Introduction to Slicer

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Overview

In the context of current medicine there are multiple options for recording and capturing images of the human body or parts of it, for the purpose of diagnosis and examination of different pathologies. These methods produce information in the form of images, called medical image.

Diagnostic by images

The medical image is often used to designate the set of techniques that produce images of internal aspects of the body (without having to open it). Imaging allows physicians to look inside the body for signs of a pathology, as they allow the observation of anatomical structures in the living subject and their movement in normal and abnormal situations.

A variety of devices and techniques can create images of structures and activities inside the human body. The type of image the practitioner uses will depend on your symptoms and the part of the body being examined. Here are some of them:

• X-rays
• Computerized tomography
• Magnetic resonance
• Ultrasound
• Nuclear medicine techniques

Clinical Context

In the clinical context there are two professional profiles: on the one hand the professional that is responsible for the acquisition of medical images with quality of diagnosis and on the other hand the doctor who interprets these images and makes diagnostic decisions based on them. Depending on the device, and the immediacy of the data provided by the device, the two profiles can coincide in one, being the facultative one that captures the image and interprets it.

Scientific research

As a field of scientific research, medical imaging constitutes a subdiscipline of biomedical engineering, medical physics or medicine, depending on the context: research and development in the area of instrumentation, image acquisition, modeling and quantification are normally reserved for biomedical engineering, medical physics and computer science; research into the application and interpretation of medical images is normally reserved for radiology and relevant medical subdisciplines in medical illness or area of medical science (neuroscience, cardiology, psychiatry, psychology, etc.) under investigation. Many of the techniques developed for medical imaging are also scientific and industrial applications.

The DICOM format

These images are captured directly in digital format, to difference, for example, of the images of conventional X-ray that remain registered in an acetate support. In medical image there is a standard recognised format worldwide, that is the DICOM (Digital Imaging *and Communication *in Medicine).

This format has been formulated for the handle, visualisation, storage, impression and transmission of the medical images. It includes the definition of a format of file and of a protocol of communication of network (applies the protocol *TCP/IP. And it allows that different entities share the *imformación and this keep its usability and legibility.

DICOM Allows the integration of scanners, servers, workstations, printers and network hardware from multiple providers inside a system of storage and communication of images. The different machines, servers and workstations have a certificate of conformity DICOM (conformance statements) that establishes clearly the classes DICOM that bear. DICOM Has been adopted widely by hospitals, managed by means of systems PACS.

Software: 3D Slicer

3D Slicer is a tool of software that allows the load and manipulation of DICOM images; it is designed for analysis of image and scientific visualisation. This licence does not present restrictions of use in commercial projects or academicians. It treats of a platform of investigation translational, no for clinical use, although it can be used in experimental procedures with the approval of the council of ethical and the patient involved. It is responsibility of the user the operate according to the rules and local legislation. 3D Slicer has not been approved formally for clinical use by the *FDA in the United States neither by any another regulatory organism in other countries.

Characteristics

It is a free software open source licence ([BSD]), it allows the registering of images, processing of diffusion tractographies, to serve as interface for external devices for guided by image and rendering of volumes by GPU, among other things.

It has a modular organization, which allows adding new functionalities adapted to the specific needs of each user.

It is in constant development by different international teams, based in universities and research centers (both public and private) in North America, Europe and Asia.

Functionalities

It allows the integration of multi-modal images, including all those previously mentioned as medical images; the interactive visualization possibilities include the construction of images by cuts in arbitrary planes, constructing surface models from image tags, and hardware-accelerated volume modeling. It also supports a wide range of logging skills such as fiducial, measurement utilities, custom color maps ...

Capacities

• Manage DICOM images and read / write other formats
• Interactive visualization of volumetric images of voxels, polygonal meshes and volume rendering
• Manual editing
• Fusion and co-registration of information using rigid and non-rigid algorithms
• Automatic image segmentation
• Analysis and visualization of images by diffusion tensors
• Device tracking in image-guided procedures

Hardware

The recommended hardware configuration is:

• Display: a minimum resolution of 1024x768 (1280x1024 recommended)
• 4GB of memory (8GB recommended)
• Dedicated graphics card (recommended 1GB)
• Multi CPU
• Mouse or equivalent pointing device with two buttons and scroll wheel
• Internet connection to access online documentation and tutorials

Operating system

Recommended Versions:

• Windows 7 64-bit
• Mac OS X Lion
• Linux: current versions of the most popular distributions should not present a problem (Ubuntu and Fedora, for example)