Difference between revisions of "User talk:Platel"
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- Currently working on the [http://www.na-mic.org/Wiki/index.php/OpenIGTLink Open IGT Link] network protocol. This protocol will be supported by [http://www.igstk.org/index.htm IGstk] and is designed to send information like image data, tracker locations, scanner protocols, etc. over a network. | - Currently working on the [http://www.na-mic.org/Wiki/index.php/OpenIGTLink Open IGT Link] network protocol. This protocol will be supported by [http://www.igstk.org/index.htm 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.'' | ''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.'' | ||
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'''Haying Liu''' | '''Haying Liu''' | ||
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- Slicer software engineer, involved in maintaining the software/source code. | - Slicer software engineer, involved in maintaining the software/source code. | ||
- Demo'ed the Slicer software to me and helped me [http://wiki.na-mic.org/Wiki/index.php/Slicer_Training_Basic build the application] from SVN. Showed me how to build a [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Documentation command line module] and demonstrated the use of the [http://wiki.na-mic.org/Wiki/index.php/Slicer_Training_Navigation_With_Aurora Aurora navigation system with Slicer]. | - Demo'ed the Slicer software to me and helped me [http://wiki.na-mic.org/Wiki/index.php/Slicer_Training_Basic build the application] from SVN. Showed me how to build a [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Documentation command line module] and demonstrated the use of the [http://wiki.na-mic.org/Wiki/index.php/Slicer_Training_Navigation_With_Aurora Aurora navigation system with Slicer]. | ||
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'''William (Sandy) Wells''' | '''William (Sandy) Wells''' | ||
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- 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. | - 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. | - Wells is currently working on a large study on fMRI data of Schizophrenia patients. | ||
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''Papers to consider:'' | ''Papers to consider:'' | ||
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[http://people.csail.mit.edu/pohl/publications/pohl-tmi-2007.pdf 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. ] | [http://people.csail.mit.edu/pohl/publications/pohl-tmi-2007.pdf 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. ] | ||
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'''Steve Pieper''' | '''Steve Pieper''' | ||
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- 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. | - 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. | ||
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''Note:'' | ''Note:'' | ||
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- Sending students to their masters at SPL is a good option. | - Sending students to their masters at SPL is a good option. | ||
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''Papers to consider:'' | ''Papers to consider:'' | ||
[http://vesicle.nsi.edu/users/izhikevich/publications/large-scale_model_of_human_brain.htm Large-Scale Model of Mammalian Thalamocortical Systems, Eugene M. Izhikevich and Gerald M. Edelman, PNAS (2008) 105:3593-3598] | [http://vesicle.nsi.edu/users/izhikevich/publications/large-scale_model_of_human_brain.htm Large-Scale Model of Mammalian Thalamocortical Systems, Eugene M. Izhikevich and Gerald M. Edelman, PNAS (2008) 105:3593-3598] | ||
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'''Carl-Fredrik Westin''' | '''Carl-Fredrik Westin''' | ||
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- Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. | - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. | ||
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''Papers to consider:'' | ''Papers to consider:'' | ||
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The whole [http://lmi.bwh.harvard.edu/papers/all.html publication list] is very interesting especially for [https://venus.tue.nl/ep-cgi/ep_detail.opl?on=44422&taal=US&voor_org_id=&rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&rn=19961226 Remco Duits] at the "Scale and Orientation" group of the TU/e. | The whole [http://lmi.bwh.harvard.edu/papers/all.html publication list] is very interesting especially for [https://venus.tue.nl/ep-cgi/ep_detail.opl?on=44422&taal=US&voor_org_id=&rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&rn=19961226 Remco Duits] at the "Scale and Orientation" group of the TU/e. | ||
| − | .... | + | [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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 |
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| + | [http://lmi.bwh.harvard.edu/papers/pdfs/2007/odonnellTMI07.pdf Automatic Tractography Segmentation Using a High-Dimensional White Matter Atlas], Lauren J. O'Donnell, Carl-Fredrik Westin IEEE Transactions on Medical Imaging 2007 | ||
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| + | [http://lmi.bwh.harvard.edu/papers/pdfs/2007/niethammerMICCAI07.pdf 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 | ||
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| + | [http://lmi.bwh.harvard.edu/papers/pdfs/2007/aja-fernandezMICCAI07.pdf 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 | ||
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''Keep in Mind'' | ''Keep in Mind'' | ||
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- Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation. | - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation. | ||
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''Interesting Publications:'' | ''Interesting Publications:'' | ||
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[http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Role of pre- and intraoperative imaging and neuronavigation in neurosurgery.] Expert Rev Med Devices. 2008 Jan;5(1):65-73. | [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Role of pre- and intraoperative imaging and neuronavigation in neurosurgery.] Expert Rev Med Devices. 2008 Jan;5(1):65-73. | ||
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[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16279079&query_hl=1&itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27. | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16279079&query_hl=1&itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27. | ||
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'''Bruce Fischl''' | '''Bruce Fischl''' | ||
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- Does interesting research together with [http://people.csail.mit.edu/koen/ Koen van Leemput] on automated brain segmentation in the aria of our interest, the thalamus and the surrounding nuclei. | - Does interesting research together with [http://people.csail.mit.edu/koen/ Koen van Leemput] on automated brain segmentation in the aria of our interest, the thalamus and the surrounding nuclei. | ||
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''Interesting Publications'' | ''Interesting Publications'' | ||
Revision as of 16:21, 9 April 2008
Home < User talk:PlatelContents
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
Deep Brain Stimulation (I'm meeting Benoit Dawant 14-18 April at Vanderbilt University to talk about their DBS research)
Diffusion Tensor Imaging
Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection (Interested to see Slicer's capabilities. 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.)
Integration of Medtronic's StealthLink into Slicer (OpenIGT Link) (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)
GPU Visualization, Depth Peeling (Nvidia's CUDA)
Scanner Deformation Analysis & Correction
Student Exchange Possibilities
Noby Hata is willing to come and give a colloquium/lecture
Main Contact
Nobuhiko (Noby) Hata
Contacts
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
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.
