Convert DICOM to VTI

OsiriX and Horos Course · Image and Export

In this tutorial I show how to run Linux inside a Mac via a virtual machine (preferably Parallels Desktop, but VirtualBox also works) to convert a DICOM dataset exported from OsiriX into a .vti file (VTK ImageData), useful for example in SimVascular. Step-by-step workflow: Create the virtual machine and install Ubuntu In Parallels: “+” button → choose Ubuntu → download (~2 GB) → install. (Alternative: VirtualBox with an Ubuntu ISO) Install the required libraries/tools in Ubuntu Open the Terminal and run: sudo apt-get update Install the GDCM tool that performs the conversion: sudo apt-get install libvtkgdcmtools Export the study from OsiriX as DICOM In OsiriX: export the study (ideally anonymized) to a folder (on the Desktop, for example). Copy the DICOM folder into Ubuntu In Parallels, install Parallels Tools (if needed) and restart Ubuntu. Drag the exported folder (with the .dcm files) to the Ubuntu Desktop. Convert the DICOM folder to .VTI In the Terminal, run: gdcm2vtk dicom_folder output.vti Typical example (dragging the folder and setting the destination): gdcm2vtk ~/Desktop/Exam ~/Desktop/exam.vti Watch out for the “folder inside a folder” problem If the command fails, it is usually because you pointed to the “wrong” folder (an outer folder that contains another folder where the .dcm files are). The solution is to point to the folder that directly contains the DICOM files. Result Instead of hundreds/thousands of DICOM files, you will have a single exam.vti file, usually smaller (because redundancies are removed), ready for use in VTK/SimVascular software.