https://www.na-mic.org/w/api.php?action=feedcontributions&feedformat=atom&user=Platel 2026-04-16T18:55:20Z User contributions MediaWiki 1.33.0 https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23772 2008-04-10T19:32:59Z

<p>Platel: /* Florin Talos */</p> <hr /> <div>----<br /> = Information on Bram Platel &amp; TU/e =<br /> ----<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> = Possible Topics of Collaboration =<br /> ----<br /> <br /> <br /> ==Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection==<br /> <br /> We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp 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. <br /> <br /> <br /> ==Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)==<br /> <br /> 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. <br /> <br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> <br /> ==GPU Based Visualization==<br /> <br /> 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. <br /> <br /> <br /> ==DTI Validation with Tracer/Anatomical Studies==<br /> <br /> 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 [http://lmi.bwh.harvard.edu/papers/papers/dauguetNeuroImage07.html macaque monkeys]. Perhaps we can use his groups knowledge and software for the analysis of our human and rat brain studies.<br /> <br /> <br /> ==Diffusion Tensor Imaging==<br /> <br /> Anna Vilanova's [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; 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. <br /> <br /> ===Diffusion Data Compatibly===<br /> <br /> 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). [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI More information on NAMIC's DTI / DWI]<br /> <br /> <br /> ==Note on Student Exchange Possibilities==<br /> <br /> 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. <br /> <br /> Also the students are in general Biomedical Engineering students that have limited programming knowledge/affinity in C++.<br /> <br /> <br /> ==Noby Hata is willing to come and give a colloquium/lecture==<br /> <br /> 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.<br /> <br /> <br /> ----<br /> = Main Contact =<br /> ----<br /> <br /> <br /> ==Nobuhiko (Noby) Hata==<br /> <br /> [http://www.spl.harvard.edu/pages/People/noby Personal web page]<br /> <br /> <br /> ----<br /> = Contacts =<br /> ----<br /> <br /> <br /> ==Ron Kikinis==<br /> <br /> [http://www.spl.harvard.edu/pages/People/kikinis Personal web page]<br /> <br /> - 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.<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications%3Fcollection%3D1 ''Publication List SPL'']<br /> <br /> <br /> ==Junichi Tokuda Ph.D.==<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> ==Haying Liu==<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> ==William (Sandy) Wells==<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> ==Steve Pieper==<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> ==Carl-Fredrik Westin==<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/dauguetNeuroImage07.html 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<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/dauguetMICCAI06.html 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<br /> <br /> <br /> ''Keep in Mind''<br /> <br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> ==Stephen Whalen==<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> ==Bruce Fischl==<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.<br /> <br /> <br /> ==Florin Talos==<br /> <br /> [http://www.spl.harvard.edu/pages/People/talos Personal web page]<br /> <br /> - Does very interesting research on ontology, DTI, anatomical analysis of Basal Ganglia, etc. Very related to our work.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications?authorfirst=N&amp;authorlast=Archip Archip's papers]<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications?authorfirst=N&amp;authorlast=talos Talos' papers]</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23767 2008-04-10T19:16:09Z

<p>Platel: </p> <hr /> <div>----<br /> = Information on Bram Platel &amp; TU/e =<br /> ----<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> = Possible Topics of Collaboration =<br /> ----<br /> <br /> <br /> ==Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection==<br /> <br /> We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp 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. <br /> <br /> <br /> ==Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)==<br /> <br /> 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. <br /> <br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> <br /> ==GPU Based Visualization==<br /> <br /> 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. <br /> <br /> <br /> ==DTI Validation with Tracer/Anatomical Studies==<br /> <br /> 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 [http://lmi.bwh.harvard.edu/papers/papers/dauguetNeuroImage07.html macaque monkeys]. Perhaps we can use his groups knowledge and software for the analysis of our human and rat brain studies.<br /> <br /> <br /> ==Diffusion Tensor Imaging==<br /> <br /> Anna Vilanova's [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; 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. <br /> <br /> ===Diffusion Data Compatibly===<br /> <br /> 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). [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI More information on NAMIC's DTI / DWI]<br /> <br /> <br /> ==Note on Student Exchange Possibilities==<br /> <br /> 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. <br /> <br /> Also the students are in general Biomedical Engineering students that have limited programming knowledge/affinity in C++.<br /> <br /> <br /> ==Noby Hata is willing to come and give a colloquium/lecture==<br /> <br /> 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.<br /> <br /> <br /> ----<br /> = Main Contact =<br /> ----<br /> <br /> <br /> ==Nobuhiko (Noby) Hata==<br /> <br /> [http://www.spl.harvard.edu/pages/People/noby Personal web page]<br /> <br /> <br /> ----<br /> = Contacts =<br /> ----<br /> <br /> <br /> ==Ron Kikinis==<br /> <br /> [http://www.spl.harvard.edu/pages/People/kikinis Personal web page]<br /> <br /> - 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.<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications%3Fcollection%3D1 ''Publication List SPL'']<br /> <br /> <br /> ==Junichi Tokuda Ph.D.==<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> ==Haying Liu==<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> ==William (Sandy) Wells==<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> ==Steve Pieper==<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> ==Carl-Fredrik Westin==<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/dauguetNeuroImage07.html 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<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/dauguetMICCAI06.html 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<br /> <br /> <br /> ''Keep in Mind''<br /> <br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> ==Stephen Whalen==<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> ==Bruce Fischl==<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.<br /> <br /> <br /> ==Florin Talos==<br /> <br /> [http://www.spl.harvard.edu/pages/People/talos Personal web page]<br /> <br /> - Does very interesting research on ontology, DTI, anatomical analysis of Basal Ganglia, etc.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications?authorfirst=N&amp;authorlast=Archip Archip's papers]<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications?authorfirst=N&amp;authorlast=talos Talos' papers]</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23760 2008-04-10T17:02:11Z

<p>Platel: </p> <hr /> <div>----<br /> = Information on Bram Platel &amp; TU/e =<br /> ----<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> = Possible Topics of Collaboration =<br /> ----<br /> <br /> <br /> ==Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection==<br /> <br /> We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp 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. <br /> <br /> <br /> ==Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)==<br /> <br /> 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. <br /> <br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> <br /> ==GPU Based Visualization==<br /> <br /> 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. <br /> <br /> <br /> ==DTI Validation with Tracer/Anatomical Studies==<br /> <br /> 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 [http://lmi.bwh.harvard.edu/papers/papers/dauguetNeuroImage07.html macaque monkeys]. Perhaps we can use his groups knowledge and software for the analysis of our human and rat brain studies.<br /> <br /> <br /> ==Diffusion Tensor Imaging==<br /> <br /> Anna Vilanova's [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; 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. <br /> <br /> ===Diffusion Data Compatibly===<br /> <br /> 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). [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI More information on NAMIC's DTI / DWI]<br /> <br /> <br /> ==Note on Student Exchange Possibilities==<br /> <br /> 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. <br /> <br /> Also the students are in general Biomedical Engineering students that have limited programming knowledge/affinity in C++.<br /> <br /> <br /> ==Noby Hata is willing to come and give a colloquium/lecture==<br /> <br /> 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.<br /> <br /> <br /> ----<br /> = Main Contact =<br /> ----<br /> <br /> <br /> ==Nobuhiko (Noby) Hata==<br /> <br /> [http://www.spl.harvard.edu/pages/People/noby Personal web page]<br /> <br /> <br /> ----<br /> = Contacts =<br /> ----<br /> <br /> <br /> ==Ron Kikinis==<br /> <br /> [http://www.spl.harvard.edu/pages/People/kikinis Personal web page]<br /> <br /> - 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.<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications%3Fcollection%3D1 ''Publication List SPL'']<br /> <br /> <br /> ==Junichi Tokuda Ph.D.==<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> ==Haying Liu==<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> ==William (Sandy) Wells==<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> ==Steve Pieper==<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> ==Carl-Fredrik Westin==<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/dauguetNeuroImage07.html 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<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/dauguetMICCAI06.html 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<br /> <br /> <br /> ''Keep in Mind''<br /> <br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> ==Stephen Whalen==<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> ==Bruce Fischl==<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.<br /> <br /> <br /> ==Ion-Florin Talos==<br /> <br /> [http://www.spl.harvard.edu/pages/People/talos Personal web page]<br /> <br /> - Does interesting research on ...<br /> <br /> <br /> ''Interesting Publications''</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23759 2008-04-10T17:01:53Z

<p>Platel: </p> <hr /> <div>----<br /> = Information on Bram Platel &amp; TU/e =<br /> ----<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> = Possible Topics of Collaboration =<br /> ----<br /> <br /> <br /> ==Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection==<br /> <br /> We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp 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. <br /> <br /> <br /> ==Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)==<br /> <br /> 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. <br /> <br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> <br /> ==GPU Based Visualization==<br /> <br /> 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. <br /> <br /> <br /> ==DTI Validation with Tracer/Anatomical Studies==<br /> <br /> 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 [http://lmi.bwh.harvard.edu/papers/papers/dauguetNeuroImage07.html macaque monkeys]. Perhaps we can use his groups knowledge and software for the analysis of our human and rat brain studies.<br /> <br /> <br /> ==Diffusion Tensor Imaging==<br /> <br /> Anna Vilanova's [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; 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. <br /> <br /> ===Diffusion Data Compatibly===<br /> <br /> 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). [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI More information on NAMIC's DTI / DWI]<br /> <br /> <br /> ==Note on Student Exchange Possibilities==<br /> <br /> 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. <br /> <br /> Also the students are in general Biomedical Engineering students that have limited programming knowledge/affinity in C++.<br /> <br /> <br /> ==Noby Hata is willing to come and give a colloquium/lecture==<br /> <br /> 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.<br /> <br /> <br /> ----<br /> = Main Contact =<br /> ----<br /> <br /> <br /> ==Nobuhiko (Noby) Hata==<br /> <br /> [http://www.spl.harvard.edu/pages/People/noby Personal web page]<br /> <br /> <br /> ----<br /> == Contacts ==<br /> ----<br /> <br /> <br /> ==Ron Kikinis==<br /> <br /> [http://www.spl.harvard.edu/pages/People/kikinis Personal web page]<br /> <br /> - 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.<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications%3Fcollection%3D1 ''Publication List SPL'']<br /> <br /> <br /> ==Junichi Tokuda Ph.D.==<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> ==Haying Liu==<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> ==William (Sandy) Wells==<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> ==Steve Pieper==<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> ==Carl-Fredrik Westin==<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/dauguetNeuroImage07.html 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<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/dauguetMICCAI06.html 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<br /> <br /> <br /> ''Keep in Mind''<br /> <br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> ==Stephen Whalen==<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> ==Bruce Fischl==<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.<br /> <br /> <br /> ==Ion-Florin Talos==<br /> <br /> [http://www.spl.harvard.edu/pages/People/talos Personal web page]<br /> <br /> - Does interesting research on ...<br /> <br /> <br /> ''Interesting Publications''</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23753 2008-04-10T13:47:14Z

<p>Platel: </p> <hr /> <div>----<br /> == Information on Bram Platel &amp; TU/e ==<br /> ----<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> == Possible Topics of Collaboration ==<br /> ----<br /> <br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> <br /> We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp 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. <br /> <br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> <br /> 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. <br /> <br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> <br /> '''GPU Based Visualization'''<br /> <br /> 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. <br /> <br /> <br /> '''DTI Validation with Tracer/Anatomical Studies'''<br /> <br /> 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 [http://lmi.bwh.harvard.edu/papers/papers/dauguetNeuroImage07.html macaque monkeys]. Perhaps we can use his groups knowledge and software for the analysis of our human and rat brain studies.<br /> <br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> Anna Vilanova's [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; 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. <br /> <br /> ''Diffusion Data Compatibly'' <br /> <br /> 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). [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI More information on NAMIC's DTI / DWI]<br /> <br /> <br /> ''Note on Student Exchange Possibilities''<br /> <br /> 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. <br /> <br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> 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.<br /> <br /> <br /> ----<br /> == Main Contact ==<br /> ----<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/noby Personal web page]<br /> <br /> <br /> ----<br /> == Contacts ==<br /> ----<br /> <br /> <br /> '''Ron Kikinis'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/kikinis Personal web page]<br /> <br /> - 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.<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications%3Fcollection%3D1 ''Publication List SPL'']<br /> <br /> <br /> '''Junichi Tokuda Ph.D.'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> '''Haying Liu'''<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> '''William (Sandy) Wells'''<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> '''Steve Pieper'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/dauguetNeuroImage07.html 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<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/dauguetMICCAI06.html 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<br /> <br /> <br /> ''Keep in Mind''<br /> <br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''Bruce Fischl'''<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.<br /> <br /> <br /> '''Ion-Florin Talos'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/talos Personal web page]<br /> <br /> - Does interesting research on ...<br /> <br /> <br /> ''Interesting Publications''</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23752 2008-04-10T13:43:17Z

<p>Platel: </p> <hr /> <div>----<br /> == Information on Bram Platel &amp; TU/e ==<br /> ----<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> == Possible Topics of Collaboration ==<br /> ----<br /> <br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> <br /> We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp 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. <br /> <br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> <br /> 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. <br /> <br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> <br /> '''GPU Based Visualization'''<br /> <br /> 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. <br /> <br /> <br /> '''DTI Validation with Tracer/Anatomical Studies'''<br /> <br /> 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 [http://lmi.bwh.harvard.edu/papers/papers/dauguetNeuroImage07.html macaque monkeys]. Perhaps we can use his groups knowledge and software for the analysis of our human and rat brain studies.<br /> <br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> Anna Vilanova's [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; 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. <br /> <br /> ''Diffusion Data Compatibly'' <br /> <br /> 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). [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI More information on NAMIC's DTI / DWI]<br /> <br /> <br /> ''Note on Student Exchange Possibilities''<br /> <br /> 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. <br /> <br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> 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.<br /> <br /> <br /> ----<br /> == Main Contact ==<br /> ----<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/noby Personal web page]<br /> <br /> <br /> ----<br /> == Contacts ==<br /> ----<br /> <br /> <br /> '''Ron Kikinis'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/kikinis Personal web page]<br /> <br /> - 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.<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications%3Fcollection%3D1 ''Publication List SPL'']<br /> <br /> <br /> '''Junichi Tokuda Ph.D.'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> '''Haying Liu'''<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> '''William (Sandy) Wells'''<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> '''Steve Pieper'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/dauguetNeuroImage07.html 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<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/dauguetMICCAI06.html 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<br /> <br /> <br /> ''Keep in Mind''<br /> <br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''Bruce Fischl'''<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23751 2008-04-10T13:40:52Z

<p>Platel: </p> <hr /> <div>----<br /> == Information on Bram Platel &amp; TU/e ==<br /> ----<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> == Possible Topics of Collaboration ==<br /> ----<br /> <br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> <br /> We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp 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. <br /> <br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> <br /> 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. <br /> <br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> <br /> '''GPU Based Visualization'''<br /> <br /> 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. <br /> <br /> <br /> '''DTI Validation with Tracer Studies'''<br /> <br /> 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 [http://lmi.bwh.harvard.edu/papers/papers/dauguetNeuroImage07.html Comparison of fiber tracts derived from in-vivo DTI tractography with 3D histological neural tract tracer reconstruction on a macaque brain macaque monkeys].<br /> <br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> Anna Vilanova's [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; 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. <br /> <br /> ''Diffusion Data Compatibly'' <br /> <br /> 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). [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI More information on NAMIC's DTI / DWI]<br /> <br /> <br /> ''Note on Student Exchange Possibilities''<br /> <br /> 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. <br /> <br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> 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.<br /> <br /> <br /> ----<br /> == Main Contact ==<br /> ----<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/noby Personal web page]<br /> <br /> <br /> ----<br /> == Contacts ==<br /> ----<br /> <br /> <br /> '''Ron Kikinis'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/kikinis Personal web page]<br /> <br /> - 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.<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications%3Fcollection%3D1 ''Publication List SPL'']<br /> <br /> <br /> '''Junichi Tokuda Ph.D.'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> '''Haying Liu'''<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> '''William (Sandy) Wells'''<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> '''Steve Pieper'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/dauguetNeuroImage07.html 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<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/dauguetMICCAI06.html 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<br /> <br /> <br /> ''Keep in Mind''<br /> <br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''Bruce Fischl'''<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.</div>

Platel https://www.na-mic.org/w/index.php?title=2008_Platel_visit_from_TUE&diff=23742 2008-04-09T21:23:38Z

<p>Platel: </p> <hr /> <div>=Schedule=<br /> <br /> ----<br /> <br /> March 31, Meeting Nobuhiko Hata<br /> <br /> ----<br /> <br /> -April 1, Meeting Junichi <br /> <br /> ----<br /> <br /> -April 2, 11.00h Meeting Haiying Liu<br /> <br /> -April 2, 15.30h Meeting Sandy Wells<br /> <br /> ----<br /> <br /> -April 3, 11.00h Meeting Ben Grauer<br /> <br /> -April 3, 14.00h Meeting Kerstin Kessel<br /> <br /> ----<br /> <br /> -April 4, 10.30h Meeting Steve Pieper<br /> <br /> -April 4, 13.00h Meeting Carl-Fredrik Westin &amp; Gordon Kindlmann<br /> <br /> -April 4, 14.30h Meeting Haiying Liu for demo Slicer &amp; Aurora<br /> <br /> ----<br /> <br /> -April 8, Meeting with Bruce Fischl<br /> <br /> ----<br /> <br /> -April 9, 10.30h Meeting with Stephen Whalen<br /> <br /> -April 9, 13.00h Meeting with Ron Kikinis &amp; Carl-Fredrik Westin to talk about Bram's research<br /> <br /> ----<br /> <br /> -April 10, 9.30h Meeting with Noby Hata<br /> <br /> -April 10, 14.00h Meeting with Ion-Florin Talos<br /> <br /> <br /> ----<br /> [http://wiki.na-mic.org/Wiki/index.php/User_talk:Platel Bram Platel's Wiki page]</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23741 2008-04-09T20:21:25Z

<p>Platel: </p> <hr /> <div>----<br /> == Information on Bram Platel &amp; TU/e ==<br /> ----<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> == Possible Topics of Collaboration ==<br /> ----<br /> <br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> <br /> We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp 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. <br /> <br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> <br /> 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. <br /> <br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> <br /> '''GPU Based Visualization'''<br /> <br /> 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. <br /> <br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> Anna Vilanova's [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; 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. <br /> <br /> ''Diffusion Data Compatibly'' <br /> <br /> 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). [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI More information on NAMIC's DTI / DWI]<br /> <br /> <br /> ''Note on Student Exchange Possibilities''<br /> <br /> 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. <br /> <br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> 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.<br /> <br /> <br /> ----<br /> == Main Contact ==<br /> ----<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/noby Personal web page]<br /> <br /> <br /> ----<br /> == Contacts ==<br /> ----<br /> <br /> <br /> '''Ron Kikinis'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/kikinis Personal web page]<br /> <br /> - 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.<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications%3Fcollection%3D1 ''Publication List SPL'']<br /> <br /> <br /> '''Junichi Tokuda Ph.D.'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> '''Haying Liu'''<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> '''William (Sandy) Wells'''<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> '''Steve Pieper'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> <br /> ''Keep in Mind''<br /> <br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''Bruce Fischl'''<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23740 2008-04-09T20:20:12Z

<p>Platel: </p> <hr /> <div>----<br /> == Information on Bram Platel &amp; TU/e ==<br /> ----<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> == Possible Topics of Collaboration ==<br /> ----<br /> <br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> <br /> We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp 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. <br /> <br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> <br /> 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. <br /> <br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> <br /> '''GPU Based Visualization'''<br /> <br /> 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. <br /> <br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> Anna Vilanova's [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; 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. <br /> <br /> ''Diffusion Data Compatibly'' <br /> <br /> 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).<br /> <br /> <br /> ''Note on Student Exchange Possibilities''<br /> <br /> 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. <br /> <br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> 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.<br /> <br /> <br /> ----<br /> == Main Contact ==<br /> ----<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/noby Personal web page]<br /> <br /> <br /> ----<br /> == Contacts ==<br /> ----<br /> <br /> <br /> '''Ron Kikinis'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/kikinis Personal web page]<br /> <br /> - 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.<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications%3Fcollection%3D1 ''Publication List SPL'']<br /> <br /> <br /> '''Junichi Tokuda Ph.D.'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> '''Haying Liu'''<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> '''William (Sandy) Wells'''<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> '''Steve Pieper'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> <br /> ''Keep in Mind''<br /> <br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''Bruce Fischl'''<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23739 2008-04-09T19:55:52Z

<p>Platel: </p> <hr /> <div>----<br /> == Information on Bram Platel &amp; TU/e ==<br /> ----<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> == Possible Topics of Collaboration ==<br /> ----<br /> <br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> <br /> We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp 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. <br /> <br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> <br /> 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. <br /> <br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> <br /> '''GPU Based Visualization'''<br /> <br /> 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. <br /> <br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> Anna Vilanova's [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; 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. <br /> <br /> <br /> ''Note on Student Exchange Possibilities''<br /> <br /> 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. <br /> <br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> 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.<br /> <br /> <br /> ----<br /> == Main Contact ==<br /> ----<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/noby Personal web page]<br /> <br /> <br /> ----<br /> == Contacts ==<br /> ----<br /> <br /> <br /> '''Ron Kikinis'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/kikinis Personal web page]<br /> <br /> - 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.<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications%3Fcollection%3D1 ''Publication List SPL'']<br /> <br /> <br /> '''Junichi Tokuda Ph.D.'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> '''Haying Liu'''<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> '''William (Sandy) Wells'''<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> '''Steve Pieper'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> <br /> ''Keep in Mind''<br /> <br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''Bruce Fischl'''<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23738 2008-04-09T19:29:10Z

<p>Platel: </p> <hr /> <div>----<br /> == Information on Bram Platel &amp; TU/e ==<br /> ----<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> == Possible Topics of Collaboration ==<br /> ----<br /> <br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> <br /> We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp 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. <br /> <br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> <br /> 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. <br /> <br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> <br /> '''GPU Visualization'''<br /> <br /> 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. <br /> <br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> Anna Vilanova's [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; 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. <br /> <br /> <br /> ''Note on Student Exchange Possibilities''<br /> <br /> 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. <br /> <br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> 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.<br /> <br /> <br /> ----<br /> == Main Contact ==<br /> ----<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/noby Personal web page]<br /> <br /> <br /> ----<br /> == Contacts ==<br /> ----<br /> <br /> <br /> '''Ron Kikinis'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/kikinis Personal web page]<br /> <br /> - 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.<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications%3Fcollection%3D1 ''Publication List SPL'']<br /> <br /> <br /> '''Junichi Tokuda Ph.D.'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> '''Haying Liu'''<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> '''William (Sandy) Wells'''<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> '''Steve Pieper'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> <br /> ''Keep in Mind''<br /> <br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''Bruce Fischl'''<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23737 2008-04-09T19:28:55Z

<p>Platel: </p> <hr /> <div><br /> <br /> ----<br /> == Information on Bram Platel &amp; TU/e ==<br /> ----<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> == Possible Topics of Collaboration ==<br /> ----<br /> <br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> <br /> We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp 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. <br /> <br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> <br /> 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. <br /> <br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> <br /> '''GPU Visualization'''<br /> <br /> 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. <br /> <br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> Anna Vilanova's [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; 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. <br /> <br /> <br /> ''Note on Student Exchange Possibilities''<br /> <br /> 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. <br /> <br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> 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.<br /> <br /> <br /> ----<br /> == Main Contact ==<br /> ----<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/noby Personal web page]<br /> <br /> <br /> ----<br /> == Contacts ==<br /> ----<br /> <br /> <br /> '''Ron Kikinis'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/kikinis Personal web page]<br /> <br /> - 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.<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications%3Fcollection%3D1 ''Publication List SPL'']<br /> <br /> <br /> '''Junichi Tokuda Ph.D.'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> '''Haying Liu'''<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> '''William (Sandy) Wells'''<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> '''Steve Pieper'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> <br /> ''Keep in Mind''<br /> <br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''Bruce Fischl'''<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23736 2008-04-09T19:28:20Z

<p>Platel: </p> <hr /> <div>----<br /> == Information on Bram Platel &amp; TU/e ==<br /> ----<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> == Possible Topics of Collaboration ==<br /> ----<br /> <br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> <br /> We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp 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. <br /> <br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> <br /> 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. <br /> <br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> <br /> '''GPU Visualization'''<br /> <br /> 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. <br /> <br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> Anna Vilanova's [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; 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. <br /> <br /> <br /> ''Note on Student Exchange Possibilities''<br /> <br /> 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. <br /> <br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> 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.<br /> <br /> <br /> ----<br /> == Main Contact ==<br /> ----<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/noby Personal web page]<br /> <br /> <br /> ----<br /> == Contacts ==<br /> ----<br /> <br /> <br /> '''Ron Kikinis'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/kikinis Personal web page]<br /> <br /> - 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.<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications%3Fcollection%3D1 ''Publication List SPL'']<br /> <br /> <br /> '''Junichi Tokuda Ph.D.'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> '''Haying Liu'''<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> '''William (Sandy) Wells'''<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> '''Steve Pieper'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> <br /> ''Keep in Mind''<br /> <br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''Bruce Fischl'''<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23735 2008-04-09T19:27:23Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> <br /> == Possible Topics of Collaboration ==<br /> <br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> <br /> We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp 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. <br /> <br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> <br /> 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. <br /> <br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> <br /> '''GPU Visualization'''<br /> <br /> 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. <br /> <br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> Anna Vilanova's [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; 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. <br /> <br /> <br /> ''Note on Student Exchange Possibilities''<br /> <br /> 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. <br /> <br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> 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.<br /> <br /> <br /> ----<br /> <br /> <br /> == Main Contact ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/noby Personal web page]<br /> <br /> ----<br /> <br /> <br /> == Contacts ==<br /> <br /> <br /> '''Ron Kikinis'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/kikinis Personal web page]<br /> <br /> - 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.<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications%3Fcollection%3D1 ''Publication List SPL'']<br /> <br /> <br /> '''Junichi Tokuda Ph.D.'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> '''Haying Liu'''<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> '''William (Sandy) Wells'''<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> '''Steve Pieper'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> <br /> ''Keep in Mind''<br /> <br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''Bruce Fischl'''<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23734 2008-04-09T19:23:19Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration ==<br /> <br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> <br /> We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp 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. <br /> <br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> <br /> 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. <br /> <br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> <br /> '''GPU Visualization'''<br /> <br /> 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. <br /> <br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> Anna Vilanova's [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; 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. <br /> <br /> <br /> ''Note on Student Exchange Possibilities''<br /> <br /> 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. <br /> <br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> 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.<br /> <br /> <br /> ----<br /> <br /> == Main Contact ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/noby Personal web page]<br /> <br /> ----<br /> <br /> <br /> == Contacts ==<br /> <br /> <br /> '''Ron Kikinis'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/kikinis Personal web page]<br /> <br /> - 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.<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications%3Fcollection%3D1 ''Publication List SPL'']<br /> <br /> <br /> '''Junichi Tokuda Ph.D.'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> '''Haying Liu'''<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> '''William (Sandy) Wells'''<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> '''Steve Pieper'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> <br /> ''Keep in Mind''<br /> <br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''Bruce Fischl'''<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23733 2008-04-09T19:11:48Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration ==<br /> <br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> Anna Vilanova's [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; 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. <br /> <br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> <br /> We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp 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. <br /> <br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> <br /> 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. <br /> <br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> <br /> '''GPU Visualization'''<br /> <br /> 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. <br /> <br /> <br /> ''Note on Student Exchange Possibilities''<br /> <br /> 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. <br /> <br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> 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.<br /> <br /> <br /> ----<br /> <br /> == Main Contact ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/noby Personal web page]<br /> <br /> ----<br /> <br /> <br /> == Contacts ==<br /> <br /> <br /> '''Ron Kikinis'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/kikinis Personal web page]<br /> <br /> - 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.<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications%3Fcollection%3D1 ''Publication List SPL'']<br /> <br /> <br /> '''Junichi Tokuda Ph.D.'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> '''Haying Liu'''<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> '''William (Sandy) Wells'''<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> '''Steve Pieper'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> <br /> ''Keep in Mind''<br /> <br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''Bruce Fischl'''<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23732 2008-04-09T19:07:45Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration ==<br /> <br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> Anna Vilanova's [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; 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. <br /> <br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> <br /> We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp 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. <br /> <br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> <br /> 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. <br /> <br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> <br /> '''GPU Visualization'''<br /> <br /> 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. <br /> <br /> <br /> ''Note on Student Exchange Possibilities''<br /> <br /> 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. <br /> <br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> 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.<br /> <br /> <br /> ----<br /> <br /> == Main Contact ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Contacts ==<br /> <br /> <br /> '''Ron Kikinis'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/kikinis Personal web page]<br /> <br /> - 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.<br /> <br /> [http://www.spl.harvard.edu/pages/Special:Publications%3Fcollection%3D1 ''Publication List SPL'']<br /> <br /> <br /> '''Junichi Tokuda Ph.D.'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> '''Haying Liu'''<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> '''William (Sandy) Wells'''<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> '''Steve Pieper'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> <br /> ''Keep in Mind''<br /> <br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''Bruce Fischl'''<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23726 2008-04-09T16:24:18Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration ==<br /> <br /> <br /> '''Deep Brain Stimulation'''<br /> (I'm meeting [http://frontweb.vuse.vanderbilt.edu/vuse_web/directory/facultybio.asp?FacultyID=20802 Benoit Dawant] 14-18 April at Vanderbilt University to talk about their DBS research)<br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> (Interested to see Slicer's capabilities. We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp Medtronic Polestar N20], we would like to use pre-operative data: fMRI, DTI and register this with the Polestar data during the surgery.)<br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> '''GPU Visualization, Depth Peeling (Nvidia's CUDA)'''<br /> <br /> '''Scanner Deformation Analysis &amp; Correction'''<br /> <br /> ''Student Exchange Possibilities''<br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> <br /> ----<br /> <br /> == Main Contact ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Contacts ==<br /> <br /> <br /> '''Junichi Tokuda Ph.D.'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> '''Haying Liu'''<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> '''William (Sandy) Wells'''<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> '''Steve Pieper'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> <br /> ''Keep in Mind''<br /> <br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''Bruce Fischl'''<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23725 2008-04-09T16:21:21Z

<p>Platel: /* Contacts */</p> <hr /> <div>----<br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration ==<br /> <br /> <br /> '''Deep Brain Stimulation'''<br /> (I'm meeting [http://frontweb.vuse.vanderbilt.edu/vuse_web/directory/facultybio.asp?FacultyID=20802 Benoit Dawant] 14-18 April at Vanderbilt University to talk about their DBS research)<br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> (Interested to see Slicer's capabilities. We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp Medtronic Polestar N20], we would like to use pre-operative data: fMRI, DTI and register this with the Polestar data during the surgery.)<br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> '''GPU Visualization, Depth Peeling (Nvidia's CUDA)'''<br /> <br /> '''Scanner Deformation Analysis &amp; Correction'''<br /> <br /> ''Student Exchange Possibilities''<br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> <br /> ----<br /> <br /> == Main Contact ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Contacts ==<br /> <br /> <br /> '''Junichi Tokuda Ph.D.'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> <br /> '''Haying Liu'''<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> <br /> '''William (Sandy) Wells'''<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> <br /> '''Steve Pieper'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> [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<br /> <br /> <br /> ''Keep in Mind''<br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''Bruce Fischl'''<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23724 2008-04-09T16:12:54Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration ==<br /> <br /> <br /> '''Deep Brain Stimulation'''<br /> (I'm meeting [http://frontweb.vuse.vanderbilt.edu/vuse_web/directory/facultybio.asp?FacultyID=20802 Benoit Dawant] 14-18 April at Vanderbilt University to talk about their DBS research)<br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> (Interested to see Slicer's capabilities. We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp Medtronic Polestar N20], we would like to use pre-operative data: fMRI, DTI and register this with the Polestar data during the surgery.)<br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> '''GPU Visualization, Depth Peeling (Nvidia's CUDA)'''<br /> <br /> '''Scanner Deformation Analysis &amp; Correction'''<br /> <br /> ''Student Exchange Possibilities''<br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> <br /> ----<br /> <br /> == Main Contact ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Contacts ==<br /> <br /> <br /> '''Junichi Tokuda Ph.D.'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> '''Haying Liu'''<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> '''William (Sandy) Wells'''<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> '''Steve Pieper'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> .... As soon as the LMI page is up again I will update the interesting publications list....<br /> <br /> ''Keep in Mind''<br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> '''Bruce Fischl'''<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - 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.<br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23723 2008-04-09T16:03:30Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration ==<br /> <br /> <br /> '''Deep Brain Stimulation'''<br /> (I'm meeting [http://frontweb.vuse.vanderbilt.edu/vuse_web/directory/facultybio.asp?FacultyID=20802 Benoit Dawant] 14-18 April at Vanderbilt University to talk about their DBS research)<br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> (Interested to see Slicer's capabilities. We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp Medtronic Polestar N20], we would like to use pre-operative data: fMRI, DTI and register this with the Polestar data during the surgery.)<br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> '''GPU Visualization, Depth Peeling (Nvidia's CUDA)'''<br /> <br /> '''Scanner Deformation Analysis &amp; Correction'''<br /> <br /> ''Student Exchange Possibilities''<br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> <br /> ----<br /> <br /> == Main Contact ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Contacts ==<br /> <br /> <br /> '''Junichi Tokuda Ph.D.'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> '''Haying Liu'''<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> '''William (Sandy) Wells'''<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> '''Steve Pieper'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> .... As soon as the LMI page is up again I will update the interesting publications list....<br /> <br /> ''Keep in Mind''<br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> [http://golbylab.bwh.harvard.edu/people_stephen.html Personal web page]<br /> <br /> - Does interesting research on presenting fMRI and DTI data to surgeons prior to the operation.<br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> '''Bruce Fischl'''<br /> <br /> [http://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=56 Personal web page]<br /> <br /> [http://surfer.nmr.mgh.harvard.edu/fswiki/ Lab's Wiki page]<br /> <br /> - Does interesting research together with Koen van Leemput on automated brain segmentation in the aria of our interest, the thalamus and the surrounding nuclei.<br /> <br /> ''Interesting Publications''<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf 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.<br /> <br /> [http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf 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.<br /> <br /> [https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf 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.<br /> <br /> - I have contacted Koen van Leemput for more publications on the matter of automatic segmentation.</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23638 2008-04-07T15:33:01Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration ==<br /> <br /> <br /> '''Deep Brain Stimulation'''<br /> (I'm meeting [http://frontweb.vuse.vanderbilt.edu/vuse_web/directory/facultybio.asp?FacultyID=20802 Benoit Dawant] 14-18 April at Vanderbilt University to talk about their DBS research)<br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> (Interested to see Slicer's capabilities. We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp Medtronic Polestar N20], we would like to use pre-operative data: fMRI, DTI and register this with the Polestar data during the surgery.)<br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> '''GPU Visualization, Depth Peeling (Nvidia's CUDA)'''<br /> <br /> '''Scanner Deformation Analysis &amp; Correction'''<br /> <br /> ''Student Exchange Possibilities''<br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> <br /> ----<br /> <br /> == Main Contact ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Contacts ==<br /> <br /> <br /> '''Junichi Tokuda Ph.D.'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/tokuda Personal web page]<br /> <br /> - Built robot for prostate cancer biopsy, this robot is currently no longer in use since the open MR-scanner is out of business.<br /> <br /> - 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.<br /> ''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.''<br /> <br /> '''Haying Liu'''<br /> <br /> - Slicer software engineer, involved in maintaining the software/source code. <br /> - 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].<br /> <br /> '''William (Sandy) Wells'''<br /> <br /> [http://people.csail.mit.edu/sw/ Personal web page]<br /> <br /> - 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. <br /> - Wells is currently working on a large study on fMRI data of Schizophrenia patients.<br /> <br /> ''Papers to consider:''<br /> <br /> [http://www.spl.harvard.edu/pages/Special:PubDB_View%3Fdspaceid%3D58 A Bayesian Model for Joint Segmentation and Registration], Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage 31, 2006<br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html 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<br /> <br /> [http://www.springerlink.com/index/m318851t513802h2.pdf 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<br /> <br /> [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. ]<br /> <br /> '''Steve Pieper'''<br /> <br /> [http://www.spl.harvard.edu/pages/People/pieper Personal web page]<br /> <br /> - At the SPL, Steve is the Engineering Core PI on the Neuroimage Analysis Center.<br /> <br /> - 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.<br /> <br /> - [http://pnl.bwh.harvard.edu/people/profiles/kubicki.html 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''. <br /> <br /> - 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.<br /> <br /> ''Note:''<br /> - Steve pointed out a [http://www.na-mic.org/Wiki/index.php/Events:June-Germany Slicer training event] in Germany June 16/17 that might be interesting for our students.<br /> <br /> - Sending students to their masters at SPL is a good option.<br /> <br /> ''Papers to consider:''<br /> <br /> [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]<br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> [http://lmi.bwh.harvard.edu/~westin/ Personal web page]<br /> <br /> - Carl-Fredrik Westin is the Director of the Laboratory of Mathematics in Imaging (LMI) and Associate Professor of Radiology, Harvard Medical School.<br /> <br /> - Together with [http://lmi.bwh.harvard.edu/~gk/ Gordon Kindlmann] we discussed our research. <br /> <br /> ''Papers to consider:''<br /> <br /> 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e.<br /> <br /> .... As soon as the LMI page is up again I will update the interesting publications list....<br /> <br /> ''Keep in Mind''<br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> Research Assistant<br /> Golby Lab<br /> Brigham and Women's Hospital<br /> Department of Neurosurgery<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/17289403?dopt=AbstractPlus Non-rigid alignment of preoperative MRI, fMRI and DT-MRI with intraoperative MRI to enhance visualization and navigation in image-guided neurosurgery.] Neuroimage, 2007 Apr 1;35(2):609-624. <br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.</div>

Platel https://www.na-mic.org/w/index.php?title=2008_Platel_visit_from_TUE&diff=23618 2008-04-04T20:14:38Z

<p>Platel: </p> <hr /> <div>=Schedule=<br /> <br /> ----<br /> <br /> March 31, Meeting Nobuhiko Hata<br /> <br /> ----<br /> <br /> -April 1, Meeting Junichi <br /> <br /> ----<br /> <br /> -April 2, 11.00h Meeting Haiying Liu<br /> <br /> -April 2, 15.30h Meeting Sandy Wells<br /> <br /> ----<br /> <br /> -April 3, 11.00h Meeting Ben Grauer<br /> <br /> -April 3, 14.00h Meeting Kerstin Kessel<br /> <br /> ----<br /> <br /> -April 4, 10.30h Meeting Steve Pieper<br /> <br /> -April 4, 13.00h Meeting Carl-Fredrik Westin &amp; Gordon Kindlmann<br /> <br /> -April 4, 14.30h Meeting Haiying Liu for demo Slicer &amp; Aurora<br /> <br /> ----<br /> <br /> -April 8, Meeting with Bruce Fischl<br /> <br /> ----<br /> <br /> -April 9, 10.30h Meeting with Stephen Whalen<br /> <br /> -April 9, 13.00h Meeting with Carl-Fredrik Westin &amp; Ron Kikinis to talk about Bram's DBS research<br /> <br /> ----<br /> <br /> -April 10, 14.00h Meeting with Ion-Florin Talos</div>

Platel https://www.na-mic.org/w/index.php?title=2008_Platel_visit_from_TUE&diff=23617 2008-04-04T20:01:29Z

<p>Platel: </p> <hr /> <div>=Schedule=<br /> <br /> ----<br /> <br /> March 31, Meeting Nobuhiko Hata<br /> <br /> ----<br /> <br /> -April 1, Meeting Junichi <br /> <br /> ----<br /> <br /> -April 2, 11.00h Meeting Haiying Liu<br /> <br /> -April 2, 15.30h Meeting Sandy Wells<br /> <br /> ----<br /> <br /> -April 3, 11.00h Meeting Ben Grauer<br /> <br /> -April 3, 14.00h Meeting Kerstin Kessel<br /> <br /> ----<br /> <br /> -April 4, 10.30h Meeting Steve Pieper<br /> <br /> -April 4, 13.00h Meeting Carl-Fredrik Westin &amp; Gordon Kindlmann<br /> <br /> -April 4, 14.30h Meeting Haiying Liu for demo Slicer &amp; Aurora<br /> <br /> ----<br /> <br /> -April 8, Meeting with Bruce Fischl<br /> <br /> ----<br /> <br /> -April 9, 13.00h Meeting with Carl-Fredrik Westin &amp; Ron Kikinis to talk about Bram's DBS research<br /> <br /> ----<br /> <br /> -April 10, 14.00h Meeting with Ion-Florin Talos</div>

Platel https://www.na-mic.org/w/index.php?title=2008_Platel_visit_from_TUE&diff=23616 2008-04-04T19:37:16Z

<p>Platel: </p> <hr /> <div>=Schedule=<br /> <br /> ----<br /> <br /> March 31, Meeting Nobuhiko Hata<br /> <br /> ----<br /> <br /> -April 1, Meeting Junichi <br /> <br /> ----<br /> <br /> -April 2, 11.00h Meeting Haiying Liu<br /> <br /> -April 2, 15.30h Meeting Sandy Wells<br /> <br /> ----<br /> <br /> -April 3, 11.00h Meeting Ben Grauer<br /> <br /> -April 3, 14.00h Meeting Kerstin Kessel<br /> <br /> ----<br /> <br /> -April 4, 10.30h Meeting Steve Pieper<br /> <br /> -April 4, 13.00h Meeting Carl-Fredrik Westin &amp; Gordon Kindlmann<br /> <br /> -April 4, 14.30h Meeting Haiying Liu for demo Slicer &amp; Aurora<br /> <br /> ----<br /> <br /> -April 9, 13.00h Meeting with Carl-Fredrik Westin &amp; Ron Kikinis to talk about Bram's DBS research<br /> <br /> ----<br /> <br /> -April 10, 14.00h Meeting with Ion-Florin Talos</div>

Platel https://www.na-mic.org/w/index.php?title=2008_Platel_visit_from_TUE&diff=23611 2008-04-04T16:39:12Z

<p>Platel: </p> <hr /> <div>=Schedule=<br /> <br /> ----<br /> <br /> March 31, Meeting Nobuhiko Hata<br /> <br /> ----<br /> <br /> -April 1, Meeting Junichi <br /> <br /> ----<br /> <br /> -April 2, 11.00h Meeting Haiying Liu<br /> <br /> -April 2, 15.30h Meeting Sandy Wells<br /> <br /> ----<br /> <br /> -April 3, 11.00h Meeting Ben Grauer<br /> <br /> -April 3, 14.00h Meeting Kerstin Kessel<br /> <br /> ----<br /> <br /> -April 4, 10.30h Meeting Steve Pieper<br /> <br /> -April 4, 13.00h Meeting Carl-Fredrik Westin &amp; Gordon Kindlmann<br /> <br /> -April 4, 14.30h Meeting Haiying Liu for demo Slicer &amp; Aurora<br /> <br /> ----</div>

Platel https://www.na-mic.org/w/index.php?title=2008_Platel_visit_from_TUE&diff=23610 2008-04-04T16:38:28Z

<p>Platel: </p> <hr /> <div>=Schedule=<br /> <br /> <br /> ----<br /> -April 1, Meeting Junichi <br /> <br /> ----<br /> <br /> -April 2, 11.00h Meeting Haiying Liu<br /> <br /> -April 2, 15.30h Meeting Sandy Wells<br /> <br /> ----<br /> <br /> -April 3, 11.00h Meeting Ben Grauer<br /> <br /> -April 3, 14.00h Meeting Kerstin Kessel<br /> <br /> ----<br /> <br /> -April 4, 10.30h Meeting Steve Pieper<br /> <br /> -April 4, 13.00h Meeting Carl-Fredrik Westin &amp; Gordon Kindlmann<br /> <br /> -April 4, 14.30h Meeting Haiying Liu for demo Slicer &amp; Aurora<br /> <br /> ----</div>

Platel https://www.na-mic.org/w/index.php?title=2008_Platel_visit_from_TUE&diff=23609 2008-04-04T16:26:06Z

<p>Platel: </p> <hr /> <div>=Schedule=<br /> <br /> <br /> ----<br /> -April 1, Meeting Junichi <br /> <br /> ----<br /> <br /> -April 2, 11.00h Meeting Haiying Liu<br /> <br /> -April 2, 15.30h Meeting Sandy Wells<br /> <br /> ----<br /> <br /> -April 3, 11.00h Meeting Ben Grauer<br /> <br /> -April 3, 14.00h Meeting Kerstin Kessel<br /> <br /> ----<br /> <br /> -April 4, 10.30h Meeting Steve Pieper<br /> <br /> -April 4, 13.00h Meeting Carl-Fredrik Westin<br /> <br /> -April 4, 14.30h Meeting Haiying Liu for demo Slicer &amp; Aurora<br /> <br /> ----</div>

Platel https://www.na-mic.org/w/index.php?title=2008_Platel_visit_from_TUE&diff=23605 2008-04-03T20:04:08Z

<p>Platel: </p> <hr /> <div>=Schedule=<br /> <br /> <br /> ----<br /> -April 1, Meeting Junichi <br /> <br /> ----<br /> <br /> -April 2, 11.00h Meeting Haiying Liu<br /> <br /> -April 2, 15.30h Meeting Sandy Wells<br /> <br /> ----<br /> <br /> -April 3, 11.00h Meeting Ben Grauer<br /> <br /> ----<br /> <br /> -April 4, 10.30h Meeting Steve Pieper<br /> <br /> -April 4, 13.00h Meeting Carl-Fredrik Westin<br /> <br /> -April 4, 14.30h Meeting Haiying Liu for demo Slicer &amp; Aurora<br /> <br /> ----</div>

Platel https://www.na-mic.org/w/index.php?title=2008_Platel_visit_from_TUE&diff=23548 2008-04-02T16:54:24Z

<p>Platel: </p> <hr /> <div>=Schedule=<br /> <br /> <br /> ----<br /> -April 1, Meeting Junichi <br /> <br /> ----<br /> <br /> -April 2, 11.00h Meeting Haiying Liu<br /> <br /> -April 2, 15.30h Meeting Sandy Wells<br /> <br /> ----<br /> <br /> -April 4, 11.00h Meeting Ben Grauer<br /> <br /> -April 4, 13.00h Meeting Carl-Fredrik Westin<br /> <br /> -April 4, 14.30h Meeting Haiying Liu for demo Slicer &amp; Aurora<br /> <br /> ----</div>

Platel https://www.na-mic.org/w/index.php?title=2008_Platel_visit_from_TUE&diff=23541 2008-04-02T16:22:09Z

<p>Platel: </p> <hr /> <div>=Schedule=<br /> <br /> -April 1, Meeting Junichi <br /> <br /> -April 2, 11.00h Meeting Haiying Liu<br /> <br /> -April 2, 15.30h Meeting Sandy Wells<br /> <br /> -April 4, 11.00h Meeting Ben Grauer<br /> <br /> -April 4, 13.00h Meeting Carl-Fredrik Westin<br /> <br /> -April 4, 14.30h Meeting Haiying Liu for demo Slicer &amp; Aurora</div>

Platel https://www.na-mic.org/w/index.php?title=2008_Platel_visit_from_TUE&diff=23540 2008-04-02T16:10:29Z

<p>Platel: </p> <hr /> <div>=Schedule=<br /> <br /> -April 1, Meeting Junichi <br /> <br /> -April 2, 11.00h Meeting Haiying Liu<br /> <br /> -April 2, 15.30h Meeting Sandy Wells<br /> <br /> -April 4, 13.00h Meeting Carl-Fredrik Westin<br /> <br /> -April 4, 14.30h Meeting Haiying Liu for demo Slicer &amp; Aurora<br /> <br /> -Meeting Ben Grauer</div>

Platel https://www.na-mic.org/w/index.php?title=2008_Platel_visit_from_TUE&diff=23539 2008-04-02T15:01:39Z

<p>Platel: </p> <hr /> <div>=Schedule=<br /> <br /> -April 1, Meeting Junichi <br /> <br /> -April 2, 11.00h Meeting Haiying Liu<br /> <br /> -April 2, 15.30h Meeting Sandy Wells<br /> <br /> -April 4, 13.00h Meeting Carl-Fredrik Westin<br /> <br /> -Meeting Ben Grauer</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23532 2008-04-02T11:49:58Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration ==<br /> <br /> <br /> '''Deep Brain Stimulation'''<br /> (I'm meeting [http://frontweb.vuse.vanderbilt.edu/vuse_web/directory/facultybio.asp?FacultyID=20802 Benoit Dawant] 14-18 April at Vanderbilt University to talk about their DBS research)<br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> (Interested to see Slicer's capabilities. We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp Medtronic Polestar N20], we would like to use pre-operative data: fMRI, DTI and register this with the Polestar data during the surgery.)<br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> '''GPU Visualization, Depth Peeling (Nvidia's CUDA)'''<br /> <br /> '''Scanner Deformation Analysis &amp; Correction'''<br /> <br /> ''Student Exchange Possibilities''<br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> <br /> ----<br /> <br /> == Main Contact ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Interesting Contacts ==<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> Director, Laboratory of Mathematics in Imaging (LMI) <br /> Associate Professor of Radiology, Harvard Medical School<br /> <br /> <br /> ''Keep in Mind''<br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html A Mathematical Framework for Incorporating Anatomical Knowledge in DT-MRI analysis]<br /> Mahnaz Maddah, Lilla Zöllei, W. Eric L. Grimson, Carl-Fredrik Westin, William M. Wells<br /> Biomedical Imaging: From Nano to Macro, 2008. ISBI 2008. 5th IEEE International Symposium on Biomedical Imaging, Paris, France<br /> 2008<br /> <br /> <br /> ... 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e ...<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> Research Assistant<br /> Golby Lab<br /> Brigham and Women's Hospital<br /> Department of Neurosurgery<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/17289403?dopt=AbstractPlus Non-rigid alignment of preoperative MRI, fMRI and DT-MRI with intraoperative MRI to enhance visualization and navigation in image-guided neurosurgery.] Neuroimage, 2007 Apr 1;35(2):609-624. <br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''William M. Wells III, (aka Sandy Wells)'''<br /> <br /> Associate Professor <br /> Department of Radiology <br /> Harvard Medical School and <br /> Brigham and Women's Hospital<br /> <br /> <br /> My work has focused primarily on the analysis of structural and functional MRI. Areas of research include the segmentation and registration of MRI, with some emphasis on applications in image-guided surgery. The figure on the upper right illustrates the white matter surface of a brain that was segmented from MRI using Adaptive Segmentation of MRI (the &quot;EM Segmenter&quot;) .<br /> My research in medical image registration concerns the use of Mutual Information as a criterion for image fusion. This approach has become the de-facto standard for multi-modality problems. Implementations of this method are available in 3D Slicer, our open-source platform for medical image analysis, and in ITK, an NIH sponsored segmentation and registration library.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> A Bayesian Model for Joint Segmentation and Registration. Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage (to appear)<br /> <br /> [http://people.csail.mit.edu/welg/papers/integrated2001.pdf An Integrated Visualization System for Surgical Planning and Guidance Using Image Fusion and an Open MR.] Gering D, Nabavi A, Kikinis R, Hata N, O'Donnell L, Grimson E, Jolesz F, Black P, Wells WM. JMRI 2001; 13:967-975<br /> <br /> <br /> '''Benjamin Grauer'''<br /> <br /> <br /> Have a look at [http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week_VolumeRendering 2008 Winter Project Week VolumeRendering]<br /> <br /> <br /> '''Junichi Tokuda'''<br /> <br /> <br /> Junichi Tokuda is a Research Fellow of Brigham and Women's Hospital and Harvard Medical School. He received a B.S in Engineering in 2002, a M.S. in Information Science and Technology in 2004, and a Ph.D. in Information Science and Technology in 2007, from The University of Tokyo, Japan. His main research interest is MRI guided therapy including MR pulse sequence, navigation software, MRI-compatible robot and integration of these technologies for operating environment. He has been working on this area since 2001, and has broad experience in developing software and devices for these applications. For example, the software to assist MRI-guided microwave coagulation therapy of liver tumor, which he developed at Shiga University of Medical Science, Japan, has already been used in more than 100 clinical cases. He joined the Image Guided Therapy Program at Brigham and Women's Hospital since April 2007, and continues to work on MR-guided therapy.<br /> <br /> Busy with a robot for taking biopsies from the prostate and in future from the liver. Currently developing the OpenIGTLink protocol for the communication of scanners/trackers/etc. with 3D Slicer. The protocol is well defined, open, and useful for many cases.<br /> <br /> <br /> '''Haiying Liu'''<br /> <br /> <br /> Talk about: Slicer, OpenIGT Link, tutorial, tools, engineering</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23482 2008-04-01T12:17:13Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration ==<br /> <br /> <br /> '''Deep Brain Stimulation'''<br /> (I'm meeting [http://frontweb.vuse.vanderbilt.edu/vuse_web/directory/facultybio.asp?FacultyID=20802 Benoit Dawant] 14-18 April at Vanderbilt University to talk about their DBS research)<br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> (Interested to see Slicer's capabilities. We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp Medtronic Polestar N20], we would like to use pre-operative data: fMRI, DTI and register this with the Polestar data during the surgery.)<br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> '''GPU Visualization, Depth Peeling (Nvidia's CUDA)'''<br /> <br /> '''Scanner Deformation Analysis &amp; Correction'''<br /> <br /> ''Student Exchange Possibilities''<br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> <br /> ----<br /> <br /> == Main Contact ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Interesting Contacts ==<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> Director, Laboratory of Mathematics in Imaging (LMI) <br /> Associate Professor of Radiology, Harvard Medical School<br /> <br /> <br /> ''Keep in Mind''<br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html A Mathematical Framework for Incorporating Anatomical Knowledge in DT-MRI analysis]<br /> Mahnaz Maddah, Lilla Zöllei, W. Eric L. Grimson, Carl-Fredrik Westin, William M. Wells<br /> Biomedical Imaging: From Nano to Macro, 2008. ISBI 2008. 5th IEEE International Symposium on Biomedical Imaging, Paris, France<br /> 2008<br /> <br /> <br /> ... 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e ...<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> Research Assistant<br /> Golby Lab<br /> Brigham and Women's Hospital<br /> Department of Neurosurgery<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/17289403?dopt=AbstractPlus Non-rigid alignment of preoperative MRI, fMRI and DT-MRI with intraoperative MRI to enhance visualization and navigation in image-guided neurosurgery.] Neuroimage, 2007 Apr 1;35(2):609-624. <br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''William M. Wells III, (aka Sandy Wells)'''<br /> <br /> Associate Professor <br /> Department of Radiology <br /> Harvard Medical School and <br /> Brigham and Women's Hospital<br /> <br /> <br /> My work has focused primarily on the analysis of structural and functional MRI. Areas of research include the segmentation and registration of MRI, with some emphasis on applications in image-guided surgery. The figure on the upper right illustrates the white matter surface of a brain that was segmented from MRI using Adaptive Segmentation of MRI (the &quot;EM Segmenter&quot;) .<br /> My research in medical image registration concerns the use of Mutual Information as a criterion for image fusion. This approach has become the de-facto standard for multi-modality problems. Implementations of this method are available in 3D Slicer, our open-source platform for medical image analysis, and in ITK, an NIH sponsored segmentation and registration library.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> A Bayesian Model for Joint Segmentation and Registration. Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage (to appear)<br /> <br /> [http://people.csail.mit.edu/welg/papers/integrated2001.pdf An Integrated Visualization System for Surgical Planning and Guidance Using Image Fusion and an Open MR.] Gering D, Nabavi A, Kikinis R, Hata N, O'Donnell L, Grimson E, Jolesz F, Black P, Wells WM. JMRI 2001; 13:967-975<br /> <br /> <br /> '''Benjamin Grauer'''<br /> <br /> <br /> Have a look at [http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week_VolumeRendering 2008 Winter Project Week VolumeRendering]<br /> <br /> <br /> '''Junichi Tokuda'''<br /> <br /> <br /> Junichi Tokuda is a Research Fellow of Brigham and Women's Hospital and Harvard Medical School. He received a B.S in Engineering in 2002, a M.S. in Information Science and Technology in 2004, and a Ph.D. in Information Science and Technology in 2007, from The University of Tokyo, Japan. His main research interest is MRI guided therapy including MR pulse sequence, navigation software, MRI-compatible robot and integration of these technologies for operating environment. He has been working on this area since 2001, and has broad experience in developing software and devices for these applications. For example, the software to assist MRI-guided microwave coagulation therapy of liver tumor, which he developed at Shiga University of Medical Science, Japan, has already been used in more than 100 clinical cases. He joined the Image Guided Therapy Program at Brigham and Women's Hospital since April 2007, and continues to work on MR-guided therapy.<br /> <br /> <br /> '''Haiying Liu'''<br /> <br /> <br /> Talk about: Slicer, OpenIGT Link, tutorial, tools, engineering</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23481 2008-04-01T12:07:05Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration: ==<br /> <br /> <br /> '''Deep Brain Stimulation'''<br /> (I'm meeting [http://frontweb.vuse.vanderbilt.edu/vuse_web/directory/facultybio.asp?FacultyID=20802 Benoit Dawant] 14-18 April at Vanderbilt University to talk about their DBS research)<br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> (Interested to see Slicer's capabilities. We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp Medtronic Polestar N20], we would like to use pre-operative data: fMRI, DTI and register this with the Polestar data during the surgery.)<br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> '''GPU Visualization, Depth Peeling (Nvidia's CUDA)'''<br /> <br /> '''Scanner Deformation Analysis &amp; Correction'''<br /> <br /> ''Student Exchange Possibilities''<br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> <br /> ----<br /> <br /> == Main Contact: ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Interesting Contacts: ==<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> Director, Laboratory of Mathematics in Imaging (LMI) <br /> Associate Professor of Radiology, Harvard Medical School<br /> <br /> <br /> ''Keep in Mind''<br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html A Mathematical Framework for Incorporating Anatomical Knowledge in DT-MRI analysis]<br /> Mahnaz Maddah, Lilla Zöllei, W. Eric L. Grimson, Carl-Fredrik Westin, William M. Wells<br /> Biomedical Imaging: From Nano to Macro, 2008. ISBI 2008. 5th IEEE International Symposium on Biomedical Imaging, Paris, France<br /> 2008<br /> <br /> <br /> ... 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e ...<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> Research Assistant<br /> Golby Lab<br /> Brigham and Women's Hospital<br /> Department of Neurosurgery<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/17289403?dopt=AbstractPlus Non-rigid alignment of preoperative MRI, fMRI and DT-MRI with intraoperative MRI to enhance visualization and navigation in image-guided neurosurgery.] Neuroimage, 2007 Apr 1;35(2):609-624. <br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''William M. Wells III, (aka Sandy Wells)'''<br /> <br /> Associate Professor <br /> Department of Radiology <br /> Harvard Medical School and <br /> Brigham and Women's Hospital<br /> <br /> <br /> My work has focused primarily on the analysis of structural and functional MRI. Areas of research include the segmentation and registration of MRI, with some emphasis on applications in image-guided surgery. The figure on the upper right illustrates the white matter surface of a brain that was segmented from MRI using Adaptive Segmentation of MRI (the &quot;EM Segmenter&quot;) .<br /> My research in medical image registration concerns the use of Mutual Information as a criterion for image fusion. This approach has become the de-facto standard for multi-modality problems. Implementations of this method are available in 3D Slicer, our open-source platform for medical image analysis, and in ITK, an NIH sponsored segmentation and registration library.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> A Bayesian Model for Joint Segmentation and Registration. Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage (to appear)<br /> <br /> [http://people.csail.mit.edu/welg/papers/integrated2001.pdf An Integrated Visualization System for Surgical Planning and Guidance Using Image Fusion and an Open MR.] Gering D, Nabavi A, Kikinis R, Hata N, O'Donnell L, Grimson E, Jolesz F, Black P, Wells WM. JMRI 2001; 13:967-975<br /> <br /> <br /> '''Benjamin Grauer'''<br /> <br /> <br /> Have a look at [http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week_VolumeRendering 2008 Winter Project Week VolumeRendering]<br /> <br /> <br /> '''Junichi Tokuda'''<br /> <br /> <br /> Junichi Tokuda is a Research Fellow of Brigham and Women's Hospital and Harvard Medical School. He received a B.S in Engineering in 2002, a M.S. in Information Science and Technology in 2004, and a Ph.D. in Information Science and Technology in 2007, from The University of Tokyo, Japan. His main research interest is MRI guided therapy including MR pulse sequence, navigation software, MRI-compatible robot and integration of these technologies for operating environment. He has been working on this area since 2001, and has broad experience in developing software and devices for these applications. For example, the software to assist MRI-guided microwave coagulation therapy of liver tumor, which he developed at Shiga University of Medical Science, Japan, has already been used in more than 100 clinical cases. He joined the Image Guided Therapy Program at Brigham and Women's Hospital since April 2007, and continues to work on MR-guided therapy.<br /> <br /> <br /> '''Haiying Liu'''<br /> <br /> <br /> Talk about: Slicer, OpenIGT Link, tutorial, tools, engineering</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23480 2008-04-01T12:06:04Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration: ==<br /> <br /> <br /> '''Deep Brain Stimulation'''<br /> (I'm meeting [http://frontweb.vuse.vanderbilt.edu/vuse_web/directory/facultybio.asp?FacultyID=20802 Benoit Dawant] 14-18 April at Vanderbilt University to talk about their DBS research)<br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> '''Surgical Planning / Intra-Operative Guidance for Brain Tumor Resection'''<br /> (Interested to see Slicer's capabilities. We have a [http://www.medtronicnavigation.com/procedures/intraoperative/polestar.jsp Medtronic Polestar N20], we would like to use pre-operative data: fMRI, DTI and register this with the Polestar data during the surgery.<br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> '''GPU Visualization, Depth Peeling (Nvidia's CUDA)'''<br /> <br /> '''Scanner Deformation Analysis &amp; Correction'''<br /> <br /> ''Student Exchange Possibilities''<br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> <br /> ----<br /> <br /> == Main Contact: ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Interesting Contacts: ==<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> Director, Laboratory of Mathematics in Imaging (LMI) <br /> Associate Professor of Radiology, Harvard Medical School<br /> <br /> <br /> ''Keep in Mind''<br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html A Mathematical Framework for Incorporating Anatomical Knowledge in DT-MRI analysis]<br /> Mahnaz Maddah, Lilla Zöllei, W. Eric L. Grimson, Carl-Fredrik Westin, William M. Wells<br /> Biomedical Imaging: From Nano to Macro, 2008. ISBI 2008. 5th IEEE International Symposium on Biomedical Imaging, Paris, France<br /> 2008<br /> <br /> <br /> ... 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e ...<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> Research Assistant<br /> Golby Lab<br /> Brigham and Women's Hospital<br /> Department of Neurosurgery<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/17289403?dopt=AbstractPlus Non-rigid alignment of preoperative MRI, fMRI and DT-MRI with intraoperative MRI to enhance visualization and navigation in image-guided neurosurgery.] Neuroimage, 2007 Apr 1;35(2):609-624. <br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''William M. Wells III, (aka Sandy Wells)'''<br /> <br /> Associate Professor <br /> Department of Radiology <br /> Harvard Medical School and <br /> Brigham and Women's Hospital<br /> <br /> <br /> My work has focused primarily on the analysis of structural and functional MRI. Areas of research include the segmentation and registration of MRI, with some emphasis on applications in image-guided surgery. The figure on the upper right illustrates the white matter surface of a brain that was segmented from MRI using Adaptive Segmentation of MRI (the &quot;EM Segmenter&quot;) .<br /> My research in medical image registration concerns the use of Mutual Information as a criterion for image fusion. This approach has become the de-facto standard for multi-modality problems. Implementations of this method are available in 3D Slicer, our open-source platform for medical image analysis, and in ITK, an NIH sponsored segmentation and registration library.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> A Bayesian Model for Joint Segmentation and Registration. Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage (to appear)<br /> <br /> [http://people.csail.mit.edu/welg/papers/integrated2001.pdf An Integrated Visualization System for Surgical Planning and Guidance Using Image Fusion and an Open MR.] Gering D, Nabavi A, Kikinis R, Hata N, O'Donnell L, Grimson E, Jolesz F, Black P, Wells WM. JMRI 2001; 13:967-975<br /> <br /> <br /> '''Benjamin Grauer'''<br /> <br /> <br /> Have a look at [http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week_VolumeRendering 2008 Winter Project Week VolumeRendering]<br /> <br /> <br /> '''Junichi Tokuda'''<br /> <br /> <br /> Junichi Tokuda is a Research Fellow of Brigham and Women's Hospital and Harvard Medical School. He received a B.S in Engineering in 2002, a M.S. in Information Science and Technology in 2004, and a Ph.D. in Information Science and Technology in 2007, from The University of Tokyo, Japan. His main research interest is MRI guided therapy including MR pulse sequence, navigation software, MRI-compatible robot and integration of these technologies for operating environment. He has been working on this area since 2001, and has broad experience in developing software and devices for these applications. For example, the software to assist MRI-guided microwave coagulation therapy of liver tumor, which he developed at Shiga University of Medical Science, Japan, has already been used in more than 100 clinical cases. He joined the Image Guided Therapy Program at Brigham and Women's Hospital since April 2007, and continues to work on MR-guided therapy.<br /> <br /> <br /> '''Haiying Liu'''<br /> <br /> <br /> Talk about: Slicer, OpenIGT Link, tutorial, tools, engineering</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23466 2008-03-31T22:13:25Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration: ==<br /> <br /> <br /> '''Deep Brain Stimulation'''<br /> (I'm meeting [http://frontweb.vuse.vanderbilt.edu/vuse_web/directory/facultybio.asp?FacultyID=20802 Benoit Dawant] 14-18 April at Vanderbilt University to talk about their DBS research)<br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> (I'm meeting Leslie Holton, StealthLink Coordinator of Medtronic on the 22nd of April)<br /> <br /> '''GPU Visualization, Depth Peeling (Nvidia's CUDA)'''<br /> <br /> '''Scanner Deformation Analysis &amp; Correction'''<br /> <br /> ''Student Exchange Possibilities''<br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> <br /> ----<br /> <br /> == Main Contact: ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Interesting Contacts: ==<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> Director, Laboratory of Mathematics in Imaging (LMI) <br /> Associate Professor of Radiology, Harvard Medical School<br /> <br /> <br /> ''Keep in Mind''<br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html A Mathematical Framework for Incorporating Anatomical Knowledge in DT-MRI analysis]<br /> Mahnaz Maddah, Lilla Zöllei, W. Eric L. Grimson, Carl-Fredrik Westin, William M. Wells<br /> Biomedical Imaging: From Nano to Macro, 2008. ISBI 2008. 5th IEEE International Symposium on Biomedical Imaging, Paris, France<br /> 2008<br /> <br /> <br /> ... 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e ...<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> Research Assistant<br /> Golby Lab<br /> Brigham and Women's Hospital<br /> Department of Neurosurgery<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/17289403?dopt=AbstractPlus Non-rigid alignment of preoperative MRI, fMRI and DT-MRI with intraoperative MRI to enhance visualization and navigation in image-guided neurosurgery.] Neuroimage, 2007 Apr 1;35(2):609-624. <br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''William M. Wells III, (aka Sandy Wells)'''<br /> <br /> Associate Professor <br /> Department of Radiology <br /> Harvard Medical School and <br /> Brigham and Women's Hospital<br /> <br /> <br /> My work has focused primarily on the analysis of structural and functional MRI. Areas of research include the segmentation and registration of MRI, with some emphasis on applications in image-guided surgery. The figure on the upper right illustrates the white matter surface of a brain that was segmented from MRI using Adaptive Segmentation of MRI (the &quot;EM Segmenter&quot;) .<br /> My research in medical image registration concerns the use of Mutual Information as a criterion for image fusion. This approach has become the de-facto standard for multi-modality problems. Implementations of this method are available in 3D Slicer, our open-source platform for medical image analysis, and in ITK, an NIH sponsored segmentation and registration library.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> A Bayesian Model for Joint Segmentation and Registration. Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage (to appear)<br /> <br /> [http://people.csail.mit.edu/welg/papers/integrated2001.pdf An Integrated Visualization System for Surgical Planning and Guidance Using Image Fusion and an Open MR.] Gering D, Nabavi A, Kikinis R, Hata N, O'Donnell L, Grimson E, Jolesz F, Black P, Wells WM. JMRI 2001; 13:967-975<br /> <br /> <br /> '''Benjamin Grauer'''<br /> <br /> <br /> Have a look at [http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week_VolumeRendering 2008 Winter Project Week VolumeRendering]<br /> <br /> <br /> '''Junichi Tokuda'''<br /> <br /> <br /> Junichi Tokuda is a Research Fellow of Brigham and Women's Hospital and Harvard Medical School. He received a B.S in Engineering in 2002, a M.S. in Information Science and Technology in 2004, and a Ph.D. in Information Science and Technology in 2007, from The University of Tokyo, Japan. His main research interest is MRI guided therapy including MR pulse sequence, navigation software, MRI-compatible robot and integration of these technologies for operating environment. He has been working on this area since 2001, and has broad experience in developing software and devices for these applications. For example, the software to assist MRI-guided microwave coagulation therapy of liver tumor, which he developed at Shiga University of Medical Science, Japan, has already been used in more than 100 clinical cases. He joined the Image Guided Therapy Program at Brigham and Women's Hospital since April 2007, and continues to work on MR-guided therapy.<br /> <br /> <br /> '''Haiying Liu'''<br /> <br /> <br /> Talk about: Slicer, OpenIGT Link, tutorial, tools, engineering</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23465 2008-03-31T22:03:20Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration: ==<br /> <br /> <br /> '''Deep Brain Stimulation'''<br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> '''Integration of Medtronic's StealthLink into Slicer (OpenIGT Link)'''<br /> <br /> '''GPU Visualization, Depth Peeling (Nvidia's CUDA)'''<br /> <br /> '''Scanner Deformation Analysis &amp; Correction'''<br /> <br /> ''Student Exchange Possibilities''<br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> <br /> ----<br /> <br /> == Main Contact: ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Interesting Contacts: ==<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> Director, Laboratory of Mathematics in Imaging (LMI) <br /> Associate Professor of Radiology, Harvard Medical School<br /> <br /> <br /> ''Keep in Mind''<br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html A Mathematical Framework for Incorporating Anatomical Knowledge in DT-MRI analysis]<br /> Mahnaz Maddah, Lilla Zöllei, W. Eric L. Grimson, Carl-Fredrik Westin, William M. Wells<br /> Biomedical Imaging: From Nano to Macro, 2008. ISBI 2008. 5th IEEE International Symposium on Biomedical Imaging, Paris, France<br /> 2008<br /> <br /> <br /> ... 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e ...<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> Research Assistant<br /> Golby Lab<br /> Brigham and Women's Hospital<br /> Department of Neurosurgery<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/17289403?dopt=AbstractPlus Non-rigid alignment of preoperative MRI, fMRI and DT-MRI with intraoperative MRI to enhance visualization and navigation in image-guided neurosurgery.] Neuroimage, 2007 Apr 1;35(2):609-624. <br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''William M. Wells III, (aka Sandy Wells)'''<br /> <br /> Associate Professor <br /> Department of Radiology <br /> Harvard Medical School and <br /> Brigham and Women's Hospital<br /> <br /> <br /> My work has focused primarily on the analysis of structural and functional MRI. Areas of research include the segmentation and registration of MRI, with some emphasis on applications in image-guided surgery. The figure on the upper right illustrates the white matter surface of a brain that was segmented from MRI using Adaptive Segmentation of MRI (the &quot;EM Segmenter&quot;) .<br /> My research in medical image registration concerns the use of Mutual Information as a criterion for image fusion. This approach has become the de-facto standard for multi-modality problems. Implementations of this method are available in 3D Slicer, our open-source platform for medical image analysis, and in ITK, an NIH sponsored segmentation and registration library.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> A Bayesian Model for Joint Segmentation and Registration. Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage (to appear)<br /> <br /> [http://people.csail.mit.edu/welg/papers/integrated2001.pdf An Integrated Visualization System for Surgical Planning and Guidance Using Image Fusion and an Open MR.] Gering D, Nabavi A, Kikinis R, Hata N, O'Donnell L, Grimson E, Jolesz F, Black P, Wells WM. JMRI 2001; 13:967-975<br /> <br /> <br /> '''Benjamin Grauer'''<br /> <br /> <br /> Have a look at [http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week_VolumeRendering 2008 Winter Project Week VolumeRendering]<br /> <br /> <br /> '''Junichi Tokuda'''<br /> <br /> <br /> Junichi Tokuda is a Research Fellow of Brigham and Women's Hospital and Harvard Medical School. He received a B.S in Engineering in 2002, a M.S. in Information Science and Technology in 2004, and a Ph.D. in Information Science and Technology in 2007, from The University of Tokyo, Japan. His main research interest is MRI guided therapy including MR pulse sequence, navigation software, MRI-compatible robot and integration of these technologies for operating environment. He has been working on this area since 2001, and has broad experience in developing software and devices for these applications. For example, the software to assist MRI-guided microwave coagulation therapy of liver tumor, which he developed at Shiga University of Medical Science, Japan, has already been used in more than 100 clinical cases. He joined the Image Guided Therapy Program at Brigham and Women's Hospital since April 2007, and continues to work on MR-guided therapy.<br /> <br /> <br /> '''Haiying Liu'''<br /> <br /> <br /> Talk about: Slicer, OpenIGT Link, tutorial, tools, engineering</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23464 2008-03-31T22:02:36Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration: ==<br /> <br /> <br /> '''Deep Brain Stimulation'''<br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> '''Integration of Medtronic's StealthLink into Slicer'''<br /> <br /> '''GPU Visualization, Depth Peeling'''<br /> <br /> '''Scanner Deformation Analysis &amp; Correction'''<br /> <br /> ''Student Exchange Possibilities''<br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> <br /> ----<br /> <br /> == Main Contact: ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Interesting Contacts: ==<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> <br /> Director, Laboratory of Mathematics in Imaging (LMI) <br /> Associate Professor of Radiology, Harvard Medical School<br /> <br /> <br /> ''Keep in Mind''<br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html A Mathematical Framework for Incorporating Anatomical Knowledge in DT-MRI analysis]<br /> Mahnaz Maddah, Lilla Zöllei, W. Eric L. Grimson, Carl-Fredrik Westin, William M. Wells<br /> Biomedical Imaging: From Nano to Macro, 2008. ISBI 2008. 5th IEEE International Symposium on Biomedical Imaging, Paris, France<br /> 2008<br /> <br /> <br /> ... 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e ...<br /> <br /> <br /> '''Stephen Whalen'''<br /> <br /> Research Assistant<br /> Golby Lab<br /> Brigham and Women's Hospital<br /> Department of Neurosurgery<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/17289403?dopt=AbstractPlus Non-rigid alignment of preoperative MRI, fMRI and DT-MRI with intraoperative MRI to enhance visualization and navigation in image-guided neurosurgery.] Neuroimage, 2007 Apr 1;35(2):609-624. <br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''William M. Wells III, (aka Sandy Wells)'''<br /> <br /> Associate Professor <br /> Department of Radiology <br /> Harvard Medical School and <br /> Brigham and Women's Hospital<br /> <br /> <br /> My work has focused primarily on the analysis of structural and functional MRI. Areas of research include the segmentation and registration of MRI, with some emphasis on applications in image-guided surgery. The figure on the upper right illustrates the white matter surface of a brain that was segmented from MRI using Adaptive Segmentation of MRI (the &quot;EM Segmenter&quot;) .<br /> My research in medical image registration concerns the use of Mutual Information as a criterion for image fusion. This approach has become the de-facto standard for multi-modality problems. Implementations of this method are available in 3D Slicer, our open-source platform for medical image analysis, and in ITK, an NIH sponsored segmentation and registration library.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> A Bayesian Model for Joint Segmentation and Registration. Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage (to appear)<br /> <br /> [http://people.csail.mit.edu/welg/papers/integrated2001.pdf An Integrated Visualization System for Surgical Planning and Guidance Using Image Fusion and an Open MR.] Gering D, Nabavi A, Kikinis R, Hata N, O'Donnell L, Grimson E, Jolesz F, Black P, Wells WM. JMRI 2001; 13:967-975<br /> <br /> <br /> '''Benjamin Grauer'''<br /> <br /> <br /> Have a look at [http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week_VolumeRendering 2008 Winter Project Week VolumeRendering]<br /> <br /> <br /> '''Junichi Tokuda'''<br /> <br /> <br /> Junichi Tokuda is a Research Fellow of Brigham and Women's Hospital and Harvard Medical School. He received a B.S in Engineering in 2002, a M.S. in Information Science and Technology in 2004, and a Ph.D. in Information Science and Technology in 2007, from The University of Tokyo, Japan. His main research interest is MRI guided therapy including MR pulse sequence, navigation software, MRI-compatible robot and integration of these technologies for operating environment. He has been working on this area since 2001, and has broad experience in developing software and devices for these applications. For example, the software to assist MRI-guided microwave coagulation therapy of liver tumor, which he developed at Shiga University of Medical Science, Japan, has already been used in more than 100 clinical cases. He joined the Image Guided Therapy Program at Brigham and Women's Hospital since April 2007, and continues to work on MR-guided therapy.<br /> <br /> <br /> '''Haiying Liu'''<br /> <br /> <br /> Talk about: Slicer, OpenIGT Link, tutorial, tools, engineering</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23463 2008-03-31T22:02:02Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration: ==<br /> <br /> <br /> '''Deep Brain Stimulation'''<br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> '''Integration of Medtronic's StealthLink into Slicer'''<br /> <br /> '''GPU Visualization, Depth Peeling'''<br /> <br /> '''Scanner Deformation Analysis &amp; Correction'''<br /> <br /> ''Student Exchange Possibilities''<br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> <br /> ----<br /> <br /> == Main Contact: ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Interesting Contacts: ==<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> Director, Laboratory of Mathematics in Imaging (LMI) <br /> Associate Professor of Radiology, Harvard Medical School<br /> <br /> <br /> ''Keep in Mind''<br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html A Mathematical Framework for Incorporating Anatomical Knowledge in DT-MRI analysis]<br /> Mahnaz Maddah, Lilla Zöllei, W. Eric L. Grimson, Carl-Fredrik Westin, William M. Wells<br /> Biomedical Imaging: From Nano to Macro, 2008. ISBI 2008. 5th IEEE International Symposium on Biomedical Imaging, Paris, France<br /> 2008<br /> <br /> <br /> ... 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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e ...<br /> <br /> <br /> '''Stephen Whalen'''<br /> Research Assistant<br /> Golby Lab<br /> Brigham and Women's Hospital<br /> Department of Neurosurgery<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/17289403?dopt=AbstractPlus Non-rigid alignment of preoperative MRI, fMRI and DT-MRI with intraoperative MRI to enhance visualization and navigation in image-guided neurosurgery.] Neuroimage, 2007 Apr 1;35(2):609-624. <br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''William M. Wells III, (aka Sandy Wells)'''<br /> Associate Professor <br /> Department of Radiology <br /> Harvard Medical School and <br /> Brigham and Women's Hospital<br /> <br /> <br /> My work has focused primarily on the analysis of structural and functional MRI. Areas of research include the segmentation and registration of MRI, with some emphasis on applications in image-guided surgery. The figure on the upper right illustrates the white matter surface of a brain that was segmented from MRI using Adaptive Segmentation of MRI (the &quot;EM Segmenter&quot;) .<br /> My research in medical image registration concerns the use of Mutual Information as a criterion for image fusion. This approach has become the de-facto standard for multi-modality problems. Implementations of this method are available in 3D Slicer, our open-source platform for medical image analysis, and in ITK, an NIH sponsored segmentation and registration library.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> A Bayesian Model for Joint Segmentation and Registration. Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage (to appear)<br /> <br /> [http://people.csail.mit.edu/welg/papers/integrated2001.pdf An Integrated Visualization System for Surgical Planning and Guidance Using Image Fusion and an Open MR.] Gering D, Nabavi A, Kikinis R, Hata N, O'Donnell L, Grimson E, Jolesz F, Black P, Wells WM. JMRI 2001; 13:967-975<br /> <br /> <br /> '''Benjamin Grauer'''<br /> <br /> <br /> Have a look at [http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week_VolumeRendering 2008 Winter Project Week VolumeRendering]<br /> <br /> <br /> '''Junichi Tokuda'''<br /> <br /> <br /> Junichi Tokuda is a Research Fellow of Brigham and Women's Hospital and Harvard Medical School. He received a B.S in Engineering in 2002, a M.S. in Information Science and Technology in 2004, and a Ph.D. in Information Science and Technology in 2007, from The University of Tokyo, Japan. His main research interest is MRI guided therapy including MR pulse sequence, navigation software, MRI-compatible robot and integration of these technologies for operating environment. He has been working on this area since 2001, and has broad experience in developing software and devices for these applications. For example, the software to assist MRI-guided microwave coagulation therapy of liver tumor, which he developed at Shiga University of Medical Science, Japan, has already been used in more than 100 clinical cases. He joined the Image Guided Therapy Program at Brigham and Women's Hospital since April 2007, and continues to work on MR-guided therapy.<br /> <br /> <br /> '''Haiying Liu'''<br /> <br /> <br /> Talk about: Slicer, OpenIGT Link, tutorial, tools, engineering</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23462 2008-03-31T22:01:26Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration: ==<br /> <br /> <br /> '''Deep Brain Stimulation'''<br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> '''Integration of Medtronic's StealthLink into Slicer'''<br /> <br /> '''GPU Visualization, Depth Peeling'''<br /> <br /> '''Scanner Deformation Analysis &amp; Correction'''<br /> <br /> ''Student Exchange Possibilities''<br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> <br /> ----<br /> <br /> == Main Contact: ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Interesting Contacts: ==<br /> <br /> <br /> '''Carl-Fredrik Westin'''<br /> Director, Laboratory of Mathematics in Imaging (LMI) <br /> Associate Professor of Radiology, Harvard Medical School<br /> <br /> <br /> ''Keep in Mind''<br /> MICCAI 2008 Tutorial: [http://lmi.bwh.harvard.edu/DMRI08 Diffusion MRI: Technology trends and unsolved problems]<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://lmi.bwh.harvard.edu/papers/papers/mahnazISBI08.html A Mathematical Framework for Incorporating Anatomical Knowledge in DT-MRI analysis]<br /> Mahnaz Maddah, Lilla Zöllei, W. Eric L. Grimson, Carl-Fredrik Westin, William M. Wells<br /> Biomedical Imaging: From Nano to Macro, 2008. ISBI 2008. 5th IEEE International Symposium on Biomedical Imaging, Paris, France<br /> 2008<br /> <br /> ... The [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&amp;taal=US&amp;voor_org_id=&amp;rn=20011434 Luc Florack] and [https://venus.tue.nl/ep-cgi/ep_detail.opl?taal=NL&amp;rn=19961226 Remco Duits] at the &quot;Scale and Orientation&quot; group of the TU/e ...<br /> <br /> '''Stephen Whalen'''<br /> Research Assistant<br /> Golby Lab<br /> Brigham and Women's Hospital<br /> Department of Neurosurgery<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/17289403?dopt=AbstractPlus Non-rigid alignment of preoperative MRI, fMRI and DT-MRI with intraoperative MRI to enhance visualization and navigation in image-guided neurosurgery.] Neuroimage, 2007 Apr 1;35(2):609-624. <br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''William M. Wells III, (aka Sandy Wells)'''<br /> Associate Professor <br /> Department of Radiology <br /> Harvard Medical School and <br /> Brigham and Women's Hospital<br /> <br /> <br /> My work has focused primarily on the analysis of structural and functional MRI. Areas of research include the segmentation and registration of MRI, with some emphasis on applications in image-guided surgery. The figure on the upper right illustrates the white matter surface of a brain that was segmented from MRI using Adaptive Segmentation of MRI (the &quot;EM Segmenter&quot;) .<br /> My research in medical image registration concerns the use of Mutual Information as a criterion for image fusion. This approach has become the de-facto standard for multi-modality problems. Implementations of this method are available in 3D Slicer, our open-source platform for medical image analysis, and in ITK, an NIH sponsored segmentation and registration library.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> A Bayesian Model for Joint Segmentation and Registration. Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage (to appear)<br /> <br /> [http://people.csail.mit.edu/welg/papers/integrated2001.pdf An Integrated Visualization System for Surgical Planning and Guidance Using Image Fusion and an Open MR.] Gering D, Nabavi A, Kikinis R, Hata N, O'Donnell L, Grimson E, Jolesz F, Black P, Wells WM. JMRI 2001; 13:967-975<br /> <br /> <br /> '''Benjamin Grauer'''<br /> <br /> <br /> Have a look at [http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week_VolumeRendering 2008 Winter Project Week VolumeRendering]<br /> <br /> <br /> '''Junichi Tokuda'''<br /> <br /> <br /> Junichi Tokuda is a Research Fellow of Brigham and Women's Hospital and Harvard Medical School. He received a B.S in Engineering in 2002, a M.S. in Information Science and Technology in 2004, and a Ph.D. in Information Science and Technology in 2007, from The University of Tokyo, Japan. His main research interest is MRI guided therapy including MR pulse sequence, navigation software, MRI-compatible robot and integration of these technologies for operating environment. He has been working on this area since 2001, and has broad experience in developing software and devices for these applications. For example, the software to assist MRI-guided microwave coagulation therapy of liver tumor, which he developed at Shiga University of Medical Science, Japan, has already been used in more than 100 clinical cases. He joined the Image Guided Therapy Program at Brigham and Women's Hospital since April 2007, and continues to work on MR-guided therapy.<br /> <br /> <br /> '''Haiying Liu'''<br /> <br /> <br /> Talk about: Slicer, OpenIGT Link, tutorial, tools, engineering</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23461 2008-03-31T21:49:41Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> == Information on Bram Platel &amp; TU/e ==<br /> <br /> <br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> [http://w3.bmt.tue.nl/en/peoplebme/?no_cache=1&amp;script=showemp.php&amp;dbname=mate&amp;pid=2146&amp;all=1 Bio and Publication List of Bram Platel]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/image_guided_surgery/ Image Guided Surgery Group]<br /> <br /> [https://w3.bmt.tue.nl/en/research/divisions_bme/biomedical_imaging_modeling/biomedical_image_analysis/research/multivalued_image_analysis_visualization/ Multivalued Image Analysis &amp; Visualization]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration: ==<br /> <br /> <br /> '''Deep Brain Stimulation'''<br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> '''Integration of Medtronic's StealthLink into Slicer'''<br /> <br /> '''GPU Visualization, Depth Peeling'''<br /> <br /> '''Scanner Deformation Analysis &amp; Correction'''<br /> <br /> ''Student Exchange Possibilities''<br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> <br /> ----<br /> <br /> == Main Contact: ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Interesting Contacts: ==<br /> <br /> <br /> '''Stephen Whalen'''<br /> Research Assistant<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/17289403?dopt=AbstractPlus Non-rigid alignment of preoperative MRI, fMRI and DT-MRI with intraoperative MRI to enhance visualization and navigation in image-guided neurosurgery.] Neuroimage, 2007 Apr 1;35(2):609-624. <br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''William M. Wells III, (aka Sandy Wells)'''<br /> Associate Professor<br /> <br /> <br /> My work has focused primarily on the analysis of structural and functional MRI. Areas of research include the segmentation and registration of MRI, with some emphasis on applications in image-guided surgery. The figure on the upper right illustrates the white matter surface of a brain that was segmented from MRI using Adaptive Segmentation of MRI (the &quot;EM Segmenter&quot;) .<br /> My research in medical image registration concerns the use of Mutual Information as a criterion for image fusion. This approach has become the de-facto standard for multi-modality problems. Implementations of this method are available in 3D Slicer, our open-source platform for medical image analysis, and in ITK, an NIH sponsored segmentation and registration library.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> A Bayesian Model for Joint Segmentation and Registration. Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage (to appear)<br /> <br /> [http://people.csail.mit.edu/welg/papers/integrated2001.pdf An Integrated Visualization System for Surgical Planning and Guidance Using Image Fusion and an Open MR.] Gering D, Nabavi A, Kikinis R, Hata N, O'Donnell L, Grimson E, Jolesz F, Black P, Wells WM. JMRI 2001; 13:967-975<br /> <br /> <br /> '''Benjamin Grauer'''<br /> <br /> <br /> Have a look at [http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week_VolumeRendering 2008 Winter Project Week VolumeRendering]<br /> <br /> <br /> '''Junichi Tokuda'''<br /> <br /> <br /> Junichi Tokuda is a Research Fellow of Brigham and Women's Hospital and Harvard Medical School. He received a B.S in Engineering in 2002, a M.S. in Information Science and Technology in 2004, and a Ph.D. in Information Science and Technology in 2007, from The University of Tokyo, Japan. His main research interest is MRI guided therapy including MR pulse sequence, navigation software, MRI-compatible robot and integration of these technologies for operating environment. He has been working on this area since 2001, and has broad experience in developing software and devices for these applications. For example, the software to assist MRI-guided microwave coagulation therapy of liver tumor, which he developed at Shiga University of Medical Science, Japan, has already been used in more than 100 clinical cases. He joined the Image Guided Therapy Program at Brigham and Women's Hospital since April 2007, and continues to work on MR-guided therapy.<br /> <br /> <br /> '''Haiying Liu'''<br /> <br /> <br /> Talk about: Slicer, OpenIGT Link, tutorial, tools, engineering</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23460 2008-03-31T21:45:51Z

<p>Platel: </p> <hr /> <div><br /> ----<br /> [http://bmia.bmt.tue.nl About Image Analysis at the Eindhoven University of Technology]<br /> <br /> ----<br /> <br /> == Possible Topics of Collaboration: ==<br /> <br /> <br /> '''Deep Brain Stimulation'''<br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> '''Integration of Medtronic's StealthLink into Slicer'''<br /> <br /> '''GPU Visualization, Depth Peeling'''<br /> <br /> '''Scanner Deformation Analysis &amp; Correction'''<br /> <br /> ''Student Exchange Possibilities''<br /> <br /> ''Noby Hata is willing to come and give a colloquium/lecture''<br /> <br /> <br /> ----<br /> <br /> == Main Contact: ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Interesting Contacts: ==<br /> <br /> <br /> '''Stephen Whalen'''<br /> Research Assistant<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/17289403?dopt=AbstractPlus Non-rigid alignment of preoperative MRI, fMRI and DT-MRI with intraoperative MRI to enhance visualization and navigation in image-guided neurosurgery.] Neuroimage, 2007 Apr 1;35(2):609-624. <br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''William M. Wells III, (aka Sandy Wells)'''<br /> Associate Professor<br /> <br /> <br /> My work has focused primarily on the analysis of structural and functional MRI. Areas of research include the segmentation and registration of MRI, with some emphasis on applications in image-guided surgery. The figure on the upper right illustrates the white matter surface of a brain that was segmented from MRI using Adaptive Segmentation of MRI (the &quot;EM Segmenter&quot;) .<br /> My research in medical image registration concerns the use of Mutual Information as a criterion for image fusion. This approach has become the de-facto standard for multi-modality problems. Implementations of this method are available in 3D Slicer, our open-source platform for medical image analysis, and in ITK, an NIH sponsored segmentation and registration library.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> A Bayesian Model for Joint Segmentation and Registration. Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage (to appear)<br /> <br /> [http://people.csail.mit.edu/welg/papers/integrated2001.pdf An Integrated Visualization System for Surgical Planning and Guidance Using Image Fusion and an Open MR.] Gering D, Nabavi A, Kikinis R, Hata N, O'Donnell L, Grimson E, Jolesz F, Black P, Wells WM. JMRI 2001; 13:967-975<br /> <br /> <br /> '''Benjamin Grauer'''<br /> <br /> <br /> Have a look at [http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week_VolumeRendering 2008 Winter Project Week VolumeRendering]<br /> <br /> <br /> '''Junichi Tokuda'''<br /> <br /> <br /> Junichi Tokuda is a Research Fellow of Brigham and Women's Hospital and Harvard Medical School. He received a B.S in Engineering in 2002, a M.S. in Information Science and Technology in 2004, and a Ph.D. in Information Science and Technology in 2007, from The University of Tokyo, Japan. His main research interest is MRI guided therapy including MR pulse sequence, navigation software, MRI-compatible robot and integration of these technologies for operating environment. He has been working on this area since 2001, and has broad experience in developing software and devices for these applications. For example, the software to assist MRI-guided microwave coagulation therapy of liver tumor, which he developed at Shiga University of Medical Science, Japan, has already been used in more than 100 clinical cases. He joined the Image Guided Therapy Program at Brigham and Women's Hospital since April 2007, and continues to work on MR-guided therapy.<br /> <br /> <br /> '''Haiying Liu'''<br /> <br /> <br /> Talk about: Slicer, OpenIGT Link, tutorial, tools, engineering</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23459 2008-03-31T21:42:24Z

<p>Platel: </p> <hr /> <div><br /> ----<br /> Possible Topics of Collaboration:<br /> <br /> '''Deep Brain Stimulation'''<br /> <br /> '''Diffusion Tensor Imaging'''<br /> <br /> '''Integration of Medtronic's StealthLink into Slicer'''<br /> <br /> '''GPU Visualization, Depth Peeling'''<br /> <br /> '''Scanner Deformation Analysis &amp; Correction'''<br /> <br /> <br /> ----<br /> <br /> == Main Contact: ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Interesting Contacts: ==<br /> <br /> <br /> '''Stephen Whalen'''<br /> Research Assistant<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/17289403?dopt=AbstractPlus Non-rigid alignment of preoperative MRI, fMRI and DT-MRI with intraoperative MRI to enhance visualization and navigation in image-guided neurosurgery.] Neuroimage, 2007 Apr 1;35(2):609-624. <br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''William M. Wells III, (aka Sandy Wells)'''<br /> Associate Professor<br /> <br /> <br /> My work has focused primarily on the analysis of structural and functional MRI. Areas of research include the segmentation and registration of MRI, with some emphasis on applications in image-guided surgery. The figure on the upper right illustrates the white matter surface of a brain that was segmented from MRI using Adaptive Segmentation of MRI (the &quot;EM Segmenter&quot;) .<br /> My research in medical image registration concerns the use of Mutual Information as a criterion for image fusion. This approach has become the de-facto standard for multi-modality problems. Implementations of this method are available in 3D Slicer, our open-source platform for medical image analysis, and in ITK, an NIH sponsored segmentation and registration library.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> A Bayesian Model for Joint Segmentation and Registration. Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage (to appear)<br /> <br /> [http://people.csail.mit.edu/welg/papers/integrated2001.pdf An Integrated Visualization System for Surgical Planning and Guidance Using Image Fusion and an Open MR.] Gering D, Nabavi A, Kikinis R, Hata N, O'Donnell L, Grimson E, Jolesz F, Black P, Wells WM. JMRI 2001; 13:967-975<br /> <br /> <br /> '''Benjamin Grauer'''<br /> <br /> <br /> Have a look at [http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week_VolumeRendering 2008 Winter Project Week VolumeRendering]<br /> <br /> <br /> '''Junichi Tokuda'''<br /> <br /> <br /> Junichi Tokuda is a Research Fellow of Brigham and Women's Hospital and Harvard Medical School. He received a B.S in Engineering in 2002, a M.S. in Information Science and Technology in 2004, and a Ph.D. in Information Science and Technology in 2007, from The University of Tokyo, Japan. His main research interest is MRI guided therapy including MR pulse sequence, navigation software, MRI-compatible robot and integration of these technologies for operating environment. He has been working on this area since 2001, and has broad experience in developing software and devices for these applications. For example, the software to assist MRI-guided microwave coagulation therapy of liver tumor, which he developed at Shiga University of Medical Science, Japan, has already been used in more than 100 clinical cases. He joined the Image Guided Therapy Program at Brigham and Women's Hospital since April 2007, and continues to work on MR-guided therapy.<br /> <br /> <br /> '''Haiying Liu'''<br /> <br /> <br /> Talk about: Slicer, OpenIGT Link, tutorial, tools, engineering</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23458 2008-03-31T21:38:41Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> == Main Contact: ==<br /> <br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Interesting Contacts: ==<br /> <br /> <br /> '''Stephen Whalen'''<br /> Research Assistant<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/17289403?dopt=AbstractPlus Non-rigid alignment of preoperative MRI, fMRI and DT-MRI with intraoperative MRI to enhance visualization and navigation in image-guided neurosurgery.] Neuroimage, 2007 Apr 1;35(2):609-624. <br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''William M. Wells III, (aka Sandy Wells)'''<br /> Associate Professor<br /> <br /> <br /> My work has focused primarily on the analysis of structural and functional MRI. Areas of research include the segmentation and registration of MRI, with some emphasis on applications in image-guided surgery. The figure on the upper right illustrates the white matter surface of a brain that was segmented from MRI using Adaptive Segmentation of MRI (the &quot;EM Segmenter&quot;) .<br /> My research in medical image registration concerns the use of Mutual Information as a criterion for image fusion. This approach has become the de-facto standard for multi-modality problems. Implementations of this method are available in 3D Slicer, our open-source platform for medical image analysis, and in ITK, an NIH sponsored segmentation and registration library.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> A Bayesian Model for Joint Segmentation and Registration. Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage (to appear)<br /> <br /> [http://people.csail.mit.edu/welg/papers/integrated2001.pdf An Integrated Visualization System for Surgical Planning and Guidance Using Image Fusion and an Open MR.] Gering D, Nabavi A, Kikinis R, Hata N, O'Donnell L, Grimson E, Jolesz F, Black P, Wells WM. JMRI 2001; 13:967-975<br /> <br /> <br /> '''Benjamin Grauer'''<br /> <br /> <br /> Have a look at [http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week_VolumeRendering 2008 Winter Project Week VolumeRendering]<br /> <br /> <br /> '''Junichi Tokuda'''<br /> <br /> <br /> Junichi Tokuda is a Research Fellow of Brigham and Women's Hospital and Harvard Medical School. He received a B.S in Engineering in 2002, a M.S. in Information Science and Technology in 2004, and a Ph.D. in Information Science and Technology in 2007, from The University of Tokyo, Japan. His main research interest is MRI guided therapy including MR pulse sequence, navigation software, MRI-compatible robot and integration of these technologies for operating environment. He has been working on this area since 2001, and has broad experience in developing software and devices for these applications. For example, the software to assist MRI-guided microwave coagulation therapy of liver tumor, which he developed at Shiga University of Medical Science, Japan, has already been used in more than 100 clinical cases. He joined the Image Guided Therapy Program at Brigham and Women's Hospital since April 2007, and continues to work on MR-guided therapy.<br /> <br /> <br /> '''Haiying Liu'''<br /> <br /> <br /> Talk about: Slicer, OpenIGT Link, tutorial, tools, engineering</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23457 2008-03-31T21:38:27Z

<p>Platel: </p> <hr /> <div><br /> ----<br /> Main Contact:<br /> <br /> '''Nobuhiko (Noby) Hata'''<br /> <br /> ----<br /> <br /> <br /> == Interesting Contacts: ==<br /> <br /> <br /> '''Stephen Whalen'''<br /> Research Assistant<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/17289403?dopt=AbstractPlus Non-rigid alignment of preoperative MRI, fMRI and DT-MRI with intraoperative MRI to enhance visualization and navigation in image-guided neurosurgery.] Neuroimage, 2007 Apr 1;35(2):609-624. <br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''William M. Wells III, (aka Sandy Wells)'''<br /> Associate Professor<br /> <br /> <br /> My work has focused primarily on the analysis of structural and functional MRI. Areas of research include the segmentation and registration of MRI, with some emphasis on applications in image-guided surgery. The figure on the upper right illustrates the white matter surface of a brain that was segmented from MRI using Adaptive Segmentation of MRI (the &quot;EM Segmenter&quot;) .<br /> My research in medical image registration concerns the use of Mutual Information as a criterion for image fusion. This approach has become the de-facto standard for multi-modality problems. Implementations of this method are available in 3D Slicer, our open-source platform for medical image analysis, and in ITK, an NIH sponsored segmentation and registration library.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> A Bayesian Model for Joint Segmentation and Registration. Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage (to appear)<br /> <br /> [http://people.csail.mit.edu/welg/papers/integrated2001.pdf An Integrated Visualization System for Surgical Planning and Guidance Using Image Fusion and an Open MR.] Gering D, Nabavi A, Kikinis R, Hata N, O'Donnell L, Grimson E, Jolesz F, Black P, Wells WM. JMRI 2001; 13:967-975<br /> <br /> <br /> '''Benjamin Grauer'''<br /> <br /> <br /> Have a look at [http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week_VolumeRendering 2008 Winter Project Week VolumeRendering]<br /> <br /> <br /> '''Junichi Tokuda'''<br /> <br /> <br /> Junichi Tokuda is a Research Fellow of Brigham and Women's Hospital and Harvard Medical School. He received a B.S in Engineering in 2002, a M.S. in Information Science and Technology in 2004, and a Ph.D. in Information Science and Technology in 2007, from The University of Tokyo, Japan. His main research interest is MRI guided therapy including MR pulse sequence, navigation software, MRI-compatible robot and integration of these technologies for operating environment. He has been working on this area since 2001, and has broad experience in developing software and devices for these applications. For example, the software to assist MRI-guided microwave coagulation therapy of liver tumor, which he developed at Shiga University of Medical Science, Japan, has already been used in more than 100 clinical cases. He joined the Image Guided Therapy Program at Brigham and Women's Hospital since April 2007, and continues to work on MR-guided therapy.<br /> <br /> <br /> '''Haiying Liu'''<br /> <br /> <br /> Talk about: Slicer, OpenIGT Link, tutorial, tools, engineering</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23456 2008-03-31T21:34:39Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> <br /> == Interesting Contacts: ==<br /> <br /> <br /> '''Stephen Whalen'''<br /> Research Assistant<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/17289403?dopt=AbstractPlus Non-rigid alignment of preoperative MRI, fMRI and DT-MRI with intraoperative MRI to enhance visualization and navigation in image-guided neurosurgery.] Neuroimage, 2007 Apr 1;35(2):609-624. <br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''William M. Wells III, (aka Sandy Wells)'''<br /> Associate Professor<br /> <br /> <br /> My work has focused primarily on the analysis of structural and functional MRI. Areas of research include the segmentation and registration of MRI, with some emphasis on applications in image-guided surgery. The figure on the upper right illustrates the white matter surface of a brain that was segmented from MRI using Adaptive Segmentation of MRI (the &quot;EM Segmenter&quot;) .<br /> My research in medical image registration concerns the use of Mutual Information as a criterion for image fusion. This approach has become the de-facto standard for multi-modality problems. Implementations of this method are available in 3D Slicer, our open-source platform for medical image analysis, and in ITK, an NIH sponsored segmentation and registration library.<br /> <br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> A Bayesian Model for Joint Segmentation and Registration. Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage (to appear)<br /> <br /> [http://people.csail.mit.edu/welg/papers/integrated2001.pdf An Integrated Visualization System for Surgical Planning and Guidance Using Image Fusion and an Open MR.] Gering D, Nabavi A, Kikinis R, Hata N, O'Donnell L, Grimson E, Jolesz F, Black P, Wells WM. JMRI 2001; 13:967-975<br /> <br /> <br /> '''Benjamin Grauer'''<br /> <br /> <br /> Have a look at [http://www.na-mic.org/Wiki/index.php/2008_Winter_Project_Week_VolumeRendering 2008 Winter Project Week VolumeRendering]<br /> <br /> <br /> '''Junichi Tokuda'''<br /> <br /> <br /> Junichi Tokuda is a Research Fellow of Brigham and Women's Hospital and Harvard Medical School. He received a B.S in Engineering in 2002, a M.S. in Information Science and Technology in 2004, and a Ph.D. in Information Science and Technology in 2007, from The University of Tokyo, Japan. His main research interest is MRI guided therapy including MR pulse sequence, navigation software, MRI-compatible robot and integration of these technologies for operating environment. He has been working on this area since 2001, and has broad experience in developing software and devices for these applications. For example, the software to assist MRI-guided microwave coagulation therapy of liver tumor, which he developed at Shiga University of Medical Science, Japan, has already been used in more than 100 clinical cases. He joined the Image Guided Therapy Program at Brigham and Women's Hospital since April 2007, and continues to work on MR-guided therapy.<br /> <br /> <br /> '''Haiying Liu'''<br /> <br /> <br /> Talk about: Slicer, OpenIGT Link, tutorial, tools, engineering</div>

Platel https://www.na-mic.org/w/index.php?title=User_talk:Platel&diff=23455 2008-03-31T21:13:39Z

<p>Platel: </p> <hr /> <div>----<br /> <br /> <br /> == Interesting Contacts: ==<br /> <br /> <br /> '''Stephen Whalen'''<br /> Research Assistant<br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18095898?ordinalpos=1&amp;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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/18044565?ordinalpos=2&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Tract-based morphometry.] Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):161-8<br /> <br /> [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&amp;Cmd=ShowDetailView&amp;TermToSearch=17289403&amp;ordinalpos=3&amp;itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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.<br /> <br /> [http://www.ncbi.nlm.nih.gov/pubmed/17289403?dopt=AbstractPlus Non-rigid alignment of preoperative MRI, fMRI and DT-MRI with intraoperative MRI to enhance visualization and navigation in image-guided neurosurgery.] Neuroimage, 2007 Apr 1;35(2):609-624. <br /> <br /> [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=16279079&amp;query_hl=1&amp;itool=pubmed_docsum Robust nonrigid registration to capture brain shift from intraoperative MRI.] IEEE Trans Med Imaging. 2005 Nov;24(11):1417-27.<br /> <br /> <br /> '''William M. Wells III, (aka Sandy Wells)'''<br /> Associate Professor<br /> <br /> ''Interesting Publications:''<br /> <br /> <br /> A Bayesian Model for Joint Segmentation and Registration. Pohl K, Fisher J, Grimson WEL, Kikinis R, Wells W. Neuroimage (to appear)<br /> <br /> [http://people.csail.mit.edu/welg/papers/integrated2001.pdf An Integrated Visualization System for Surgical Planning and Guidance Using Image Fusion and an Open MR.] Gering D, Nabavi A, Kikinis R, Hata N, O'Donnell L, Grimson E, Jolesz F, Black P, Wells WM. JMRI 2001; 13:967-975</div>

Platel