DICOM Viewer

Digital Imaging and Communications in Medicine (DICOM) is an internationally recognised standard for the communication and managment of medical imaging information and related data. DICOM standard is used in several imaging modalities, such as radiography, CT, MRI...

DICOM files contain pixel information, as well as a lot of metadata about the method used to acquire the image, its orientation, study and patient information, amongst others. Allowing users to combine imaging and non-imaging data. For this reason, DICOM files are a great source of information in the field of medical imaging and image analysis and research.

This mini-app allows users to interactively visualise and explore 3D DICOM volume utilising oro.dicom and oro.nifti packages. These are to read DICOM files, display volums and extract DICOM metadata. Information about these packages can be found here: https://cran.r-project.org/web/packages/oro.dicom/index.html. The sample DICOM images displayed are from MRIs (source: https://www.osirix-viewer.com/resources/dicom-image-library/, the library is called BRAINIX).

For more information about this app you can read the dedicated blog post at http://www.aridhia.com/blog/interactively-visualising-dicom-volumes-and-header-data/.

About the app

You can select the patinet file to display using the dropdown menu on the left. Then, you can change the orientation of the image using the sliders below. The image will be displayed in the middle of the screen, you can change the view plane by clicking on the Axial', 'Sagittal' or 'Coronal' tabs just above the image. Under the image a table with the file information will be displayed. On the left-side of the screen, you will see the orthogonal position of your current view.

The button on the bottom of the page to "Extract DICOM headers to database" only works if you are using the app within a workspace, and you have a dataset called "image_analysis_findings" in your database.

Using your DICOM files

To use other DICOM files in the app, you can place the new folder inside the 'dicom_images' directory:

• Data
  • dicom_images
    • new_image_set
      • image1.dcm
      • image2.dcm
      • ...

Checkout and run

You can clone this repository by using the command:

git clone https://github.com/Aridhia-Open-Source/shiny-demo-dicom-viewer

Open the .Rproj file in RStudio and run runApp() to run the app.

Deploying to the workspace

1. Download this GitHub repo as a .zip file.
2. Create a new blank Shiny app in your workspace called "dicom-viewer".
3. Navigate to the dicom-viewer folder under "files".
4. Delete the app.R file from the dicom-viewer folder. Make sure you keep the .version file!
5. Upload the .zip file to the dicom-viewer folder.
6. Extract the .zip file. Make sure "Folder name" is blank and "Remove compressed file after extracting" is ticked.
7. Navigate into the unzipped folder.
8. Select all content of the unzipped folder, and move it to the dicom-viewer folder (so, one level up).
9. Delete the now empty unzipped folder.
10. Start the R console and run the dependencies.R script to install all R packages that the app requires.
11. Run the app in your workspace.

For more information visit https://knowledgebase.aridhia.io/article/how-to-upload-your-mini-app/