Dicom Que Es

[Liese Hittson]

DICOMstores within the Cloud Healthcare API support a subset of the RESTful webservices specified in the DICOM PS3.18 - Web Servicesstandard (commonly referred to as DICOMweb). Specifically, they support theStudies Service and Resources(previously referred to as the WADO-RS, STOW-RS, and QIDO-RS services).

A transfer syntax of * allows the user to request no transcoding be done, sothe transfer syntax of the uploaded file will be used. For application/octet-streamthe bulk data will be returned in whatever format it appears in the uploaded DICOMfile.

By default, RetrieveMetadata doesn't return any attribute which has a DICOMValue Representation of OB, OW, or UN. To return BulkDataURIs for tags matchingthe PreviewBulkdata definition,use thePreview version.

DICOM sequence tags containing more than approximately 1 MiB of data will notbe returned in metadata resources. This limitation applies to metadata resourcesonly. DICOM resources will still contain these tags.

The above Accept headers describe what media types & transfer syntaxes you canrequest from the API, but this may not always be possible depending on the transfer syntaxof the original file that was uploaded. In particular, transcoding is only possiblefrom the following transfer syntaxes:

The store transaction either accepts Part 10 DICOM binary files directly or itaccepts splitting of a DICOM file into metadata (represented in JSON) and bulk data.These 2 versions have different semantics that are described in the followingsections.

Note that for convenience, the Store Transaction also accepts a single part HTTP requestwith a single DICOM instance with content type application/dicom. This is notpart of the official DICOMweb standard.

The first part must have a Content-Type of application/dicom+json; transfer-syntax=TransferSyntaxUIDwhere TransferSyntaxUID is the transfer syntax which was used to encode binary data in InlineBinary objects.If no InlineBinary objects are present in the metadata, the transfer-syntax parameter can be omitted.

The SpecificCharacterSet element must be set to ISO_IR 192, and the JSONmetadata must be encoded in unicode UTF-8. The TransferSyntaxUID can be set toany valid transfer syntax, except for the following unsupported transfersyntaxes:

Within the JSON metadata, the user can specify multiple BulkDataURIs for DICOM tags with VRs of OB, OW, or UN.These BulkDataURIs indicate that the binary data for the tag which contains the URI will be sent in a following part which has the Content-Location header set to the BulkDataURI.

Each instance in the JSON metadata can have at most one BulkDataURI. There must not be any duplicate BulkDataURIs in the JSON metadata. Compressed image bulk data must only be sent for the PixelData tag, and when sent, the transfer syntax specified in the bulk data part must match the value of the instance's TransferSyntaxUID element.

An alternative method to specify binary data is to encode it as an InlineBinary base64 encoded string.This is supported for all tags except PixelData, which must be sent as a bulk data part.When InlineBinary objects are used in the JSON metadata, the transfer syntax which was used for encoding must be specified in the Content-Type of the JSON metadata part.

Paging is supported using the limit and offset query parameters. There isno Warning response header if no more results are available. You must executean extra query to determine if there are more results.

limit: Maximum number of results that should be returned, up to a maximumof 5,000 for studies/series and 50,000 for instances. The default number ofresults is 100 for studies/series and 1,000 for instances.

By default, searchForInstances doesn't return any attribute which has a DICOMValue Representation of OB, OW, or UN. To return BulkDataURIs for tags matchingthe PreviewBulkdata definition,use thePreview searchForInstances.

In the case of SearchForStudies/SearchForSeries there is a potential forinconsistent study/series level metadata across multiple instances. For example,two instances could be uploaded with the same StudyInstanceUID but havedifferent StudyDates. In this case, the search behavior is not well defined.Searching by that value may work in some cases, but not others and the returnedvalue may vary across different calls.

These use the same request paths as their WADO-RS counterparts (RetrieveStudy, RetrieveSeries, and RetrieveInstance, respectively). Instead of an HTTP GET request, a DELETE request is used. The effect is that the specified study, series, or instance is deleted along with all the DICOM resources contained in it.

The DeleteStudyand DeleteSeries methods return a long running operationwhich deletes all of the instances in the study or series. Please note that instances cannot be inserted into a study or series that is being deleted by an operation until the operation completes.

Some of the above methods provide the ability to control the response formatusing HTTP Accept headers. Wildcard matching is supported at both the top level(e.g. */*) and subtype (e.g. image/*). Specifying a q value is alsosupported to indicate relative preference. If a q value is not specified foran Accept header, it is set to the default value of 1.0.

In the event that multiple Accept headers are specified and there is a tiebetween the highest preference Accept headers, the server will choose the Acceptheader. Clients should not depend on the server's choice of Accept header inthis scenario.

The Cloud Healthcare API can ingest and do basic retrieval of all DICOMSOP classes. For any retrieval that requires transcoding between image formats,see supported transfer syntaxes for transcoding for a list ofsupported transfer syntaxes.

When retrieving metadata with Preview methods, the Cloud Healthcare API will excludecertain tags that are defined as bulkdata. Instead, these tags will be returnedalongside metadata with a BulkDataURI that allows the user to retrieve contentsof these tags (seeRetrieveBulkdata).The following is the definition used by the Cloud Healthcare API:

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I noticed that the local dicom database files stick around even when you delete all the patients, and will continue growing in size as more patients are added and removed. I would like to clean up these files to prevent any issues if a computer has to process many patients.

Also, it points to the sql data file in the folder. If i just assigned that to a new path with the same data file name, would it create a new file with the given name or would i have to initialize the database somehow?

I'm using a set of dicom files for my tests, and I've been printing the "Photometric Interpretation" and the "Sample Per Pixel" values, to have a better understanding of what kind of images I'm working with.

But what is the Sample Per Pixel exactly? I thought this was representing the number of bytes (and not bits) per pixel (that would be logic to have 8 bits per pixel for a scale of gray right?)

These tell you how many bits are used to encode a pixel value (BitsAllocated) and which of these bits really contain grayscale information (BitsStored, HighBit). HighBit is zero-based and usually but not necessarily = BitsStored-1

An example to illustrate this: For CT images, it is very common to express gray values in hounsfield units which range from -1000 to +3000. These are represented by 12 bits which are stored with a 2-byte-alignment, so

Another degree of freedom is PixelRepresentation which tells you if the pixel data is encoded unsigned (0) or in 2s complement (1). I have seen both for CT images, however signed pixel data is rather unusual for image types other than CT.

I have over-simplified a bit here, especially about color images but I think this is complicated enough ;-). Basically, DICOM offers any thinkable degree of freedom to encode pixel data and describe the encoding in the header.

I think I have recommended you to have a look at the DCMTK in a recent post. The DicomImage class features a nice interface (getInterData()) which cares about all that stuff and provides the pixel data read from a DICOM file in a normalized format.

Is there a way/plugin to convert a non-standard DICOM file to a standards compliant DICOM P10 file? I am currently using orthanc as a WADO server, and cornerstone on the frontend to display the DICOM images. cornerstone's dicomParser is very strict with standard-compliance, and keeps throwing the following error:Uncaught dicomParser.parseDicom: DICM prefix not found at location 132I had posted this question on cornerstone platform's group below: !topic/cornerstone-platform/n6lSGyjoS8gIs there any way around this?

DICOM (Digital Imaging and Communications in Medicine) enables the transfer of medical images in a multi-vendor environment and facilitates the development and expansion of picture archiving and communication systems. The DICOM Standard is available for download at no charge at www.dicomstandard.org.

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I have been trying to upload some DICOM files from a (Siemens) MEGA-PRESS acquisition into the Osprey GUI (have also tried using the command line - [MRSCont] = OspreyLoad(MRSCont) after creating an MRSCont file in the GUI).

I was playing around with some of the functions today, trying to load the DICOMs using io_loadspec_dicom() and I am getting an error "Unable to perform assignment because the size of the left side is 1024-by-1 and the size of the right side is 0-by-1. " Not sure if this is related to the issue or not (I did just try this with one or two dicoms in the folder so it may be a completely different error).

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