|Description:||Neuroimaging visualization with interactive volume rendering|
|License:||New BSD License|
|Feature(s):||Neuroimaging visualization, Brain extraction, Volume rendering|
MRIcroGL is a program for neuroimaging visualization by Chris Rorden. It is available for Windows, Linux and Macintosh as well as source code. In general it is simpler to use but also somewhat less powerful than the MRIcro and MRIcron tools. A core feature is the use of modern graphics cards to both accelerate volume rendering and provide shading based on surface orientation (e.g. emulating realistic lighting, helping the viewer to perceive the shape of the volume). It is useful tool for rendering three dimensional volumetric datasets. While it can render any 3D volume, the ability to overlay statisitical maps and to use the coordinate system popular in neuroimaging makes it particularly well suited for interactive visualization of results from neuroimaging tools such as SPM, FSL, AFNI. An important feature is the ability to view multiple images simultaneously ('overlays') allowing the viewer to see the relative locations of objects in different images. For example, the user can load an anatomical MRI scans (that shows the brain's structure) and overlay a functional map (that highlights areas that become active as an individual conducts a task). While it was designed for medical imaging (MRI, CT, ultrasound) it can also be used with any volumetric data,such as confocal microscopy. It uses the graphics card to perofrm ray casting to visualize the volume data. Compiled software and source code are available from the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC).
Here are a few features described by the manual
- Ability to load NIfTI format images (DICOM images can be converted to NIfTI using dcm2nii
- Supports 1D transfer functions
- Ability to overlay multiple images (different modalities, statistical maps)
- Color schemes and GLSL shaders are text file plug-ins
- Includes script compiler to generate animations
- Automatic object extraction to remove noise from around an object
- Edge enhancement options which can generate 'glass brains' (regions with the same appearance are made transparent).
- Clip planes and cutouts can intersect the volume (as seen in the sample images on this page)
- Creation of multislice mosaics
 Sample Datasets
- The Visible Human Project Photographed cryo-sections male ('visiblehuman' Joseph Paul Jernigan).
- T1-weighted_MRI scan of human brain ('chris_t1' Chris Rorden).
- T2-weighted MRI scan of human brain ('chris_t2' Chris Rorden).
- T1 scan after segmentation into gray matter, white matter and spinal fluid using SPM8 ('chris_seg' Chris Rorden).
- Magnetic resonance angiography Time-of-flight of human head ('chris_MRA' Chris Rorden).
- Functional magnetic resonance imaging statistical maps showing regions active during eye movements (saccades) and peripheral visual attention ('saccades', 'attention' from de Haan et al., 2008).
- X-ray computed tomography scan of human cadaver head ('ct' University of North Carolina Volume Rendering Test Data Set).