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Workaround for DICOM dictionary problem (CemrgApp v2.X on macOS)

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Jose Alonso Solis-Lemus edited this page Nov 25, 2020 · 3 revisions

One of the known issues with CemrgApp v2.X is reading some DICOMs using MITK's native DICOM reader. This issue is prevalent in macOS (since Sierra). We provided our users with an alternative DICOM reader, which can be selected on the Scar Plugin, this requires the user to install Docker.

This page presents another workaround for this problem.

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Set up steps: DO ONCE!

1. Install homebrew and wget

Homebrew is easy to install, just open a Terminal (Applications > Utilities > Terminal) and paste the following command

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

The script explains what it will do and then pauses before it does it.

To download wget, after homebrew, simply paster the following:

brew install wget

2. Create the destination folder for the dicom.dic

Create a folder somewhere in your computer, in this example, we create it in the Documents folder. You can use the macOS Finder or in a Terminal paste the following:

mkdir -p ~/Documents/CemrgAppDICOM

If you have not already, open a Terminal and navigate to the new folder:

cd ~/Documents/CemrgAppDICOM

3. Download dicom.dic using wget (do once)

On the same Terminal from the previous step paste the following command:

# cd ~/Documents/CemrgAppDICOM # previous step
wget https://raw.githubusercontent.com/InsightSoftwareConsortium/DCMTK/master/dcmdata/data/dicom.dic

Run CemrgApp: DO EVERY TIME!

Note: The Terminal window should remain open the entire time, if you close it you will have to start from this section.

The following steps you will need to do every time you want to use the native DICOM reader in CemrgApp. Open a Terminal and navigate to the folder where the dicom.dic is stored:

cd ~/Documents/CemrgAppDICOM

1. Set the dicom.dic to be recognised by CemrgApp

Paste the following command on your Terminal:

export DCMDICTPATH=$(pwd)/dicom.dic

2. Open CemrgApp from Terminal

We are assuming you installed CemrgApp in the Applications Folder.

On your Terminal paste:

/Applications/CemrgApp/CemrgApp.app/Contents/MacOS/CemrgApp

The Cardiac Electro-Mechanics Research Group (CEMRG) at King's College London applies statistical, machine learning and simulation approaches to combine experimental and clinical data with physics and biology to study the physiology, pathology, diagnosis and treatment of the heart.

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