User talk:Platel
Contents
- 1 Information on Bram Platel & TU/e
- 2 Possible Topics of Collaboration
- 2.1 Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection
- 2.2 Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)
- 2.3 GPU Based Visualization
- 2.4 DTI Validation with Tracer/Anatomical Studies
- 2.5 Diffusion Tensor Imaging
- 2.6 Note on Student Exchange Possibilities
- 2.7 Noby Hata is willing to come and give a colloquium/lecture
- 3 Main Contact
- 4 Contacts
Information on Bram Platel & TU/e
About Image Analysis at the Eindhoven University of Technology
Bio and Publication List of Bram Platel
Multivalued Image Analysis & Visualization
Possible Topics of Collaboration
Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection
We have a Medtronic Polestar N20, we would like to use pre-operative data: fMRI, DTI and register this with the Polestar data during the surgery. SPL has many researchers working on registration of these modalities. Using Slicer for the registration is a good option. Exchange of students to work on registration projects is interesting as well. We have a robust method for initialization-less registration that might be interesting for integration into Slicer.
Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)
We will use Medtronic's Stealth Station for navigation. We will have a student project to develop an interface with Medtronic's Stealth Link software. We hope that with the help of Junichi and Haiying we can develop a sort of proxy that translates Medtronic's StealthLink protocol into OpenIGT Link. This will make our software integrate with other systems and on the other hand it is useful for Medtronic, as this enables the use of their system in OpenIGT Link-compatible software like Slicer.
(I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)
GPU Based Visualization
Our group has a multi-volume ray casting engine based on VTK. This volume renderer supports multiple volumes, (transparent) geometric shapes, convex and concave clipping geometry, transferfunction editing, etc. The ray caster is based on VTK classes and could be implemented into Slicer. This could be made into a student project.
DTI Validation with Tracer/Anatomical Studies
As soon as more detailes are available on our research on DTI validation with tracer studies and anatomical slices, we will contact CF Westin who has extensive knowledge on the subject, through studies on macaque monkeys. Perhaps we can use his groups knowledge and software for the analysis of our human and rat brain studies.
Diffusion Tensor Imaging
Anna Vilanova's Multivalued Image Analysis & Visualization research group at the Eindhoven University of Technology is specialized in Diffusion Tensor Imaging. Exchange of students might be a good way to exchange knowledge. The DTI tool built by Anna's group is open source and based on VTK. Integration into Slicer would be possible.
Diffusion Data Compatibly
Steve Pieper has asked for information on the Philips DTI data structure, we will look into this and provide the information we have on importing DTI data (we have our own tool for this). More information on NAMIC's DTI / DWI
Note on Student Exchange Possibilities
Student projects should contain enough research to be acceptable as master projects. This means that they have to be well defined and should not only contain the wrapping of existing code.
Also the students are in general Biomedical Engineering students that have limited programming knowledge/affinity in C++.
Noby Hata is willing to come and give a colloquium/lecture
I will talk to Bart ter Haar Romeny to discuss the possibility for Noby to come to Eindhoven and give a lecture on the research at SPL and demonstrate Slicer.
Main Contact
Nobuhiko (Noby) Hata
Contacts
Ron Kikinis
- Dr. Kikinis is the founding Director of the Surgical Planning Laboratory, Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, and a Professor of Radiology at Harvard Medical School. This laboratory was founded in 1990.
Junichi Tokuda Ph.D.
- Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.
- Currently working on the Open IGT Link network protocol. This protocol will be supported by IGstk and is designed to send information like image data, tracker locations, scanner protocols, etc. over a network. We will have to see if this protocol is useful for us next to Medtronic's StealthLink software. Perhaps we could build a translating proxy that translates Medtronic's StealthLink protocol to Open IGT Link, so that our applications can be Open IGT Link compatible.
Haying Liu
- Slicer software engineer, involved in maintaining the software/source code. - Demo'ed the Slicer software to me and helped me build the application from SVN. Showed me how to build a command line module and demonstrated the use of the Aurora navigation system with Slicer.
William (Sandy) Wells
- Discussed the correction of the distortion of our Medtronic Polestar N20 scanner. Wells pointed out several papers on image registration that might be useful, but the scanners resolution is probably too low, with a too small FOV, and there are too many artifacts for an accurate registration. - Wells is currently working on a large study on fMRI data of Schizophrenia patients.
Papers to consider:
A Bayesian Model for Joint Segmentation and Registration, Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006
A Mathematical Framework for Incorporating Anatomical Knowledge in DT-MRI Analysis, M. Maddah, L. Zöllei, W.E.L. Grimson, C.F. Westin, W.M. Wells III, International Symposium on Biomedical Imaging (ISBI): From Nano to Macro, May 2008, Paris, France
Geometry Driven Volumetric Registration, G.M. Postelnicu, L . Zöllei, R. Desikan, B. Fischl, Information Processing in Medical Imaging (IPMI) 2007, LNCS 4584 pp. 675-686
A hierarchical algorithm for MR brain image parcellation, K.M. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R.W. McCarley, R. Kikinis, W.E.L. Grimson, M.E. Shenton, and W.M. Wells, IEEE Transactions on Medical Imaging, 26(9),pp 1201-1212, 2007. ]
Steve Pieper
- At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.
- We discussed the GPU volume rendering that Ralph Brecheisen has made in our Image Guided Surgery group. SPL is interested in our project and when back in Eindhoven, Bram should discuss the sharing of the source code with Bart ter Haar Romeny. At SPL Ben Grauer, a master student of the ETH in Zürich, is currently implementing a CUDA based real time volume renderer in Slicer.
- Marek Kubicki is working on a conversion tool for DTI data of different scanners. We also have such a tool, when back in Eindhoven, Bram should discuss the sharing of the source code with Bart ter Haar Romeny.
- Kerstin Kessel is a master student from Heidlberg University in Germany and she is working on implementing the DTI conversion tool and tensor calculation in Slicer. Immediate visualization of the fiber tracks or glyphs can help figure out the correct settings for certain DTI data.
Note:
- Steve pointed out a Slicer training event in Germany June 16/17 that might be interesting for our students.
- Sending students to their masters at SPL is a good option.
Papers to consider:
Carl-Fredrik Westin
- Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.
- Together with Gordon Kindlmann we discussed our research.
Papers to consider:
The whole publication list is very interesting especially for Luc Florack and Remco Duits at the "Scale and Orientation" group of the TU/e.
A Mathematical Framework for Incorporating Anatomical Knowledge in DT-MRI analysis, Mahnaz Maddah, Lilla Zöllei, W. Eric L. Grimson, Carl-Fredrik Westin, William M. Wells Biomedical Imaging: From Nano to Macro, 2008. ISBI 2008. 5th IEEE International Symposium on Biomedical Imaging, Paris, France 2008
Automatic Tractography Segmentation Using a High-Dimensional White Matter Atlas, Lauren J. O'Donnell, Carl-Fredrik Westin IEEE Transactions on Medical Imaging 2007
Outlier Rejection for Diffusion Weigthed Imaging, Marc Niethammer, Sylvain Bouix, Santiago Aja-Fernandez, Carl-Fredrik Westin, Martha E. Shenton Tenth International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI '07) 2007
Signal LMMSE Estimation from Multiple Samples in MRI and DT-MRI, Santiago Aja-Fernandez, Carlos Alberola-Lopez, Carl-Fredrik Westin Tenth International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI '07) 2007
Comparison of fiber tracts derived from in-vivo DTI tractography with 3D histological neural tract tracer reconstruction on a macaque brain, Julien Dauguet, Sharon Peled, Vladimir Berezovskii, Thierry Delzescaux, Simon K. Warfield, Richard Born, Carl-Fredrik Westin NeuroImage 2007
3D Histological Reconstruction of Fiber Tracts and Direct Comparison with Diffusion Tensor MRI Tractography, Julien Dauguet, Sharon Peled, Vladimir Berezovskii, Thierry Delzescaux, Simon K. Warfield, Richard Born, Carl-Fredrik Westin Ninth International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'06), Copenhagen, Denmark 2006
Keep in Mind
MICCAI 2008 Tutorial: Diffusion MRI: Technology trends and unsolved problems
Stephen Whalen
- Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.
Interesting Publications:
Role of pre- and intraoperative imaging and neuronavigation in neurosurgery. Expert Rev Med Devices. 2008 Jan;5(1):65-73.
Tract-based morphometry. Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8
Non-rigid alignment of pre-operative MRI, fMRI, and DT-MRI with intra-operative MRI for enhanced visualization and navigation in image-guided neurosurgery. Neuroimage. 2007 Apr 1;35(2):609-24. Epub 2006 Dec 23.
Robust nonrigid registration to capture brain shift from intraoperative MRI. IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.
Bruce Fischl
- Does interesting research together with Koen van Leemput on automated brain segmentation in the aria of our interest, the thalamus and the surrounding nuclei.
Interesting Publications
Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain, Fischl, B., D.H. Salat, E. Busa, M. Albert, M. Dieterich, C. Haselgrove, A. van der Kouwe, R. Killiany, D. Kennedy, S. Klaveness, A. Montillo, N. Makris, B. Rosen, and A.M. Dale, (2002). Neuron, 33:341-355.
Sequence-Independent Segmentation of Magnetic Resonance Images, Fischl, B., Salat, D.H., van der Kouwe, A.J.W., Makris, N., Ségonne, F., and Dale, A.M. (2004) NeuroImage 23:S69-S84.
Atlas Renormalization for Improved Brain MR Image Segmentation Across Scanner Platforms, Han, X. and B. Fischl, (2007). IEEE Transactions on Medical Imaging, 26(4):479-486.
- I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.
Florin Talos
- Does very interesting research on ontology, DTI, anatomical analysis of Basal Ganglia, etc. Very related to our work.
Interesting Publications
