above, because the PACS has decided to send the DICOM image using the JPEG2k transfer syntax).

Transcoding in Orthanc ¶

Orthanc 1.7.0 was the first release of Orthanc to feature built-in support for DICOM transcoding. Transcoding is available at multiple levels, as depicted by the green arrows on the following drawing:

Automated transcoding while ingesting. Orthanc can be configured to automatically transcode each DICOM instance it receives (either by DICOM protocol or by REST API) to a fixed transfer syntax. This is especially useful to either create an archive of compressed files (for long-term archiving), or to create a DICOM buffer with uncompressed files (for interfacing with DICOM modalities that do not support compressed transfer syntaxes). If the transcoding fails, the DICOM instance is still stored using its original transfer syntax.

Automated transcoding is enabled by setting the configuration option IngestTranscoding to the transfer syntax UID of interest. For instance, setting IngestTranscoding to 1.2.840.10008.1.2.1 will decompress all the received DICOM instances. Conversely, setting it to 1.2.840.10008.1.2.4.70 will compress and store images using JPEG Lossless.

NB: Starting with Orthanc 1.8.2, the option IngestTranscodingOfUncompressed (resp. IngestTranscodingOfCompressed) is available to control whether the ingest transcoding is applied to uncompressed transfer syntaxes (resp. compressed transfer syntaxes). By “uncompressed” transfer syntaxes, we mean Little Endian Implicit, Little Endian Explicit, or Big Endian Explicit. By default, these options are considered as equal to true, meaning that all the transfer syntaxes are transcoded.
Decompression while sending instances using the DICOM protocol. Orthanc can be configured to automatically decompress DICOM images on its outgoing connections, if the remote modality does not support the compressed transfer syntax of the source DICOM instances. This feature is available for both DICOM C-Move and C-Get commands. Note that Orthanc won’t transcode DICOM instances to a compressed transfer syntax over the DICOM protocol.

By default, this automated decompression is enabled. This might be undesirable if you want to limit the resources that are used by Orthanc. As a consequence, you can disable this feature either globally (by setting configuration option TranscodeDicomProtocol to false), or on a per-modality basis (by setting the option AllowTranscoding to false in the DicomModalities section).

Transcoding while sending instances to an Orthanc peer. The /peers/{id}/store route in the Orthanc REST API allows to send DICOM resources (patients, studies, series or instances) to another Orthanc server over HTTP/HTTPS. Starting with Orthanc 1.7.0, the Transcode option can be used in the JSON POST body to instruct to transcode the DICOM files before they are sent. For instance:
```
$ curl -X POST http://localhost:8042/peers/sample/store -d '{"Transcode":"1.2.840.10008.1.2.4.70","Resources":["66c8e41e-ac3a9029-0b85e42a-8195ee0a-92c2e62e"]}'
```
Transcoding using the REST API. Starting with Orthanc 1.7.0, some routes in the REST API also accept the Transcode option in their JSON POST body. Those routes notably include:
- The routes to create ZIP files or DICOMDIR archives (.../media and .../archive).
- The routes to modify DICOM resources (/{patients|studies|series|instances}/{id}/modify).

Importantly, if you need to transcode JPEG2k DICOM instances, you’ll have to install the GDCM plugin that replaces the built-in transcoder of Orthanc based on DCMTK, by the GDCM transcoder.

The following advanced configuration options are also available to control transcoding:

BuiltinDecoderTranscoderOrder controls the transcoder that is used by Orthanc. It specifies whether the built-in transcoder of Orthanc (that uses DCMTK) is applied before or after the transcoding plugins, or not applied at all. “After” means that the built-in transcoder is applied if all the transcoding plugins have failed to transcode the image.
DicomLossyTranscodingQuality controls the quality level of lossy compression (notably for JPEG transcoding).

Solutions to avoid transcoding ¶

Up to release 1.6.1, Orthanc didn’t feature support for transcoding DICOM instances. In other words, the Orthanc core never changed the transfer syntax of some DICOM instance when it had to send it to another modality using the DICOM protocol.

Three workarounds were available to bypass the need for DICOM transcoding in Orthanc <= 1.6.1. These workarounds are still valid in Orthanc >= 1.7.0, if transcoding is undesirable (e.g. if Orthanc is being run on a computer with sparse CPU/RAM resources).

Refusing transfer syntaxes ¶

The first solution consists in making Orthanc refuse to accept the transfer syntaxes that are not supported by the workstation. This is depicted in the following diagram:

If Orthanc tells the PACS that is doesn’t accept, say, DICOM JPEG2k, the source PACS will be aware of this, and will take care of transcoding the DICOM files before they are sent to Orthanc. This is the role of the following configuration options that specifies which transfer syntaxes are accepted by Orthanc:

{
  "DeflatedTransferSyntaxAccepted"     : true,
  "JpegTransferSyntaxAccepted"         : true,
  "Jpeg2000TransferSyntaxAccepted"     : true,
  "JpegLosslessTransferSyntaxAccepted" : true,
  "JpipTransferSyntaxAccepted"         : true,
  "Mpeg2TransferSyntaxAccepted"        : true,
  "RleTransferSyntaxAccepted"          : true,
  "UnknownSopClassAccepted"            : false
}

If all of those options are set to false, Orthanc will only receive uncompressed transfer syntaxes (obviously provided that the source PACS itself supports DICOM transcoding).

Using external conversion tools ¶

The second solution consists in applying an external conversion tool to every DICOM image that is received by Orthanc. The standard command-line tools gdcmconv from GDCM or dcmconv from DCMTK can be used to change the transfer syntax of a given DICOM file. These tools can be invoked from a Lua script (check out OnStoredInstance() callback) or from an Orthanc plugin (check out OrthancPluginRegisterOnStoredInstanceCallback() function). A sample Lua script that converts every incoming DICOM file to the JPEG2k transfer syntax is part of the Orthanc sources. Note that this solution makes no sense anymore in Orthanc 1.7.0, as it provides built-in support for transcoding.

Transcoding buffer ¶

Finally, as a third solution, it is possible to combine two Orthanc servers, the first one being configured to accept any transfer syntax, and the second one being responsible to serve the DICOM files after conversion to uncompressed transfer syntax (which should be compatible with any workstation):

In this solution, the first Orthanc server acts as a transient server that implements the decompression (i.e. it transcodes all the DICOM instances it receives to an uncompressed transfer syntax). To carry on the transcoding, this first Orthanc server can be:

either an instance Orthanc >= 1.7.0, with transcoding enabled, or
an instance of Orthanc (any version) equipped with a plugin or an external script to do the necessary conversions to an uncompressed transfer syntax, as explained in the second solution above.

Whenever a DICOM instance is received by the first Orthanc, the DICOM instance is thus transcoded. The first Orthanc server automatically forwards all the transcoded instances to the second instance of Orthanc, thanks to a Lua script or an external script, taking advantage of Orthanc peering.

Contrarily to the second solution, this solution has the advantage of better scalability (as decompression can be a time-consuming operation). The second instance of Orthanc can run even on a low-end computer, with any version of Orthanc.