8.10 How to upload DICOM Images

Owned by Pernille Marqvardsen
Last updated: Feb 22, 2024 by Julie Klapel
4 min read

DICOM images can be added as Resources in risr/assess. Grayscale, colour and multi slice DICOM images are supported.

Types of multi-slice DICOM formats supported:

  • single file, single slice DICOM (eg. chest-x-ray.dcm)

  • multiple file, multiple slice DICOM (eg. chest-x-ray-1.dcm, chest-x-ray-2.dcm, chest-x-ray-3.dcm)

  • single file, multiple slice DICOM (eg. chest-x-ray.dcm)

Each of these DICOM formats can be uploaded to risr/assess and will create a single Resource representing the DICOM image. When uploading DICOM images to risr/assess users need to use a ZIP ZIP file. Please see the next section for descriptions of the ZIP file structure for each of the file types above.

Supported formats

You can find more information on what DICOM formats we support here

Image size: For optimum performance we recommend that DICOM images with a maximum of 100 slices be used. Images with more than 100 slices can cause significant slowing when downloading the exams onto local devices.  

Total Exam Size: Practique supports a total exam size of 2GB. If you require larger exams than this please contact our service desk. 

Preparing a DICOM ZIP file

Single file, single slice DICOM and Single file, multi slice DICOM

These 2 cases are the simplest. In the screenshot on the left, the ZIP file structure is the same as for single-file-single-slice 

The user needs to produce a ZIP file which:

  • does not have any subfolders

  • DICOM image can have any name and/or extension

Multiple file, multiple slice DICOM

In this case, create a flat ZIP file containing only the files with individual slices of one DICOM image. In the screenshot below, the ZIP file structure would be the same as for multi-file-multi-slice. 

The user needs to produce ZIP file which:

  • does not have any subfolders

  • DICOM image can have any name and/or extension

  • Multiple slices are denoted by the increasing numeric filename

Exporting DICOM images from OsiriX

In this case risr/assess requires the user to create a hierarchical ZIP file containing only the files with individual slices of one DICOM image (See image below).

Let's consider the example database in OsiriX containing 3 patients with different DICOM imagery.

Select a patient and use the Export feature available in OsiriX.

For best results, use the export settings detailed below. There are many versions of OsiriX software which may have different export capabilities, the following information is applicable to OsiriX 14.x.

Select the OsiriX Export settings:

 

Once exported, a ZIP file will be generated. This ZIP file can be uploaded to items in risr/assess.

Filenames of the ZIP files will be the same as Patient name as that is the export option chosen.

When ZIP Files are extracted it is apparent what structure the OsiriX export achieved for various types of cases.

Notice that the structure of the ZIP files is the same for all cases. When "Patient" has multiple DICOM images (series) in OsiriX, the resulting ZIP file will contain the same number of folders as there is series, for example LC203.

 

Uploading DICOM images to risr/assess

Once user has prepared ZIP files either manually as per “Preparing DICOM ZIP file” or using OsiriX as per “Exporting DICOM images from OsiriX” ZIP files can be uploaded to risr/assess as Resources.

Keep in mind that in risr/assess one Resource corresponds to one DICOM image (can be multi-slice).

Users can use “+ Create new resource” when the ZIP file they’re uploading contains a single DICOM image (can be multiple slice).

When uploading a ZIP file (most likely export from OsiriX) which contains multiple DICOM images, (as for example LC203 mentioned above) user must use “+ Create multiple Resources” and risr/assess will create a Resource for each DICOM image which is contained within the ZIP archive.

DICOM file order

DICOMs contain many slices and the order of the slices can vary according to how the file is prepared. In risr/assess, the default display is the order the files are added in the ZIP file.

To view the DICOM file order for the resource in risr/assess, find the resource in the Resource library and click View. Find and click the link ‘Show DICOM File details’ below the DICOM image. The order of the slices are displayed.

There is an option to edit the file order once the resource is uploaded and still in a DRAFT state.

To edit the file order, find the DICOM resource in Resource library. Click View and then Edit.

DICOM File order options:

  • File - the order of the files as they are in the ZIP file

  • Alphanumeric - files are sorted alphanumerically

  • Spatial index - the order defined by the source application as part of the metadata for the slice