Hago Imagen

Spain has been on the ascendant in 2010 and continues that dominance with two terrific new programs added to this site, both very advanced and from academic centres in Spain.

The first is SATURN, an advanced visualization program for Diffusion Tensor Imaging (DTI), which comes from Ruben Cardenes and colleagues at the Image Processing Laboratory of the University of Valladolid.  This program is an excellent example of cross-platform development, in this case using the ‘Fast Light Toolkit’ FLTK.  I downloaded and ran the Mac, Windows and Linux versions of SATURN and they look and run identically.  It’s great to see the program released on all three platforms with the same version.

DTI employs data sets storing tensor data, represented by volumes of multidimensional data.  As such, the program uses fundamentally different data file formats than those used by most other imaging modalities, which store one scalar value per point.  SATURN stores tensor data in VTK and NRRD formats, the latter is new to me, it’s a library and file format for storing multidimensional raster data.  The MR data is loaded from regular data, and the higher level abstractions of model data, or fiber tracts, are stored in the VTK format.

I can’t claim to have tested this program extensively since I’m unfamiliar with the modality (I must now try to drop the terms ‘fractional anisotropy’ and ‘mean diffusivity’ into conversations), but I did open the sample data sets and have a run through the menus.  This is a major, solid scientific application and a significant addition to this active and growing field.

I know little about DTI but I have seen an increase recently in the amount of software coming out in this field.  I’ve been wondering whether to classify it as a specialization of MRI, or a modality in its own right, and have decided on the former.  There are several other sub-fields of MRI (FMRI, DSI), and it seems more likely to come, and I don’t want to fragment the categories too much.  Also, programs such as SATURN can read ‘scalar’ or regular MRIs in DICOM format just fine, so it seems it belongs under MRI.  And anyone in this highly advanced and specialized field is going to be an expert, and will know where to look for the right software.  I don’t think it’s quite got to the point where they send you home with your DTI images on a CD.

Continuing the Spanish theme, the other program added is GIMIAS, from Xavier Planes and colleagues at the Universitat Pompeu Fabra, in Barcelona.  GIMIAS is a large and comprehensive dataflow-based environment for prototyping processing in medical imaging and several other disciplines.  That’s a broad description and this framework, accordingly, covers a wide swath and requires some study before use.  This is an application for the heavy tasks, and yet as installed, is easy to use for the most common imaging tasks: you can use it to view images and I also tested query/retrieve from my DCM4CHEE PACS server.  There is also the ability to save in various formats, and many advanced imaging features including volume rendering, segmentation, ROI definition and statistics, volumetric meshes and many others, detailed in the 84-page manual and large website that includes tutorials and demonstration videos.

The real power of the GIMIAS framework, though, is enabled by its workflow capabilities.  A workflow (several are included) is defined by the user as a series of processing steps, as shown her in the AngioMorphology clinical workflow.

Each step can be anything from loading the images, to image processing, to a complex process involving the user.  The workflow is defined using a drag-and-drop editor and of course can be saved and new workflows can be downloaded.

And if that’s not enough, the framework is fully extensible through a plugin architecture and a comprehensive API; source code is also available to download.  GIMIAS makes good use of existing free software including several popular toolkits used by other programs on this site: ITK, VTK, DCMTK and MITK.  Each one of these is a leader in its field: used well, as here, in a major project from a top academic lab, and great things result.