A small tutorial about free software to process 3D images and meshes

A small tutorial about free software to process 3D images and meshes G. Subsol – LIRMM/CNRS - ODENT 1 A small tutorial about free software to process 3D images and meshes Gérard Subsol, ODENT Project, LIRMM : CNRS, France gerard.subsol@lirmm.fr http://www.lirmm.fr/ODENT/ October 15, 2008 Reading 3D medical images In general, 3D medical images (CT-Scan, MRI) are in a standard format called DICOM (Digital Imaging 1and Communications in Medicine ). This format is quite complex and includes many information about the patient and the acquisition process. For image processing purposes, it is more convenient to convert DICOM files into a very simple and standard format which includes only data about the image. 2We propose to use the Analyze 7.5 format . The image is then composed of 2 files: • The header (.hdr) which contains the image size and the resolution of the voxel. More information may be added. • The content of the image (.img) which is coded as the list of the intensities (a value which is in general between 0 and 65535 and which is coded on 2 bytes) of all the voxels. How to convert DICOM data into Analyze 7.5 format? 3You may use the MRIConvert software which is free and runs on Windows and Linux OS. This software is regularly updated. 1. Define the folder where is the DICOM series by Input/Add Folder 2. All the files of the folder will be analyzed. Validate by Okay. 3. Select Analyse 7.5 in the format ...