Application Prototypes
The application prototypes are implemented in C++ with a volume ray-casting fragment shader written in GLSL. The Qt GUI library is used for implementing the interface, the open-source Grassroots DiCoM library is for reading and parsing Dicom (Digital Imaging and Communications in Medicine) medical files, the open-source multi-dimensional image analysis SimpleITK including the medical image rgistration library SimpleElastix is for deformable registration. Codes from the open-source TIPL were used to parse NIfTI (Neuroimaging Informatics Technology Initiative) format, the CImg Library to image processing, and the OpenGL Mathematics glm library to linear-algebra-processing. To run the executable files you should be attentive to the system requirements (programmable GPU with >=1GB graphics memory and supports OpenGL-GLSL >= 4.0) before downloading one of the following files and uncompressing it.
Please reference the following papers, if you use
- Interactive Tractography: Wu Shin-Ting, Raphael Voltoline, and Rodrigo Lacerda Benito: Interactive DTI-Based Constrained Tractography using OpenGL Pipeline. Proceedings of 36th Sibgrapi (2023) ; and Shin-Ting Wu, Raphael Voltoline, Rodrigo Lacerda Benites, Brunno Machado de Campos, João Paulo Sant'Ana Santos de Souz, Enrico Ghizoni: Interactive Mining of Neural Pathways to Preoperative Neurosurgical Planning. Computers in biology and medicine (2024). doi: 10.1016/j.compbiomed.2024.109334.
- Interactive ODF Glyphs: Daniel Xavier Silva, Raphael Voltoline, and Wu Shin-Ting: An interactive triangle-based ODF glyph rendering for high angular resolution diffusion imaging. Computers & Graphics (2023). doi: 10.1016/j.cag.2023.08.027
- Tensor Glyphs Interactive Visualization: Voltoline Raphael and Shin-Ting Wu: Multimodal visualization of complementary color-coded FA map and tensor glyphs for interactive tractography ROI seeding. Computers Graphics (2021)
- Image-guided Digitizing: Shin-Ting Wu, José Angle Iván Rubianes Silva, Sérgio Luiz Novi, Nicholas Gabriel S.R. de Souza, Edwin Johan Forero, and Rickson C. Mesquita: Accurate Image-guided (Re)Placement of NIRS Probes. Computer Methods and Programs in Biomedicine (2021)
- Curvilinear Reformatting for Surgical Planning: Shin-Ting Wu, Wallace Souza Loos, Dayvid Leonardo de Castro Oliveira, Fernando Cendes, Clarissa L. Yasuda, and Enrico Ghizoni: Interactive Patient-Customized Curvilinear Reformatting for Improving Neurosurgical Planning. International Journal of Computer Assisted Radiology and Surgery (2021)
- Multimodal rendering: Shin-Ting Wu, Raphael Voltoline, Wallace Souza Loos, Jose Angel Ivan Rubianes Silva, Lionis de Souza Watanabe, Barbara Amorim, Ana Carolina Coan, Fernando Cendes, and Clarissa L. Yasuda: Toward a Multimodal Diagnostic Exploratory Visualization of Focal Cortical Dysplasia. IEEE Computer Graphics and Applications 38(3): 73-89 (2018)
- Rigid co-registration: Shin-Ting Wu, Augusto Cavalcante Valente, Lionis de Souza Watanabe, Clarissa Lin Yasuda, Ana Carolina Coan, and Fernando Cendes: Pre-alignment for Co-registration in Native Space. SIBGRAPI 2014: 41-48
- Coordinated views: Shin-Ting Wu, José Elías Yauri Vidalón, Wallace Souza Loos, and Ana Carolina Coan: Query Tools for Interactive Exploration of 3D Neuroimages: Cropping, Probe and Lens. SIBGRAPI 2013: 250-257
- Curvilinear reformatting: Shin-Ting Wu, Clarissa L. Yasuda, and Fernando Cendes: Interactive Curvilinear Reformatting in Native. IEEE Transactions on Visualization and Computer Graphics (2012)
- 3D Cursor: Shin-Ting Wu, José Elías Yauri Vidalón, and Lionis de Souza Watanabe: Snapping a Cursor on Volume Data. SIBGRAPI 2011: 109-116
VMTK-Neuro 4.0
Neuroimage-guided Placemento of Sensors on a Head
It only works with the Polhemus Fastrak digitizer connected to the computer's serial port running the application.
Last update: ( , )
- MacOS Intel Binary (64-bit, OSX 10.13+) ( MB)
- Linux Binary (64-bits, Ubuntu 16.04) ( MB)
- Windows Binary (64-bit, Window 10+) ( MB)
Copyright (C) José Angel Iván Rubianes Silva, Raphael Voltoline Ramos, and Wu Shin-Ting.
Automated Anatomical Labeling of Gross Neuroanatomy
SimpleElastix is integrated in the executable file, Talairach and MNI-ICB2009c atlases are included in the compressed file.
Last update: (December, 2023)
- MacOS Intel Binary (64-bit, OSX 10.13+) (46.6 MB) : The Atlases folder must be placed in the user's Desktop.
- Linux Binary (64-bits, Ubuntu 16.04) (194.4 MB): The Atlases folder must be placed in the same folder as the executable file.
- Windows Binary (64-bit, Window 10+) (44.5 MB) : The Atlases folder must be placed in the same folder as the executable file.
Copyright (C) Felippe Trigueiro Angelo, Raphael Voltoline Ramos, José Angel Iván Rubianes Silva, and Wu Shin-Ting.
Visual Analytics of Neural Connections for Neurosurgical Planning
SimpleElastix is integrated in the executable file.
Last update: (July, 2024)
- MacOS Intel Binary (64-bit, OSX 10.13+) (zip, 31.8 MB)
- Linux Binary (64-bits, Ubuntu 16.04) (178.9 MB)
- Windows Binary (64-bit, Window 10+) (31.8 MB)
Copyright (C) Raphael Voltoline Ramos, Daniel Xavier Silva, Rodrigo Lacerda Benites, José Angel Iván Rubianes Silva, and Wu Shin-Ting.
Color maps used in the tutorials: palettes.zip (1.4 KB). Just download and uncompress it in any folder. However, we recommend using your transfer functions appropriate to your data.
We have successfully loaded DICOM files from different scanners in our university hospital and some of these datasets, from which we successfully co-registered the available pair of anatomic and functional 3D images: CEREBRIX/Neuro Crane/t1_fl2d_tra and CEREBRIX/PET PETCT_CTplusFET_LM_Brain (Adult)/PET FET Cerebral.
If you have some problems, please let us know by sending an e-mail: ting at dca dot fee dot unicamp.br
LICENSE
The prototype is released under the LGPL license:
This prototype is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
This software is not certified as a medical device for primary diagnostic. It is for research purpose. Any other user is entirely in your own risk.
Old Versions
DISCLAIMER
All procedures provided by different versions of this software are intended only for scientific research. They are not certified for primary diagnostic. Use it at your own risk.
Implemented Techniques
Deterministic DTI-based Tractography
ODF Visualization: ODF Glyphs
DTI Visualization: Superquadrics and scalar maps
Neuroimage-guided Digitizing
Multi-volume Raycasting
A simplified version of the VMTK-Neuro prototype demonstrating appropriate geometric transformations in the texture space are sufficient for efficiently rendering a single image from multi-volumes:
The co-register matrix and two volumes, MRI-T1 and MRI-FLAIR, are provided for the test.
Maximization of Mutual Information based Rigid Co-registration
Multiplanar Reformatting
Curvilinear Reformatting
Coordinated Multiple Views and Interactions