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Publications

2007-01-16T00:55:11Z

Delphine: /* Peer Reviewed Conference Proceedings */

The following publications gratefully acknowledge the support of NA-MIC. Please see [[Publications:NIH_Roadmap_acknowledgement|'''NA-MIC acknowledgement instructions''']] for instructions on how to acknowledge NA-MIC in your publications.

* '''Search Medline'''

# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=EB005149 Search Medline for NAMIC-enabled publications]

List of publications from other NCBCs:

# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=RR021813 Search Medline for CCB-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=lm008748 Search Medline for I2B2-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=gm072970 Search Medline for SIMBIOS-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=DA021519 Search Medline for NCIBI-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=CA121852 Search Medline for C2B2-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=HG004028 Search Medline for Bioontology-enabled publications]

 

* ** Note: Many technical journals are not listed in Medline. Medline therefore only holds a subset of NA-MIC related refereed publications.

== Peer Reviewed Journal Papers ==

# Nakamura M, McCarley RW, Kubicki M, Dickey CC, Niznikiewicz MA, Voglmaier MM, Seidman LJ, Maier SE, Westin CF, Kikinis R, Shenton ME. Fronto-temporal disconnectivity in schizotypal personality disorder: a diffusion tensor imaging study. Biol Psychiatry. 2005 Sep 15;58(6):468-78. [[Media:Nakamura_2005BiolPsych.pdf| PDF]]
# Tuch DS, Salat DH, Wisco JJ, Zaleta AK, Hevelone ND, Rosas HD. Choice reaction time performance correlates with diffusion anisotropy in white matter pathways supporting visuospatial attention. Proc Natl Acad Sci U S A. 2005 Aug 23;102(34):12212-7. [[Media:Tuch_PNAS_2005.pdf| PDF]]
# Tuch DS, Wisco JJ, Khachaturian MH, Ekstrom LB, Kotter R, Vanduffel W. Q-ball imaging of macaque white matter architecture. Philos Trans R Soc Lond B Biol Sci. 2005 May 29;360(1457):869-79. [[Media:Tuch_PhilosTransRBiolSoc_2005.pdf| PDF]]
# Niethammer M, Vela P, Tannenbaum A. On the evolution of closed curves by means of vector distance functions. Int. Journal Computer Vision, 2006. [[Media:Niethammer_etal_VISI849-04I.pdf| PDF]]
# Niethammer M, Tannenbaum A, Angenent S. Dynamic active contours. IEEE Trans. Automatic Control. 2006; 51:562-579. [[Media:Niethammer_paper1.pdf| PDF]]
# Turner JA, Smyth P, Macciardi F, Fallon JH, Kennedy JL, Potkin SG. Imaging phenotypes and genotypes in schizophrenia. Neuroinformatics. 2006;4(1):21-49. [[Media:Media-Turner_paper.pdf| PDF]]

'''''In Press'''''
# Nain D, Haker S, Bobick A, Tannenbaum A. "Multiscale 3D Shape Representation and Segmentation using Spherical Wavelets", in press, IEEE Transactions on Medical Imaging Special issue on Computational Anatomy.
# Liu T, Young G, Huang L, Chen N-K, Wong S. “76-space Analysis of Grey Matter Diffusivity: Methods and Applications,” in press, NeuroImage.
# O’Donnell L, Kubicki M, Shenton ME, Dreusicke MH, Grimson WEL, Westin CF. A method for clustering white matter fiber tracts. AJNR (In Press).
# Koo MS, Levitt JJ, McCarley RW, Seidman LJ, Dickey CC, Niznikiewicz MA, Voglmaier MM, Zamani P, Long KL, Kim SS, Shenton ME. Reduction of caudate volume in neuroleptic-naive female subjects with schizotypal personality disorder. Biol Psychiatry (In Press).
# Kuroki N, Kubicki M, Nestor PG, Salisbury DF, Park HJ, Levitt JJ, Woolston S, Frumin M, Niznikiewicz M, Westin CF, Maier SE, McCarley RW, Shenton ME. Fornix integrity and hippocampal volume in male schizophrenic patients. Biol Psychiatry (In Press).
# Onitsuka T, Niznikiewicz MA, Spencer KM, Frumin M, Kuroki N, Lucia LC, Shenton ME, McCarley RW. Schizophrenia is associated with functional and structural deficits in brain regions subserving face processing. Am J Psychiatry (In Press).
# Niethammer M, Tannenbaum A, Kalies W, Mischaikow K. Detecting simple points in higher dimensions. IEEE Image Processing, 2006. (In Press).
# Rathi Y, Dambreville S, Tannenbaum A. Comparative analysis of kernel methods for statistical shape learning. CVAMIA'06, 2006. (In Press).
# Roth RM, Koven, NS, Randolph JJ, Flashman LA, Pixley HS, Ricketts SM, Wishart HA, Saykin AJ. Event-Related fMRI study of Functional magnetic resonance imaging of executive control in bipolar disorder. NeuroReport, 2006 (In Press).
# Pohl KM, Fisher J, Grimson WEL, Kikinis R, Wells WM. [[Media:Pohl-ni-2006.pdf| A bayesian model for joint segmentation and registration.]] NeuroImage, 2006 (In Press).
# Fletcher PT, Joshi S. Riemannian Geometry for the Statistical Analysis of Diffusion Tensor Data. Signal Processing, 2006. (In Press).

== Peer Reviewed Conference Proceedings ==

'''Conferences included here represent the major high quality conferences in medical image analysis (MICCAI, IPMI, MMBIA, ISBI). These conferences only accept submission of full papers and guarantee a peer review process by at least three reviewers and an area chair. Acceptance rates are below 40% for MICCAI, IPMI and MMBIA and around 50% for ISBI.'''

# D. Nain, M. Styner, M. Niethammer, J. J. Levitt, M E Shenton, G Gerig, A. Bobick, A. Tannenbaum. Statistical Shape Analysis of Brain Structures using Spherical Wavelets. Accepted in The Fourth IEEE International Symposium on Biomedical Imaging (ISBI ’07), April 12-15, 2007, Washington DC, USA.
# Kim S, Smyth P. Hierarchical Dirichlet processes with random effects. Advances in Neural Information Processing Systems 19, to appear, 2006. [[Media:Nips_hMDP_RE.pdf| PDF ]]
# Kim S, Smyth P, Stern H. A nonparametric Bayesian approach to detecting spatial activation patterns in fMRI data. To appear in MICCAI, Oct 2-5, 2006.[[Media:InfMM_miccai.pdf| PDF ]]
# Nain D, Haker S, Bobick A, Tannenbaum A. Shape-driven surface segmentation using spherical wavelets. MICCAI, LNCS 4190, Oct 2-5, 2006.
# Styner M, Jomier M, Gerig G: Closed and Open Source Neuroimage Analysis Tools and Libraries at UNC. IEEE Symposium on Biomedical Imaging ISBI. 2006; 702-705. [[Media:ISBI06_Neurolib.pdf| PDF ]]
# Gerig G, Joshi S, Fletcher T, Gorczowski K, Xu S, Pizer SM, Styner M. Statistics of populations of images and its embedded objects: Driving applications in neuroimaging. IEEE Symposium on Biomedical Imaging ISBI. 2006; 1120-1123.[[Media:ISBI06-GerigShape.pdf| PDF]]
# Pieper S, Lorensen W, Schroeder W, Kikinis R. [[Media:Pieper-ISBI-2006-revised.pdf| The NA-MIC Kit: ITK, VTK, Pipelines, Grids and 3D Slicer as An Open Platform for the Medical Image Computing Community.]] IEEE Symposium on Biomedical Imaging ISBI. 2006; 698-701.
# Pichon E, Westin CF, and Tannenbaum A. A Hamilton-Jacobi-Bellman approach to high angular diffusion tractography. Proceedings of MICCAI, 2005. [[Media:Pichon-miccai05.pdf| PDF]]
# Yang Y, Zhu L, Haker S, Tannenbaum A. On the harmonic skeleton and vessel data. Proceeedings of MICCAI, 2005. [[Media:YangMICCAI2005.pdf| PDF]]
# Styner M, Gimpel Smith R, Cascio C, Oguz I, Jomier M. Corpus Callosum Subdivision based on a Probabilistic Model of Inter-hemispheric Connectivity. Medical Image Computing and Computer Assisted Interventions MICCAI. 2005 LNCS 3750;765-772. [[Media:MICCAI05CCSubdiv.pdf| PDF]]
# Liu T, Young G, Huang L, Chen N-K, Wong S. “76-space Analysis of Grey Matter Diffusivity: Methods and Applications,” MICCAI 2005.[[Media:MICCAI-2005--461-Liu.pdf| PDF]]
# Pichon E, Tannenbaum A. Curve segmentation using directional information, relation to pattern detection. Proc IEEE International Conference on Image Processing (ICIP), 2005
# Nain D, Haker S, Bobick A, Tannenbaum A. [[Media:Nain.miccai2005.pdf| Multiscale 3D Shape Analysis using Spherical Wavelets]]. Proc MICCAI, LNCS 3750, Oct 26-29 2005; p 459-467.
# Corouge I, Fletcher PT, Joshi S, Gilmore JH, Gerig G. [[Media:Corouge-miccai-2005.pdf| Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis.]] Proc. MICCAI, Oct 26-29 2005; LNCS 3749, pp. 131-139
# Ou W, Golland P. From Spatial Regularization to Anatomical Priors in fMRI Analysis. Proc IPMI, Jul 10-15 2005; LNCS 3565: p 88-100. [[Media:OuGolland_IPMI2005.pdf| PDF]]
# Pohl KM, Fisher J, Levitt JJ, Shenton ME, Kikinis R, Grimson WEL, Wells WM. [[Media:Pohl-miccai-2005.pdf| A Unifying Approach to Registration, Segmentation, and Intensity Correction,]] In Proc. MICCAI 2005: Eigth International Conference on Medical Image Computing and Computer Assisted Intervention, Palm Springs, CA, USA, Springer-Verlag, Part I, vol. 3749 of Lecture Notes in Computer Science, pp. 310-318, 2005
# Pohl KM, Bouix S, Shenton ME, Grimson WEL, Kikinis R. [[Media:Pohl-miccai-short-2005.pdf| Automatic Segmentation Using Non-Rigid Registration,]] In short communications of MICCAI 2005: Eighth International Conference on Medical Image Computing and Computer Assisted Intervention, Palm Springs, CA, USA, 2005
# Martin-Fernandez M, Bouix S, Ungar L, McCarley RW, Shenton ME. Two Methods for Validating Brain Tissue Classifiers. MICCAI 2005, Palm Springs, CA, USA: Duncan J and Gerig G (Eds.): Lecture Notes in Computer Science, volume 3749, pp 515-522, 2005. Springer-Verlag Berlin Heidelberg, 2005. [[Media:Martin-fernandezMICCAI05.pdf| PDF]]
# Kim S, Smyth P, Stern H, Turner J. Parametric response surface models for analysis of multi-site fMRI data. In Proc. MICCAI 2005: Eighth International Conference on Medical Image Computing and Computer Assisted Intervention, Palm Springs, CA, USA, Springer-Verlag, Part I, vol. 3749 of Lecture Notes in Computer Science, pp. 352-359, 2005. [[Media:Seyoung-official.pdf|PDF]]
# O'Donnell L, Westin C-F. White Matter Tract Clustering and Correspondence in Populations. MICCAI 2005, Palm Springs, CA, USA: Duncan J, Gerig G (Eds.): Lecture Notes in Computer Science, volume 3749, pp 140-147, 2005. Springer-Verlag Berlin Heidelberg, 2005. [[Media:OdonnellMICCAI05.pdf| PDF]]
# M. Maddah, A. Mewes, S. Haker, W. E. L. Grimson, and S. Warfield, [http://mit.edu/~mmaddah/www/Mahnaz_Miccai2005.pdf , Automated Atlas-Based Clustering of White Matter Fiber Tracts from DTMRI]. MICCAI05, Palm Spring, CA,: Lecture Notes in Computer Science, volume 3749, pp. 188-195, 2005.
# M. Maddah, W. E. L. Grimson, and S. Warfield, [http://mit.edu/~mmaddah/www/maddahISBI.pdf , Statistical Modeling and EM Clustering of White Matter Fiber Tracts], ISBI 2006: IEEE 2006 International Symposium on Biomedical Imaging, Arlington, VA, April 6-9, 2006

== Book Chapters ==

# Nain D, Tannenbaum A, Unal G, Yezzi A, Zeitouni O. On a stochastic model of geometric snakes. Mathematical Methods in Computer Vision: A Handbook, edited by Faugeras O, Paragios N, Springer-Verlag, 2005.
# Angenent S, Tannenbaum A, Yezzi A, Zeitouni O. Curve shortening and interacting particle systems. Book chapter in a volume edited by Hamid Krim, 2005.

== Others ==

=== Insight Journal ===

# Goodlett C, Corouge I, Jomier M, Gerig G. [http://hdl.handle.net/1926/39 A Quantitative DTI Fiber Tract Analysis Suite]. Insight Journal, 2005.
# Miller JV. [http://hdl.handle.net/1926/159 "Probability distributions for the Insight Toolkit."] Insight Journal, 2006.
# Gao Y, Melonakos J, Tannenbaum A. [http://hdl.handle.net/1926/225 "Conformal Flattening ITK Filter"] Insight Journal, 2006.
# Melonakos J, Krishnan K, Tannenbaum A. [[Media:Melonakos-ISC2006-bayesian.pdf| An ITK filter for Bayesian segmentation: itkBayesianClassifierImageFilter]]. Insight Journal, Jan 2006. http://hdl.handle.net/1926/160.
# Melonakos J, Al-Hakim R, Fallon J, Tannenbaum A. [[Media:Melonakos-ISC2005-bayesian.pdf| Knowledge-based segmentation of brain MRI scans using the Insight Toolkit]]. Insight Journal, Oct 2005. http://hdl.handle.net/1926/44.

=== Conferences and Workshops ===

# Rathi Y, Olver P, Sapiro G, Tannenbaum A. Affine Invariant Surface Evolutions for 3D Image Segmentation, SPIE 2006
# Rathi Y, Dambreville S, Tannenbaum A. Comparative Analyis of Kernel Methods for Statistical Shape Learning, 2nd Workshop on Computer Vision Approaches to Medical Image Analysis (in conjunction with ECCV) 2006.
# Eric Pichon, Delphine Nain, and Marc Niethammer. [[Media:Pichon-SPIEMI2006-laplace.pdf| A Laplace Equation Approach for Shape Comparison]]. Proc SPIE Medical Imaging, 2006.
# Al-Hakim R, Fallon J, Nain D, Melonakos J, Tannenbaum A. [[Media:Dlpfc-SPIE2006-full.pdf| A Dorsolateral Prefrontal Cortex Semi-Automatic Segmenter]]. Proc SPIE Medical Imaging, 2006.
# Pohl KM, Fisher J, Kikinis R, Grimson WEL, Wells WM. [[Media:Pohl-iccv-ws-2005.pdf| Shape Based Segmentation of Anatomical Structures in Magnetic Resonance Images,]] In Proc. ICCV 2005: Computer Vision for Biomedical Image Applications: Current Techniques and Future Trend, An International Conference on Computer Vision Workshop, Beijing, China, Springer-Verlag, vol. 3765 of Lecture Notes in Computer Science, 2005
# Zöllei L, Learned-Miller E, Grimson WEL, Wells WM III. Efficient Population Registration of 3D Data. Proc ICCV 2005, Computer Vision for Biomedical Image Applications; Beijing, China
# Angenent S, Pichon E, Tannenbaum A. Mathematical methods in medical imaging. Bulletin of American Mathematical Association, 2006.
# O'Donnell L, Westin C-F. A High-Dimensional Fiber Tract Atlas. accepted to ISMRM 2006.
# Zöllei L, Wells WM III. Multi-modal Image Registration Using Dirichlet-encoded Prior Information. oral presentation at WBIR06
# Fletcher PT, Whitaker RT. Riemannian Metrics on the Space of Solid Shapes. accepted to MICCAI'06 Workshop on Mathematical Foundations of Computational Anatomy (MFCA).
# Cates J, Meyer M, Fletcher PT, Whitaker R. Entropy-Based Particle Systems for Shape Correspondence. accepted to MICCAI'06 Workshop on Mathematical Foundations of Computational Anatomy (MFCA).

=== Submitted and in Preparation ===

# Flashman LA, Roth RM, Pixley HS, Cleavinger HB, Saykin AJ, McAllister TW, Vidaver RM. (submitted). Cavum septum pellucidum in schizophrenia: Clinical and neuropsychological correlates.
# Szymczak A, Tannenbaum A, Stillman A, Mischaikow K. Vessel cores from 3D imagery: a topological approach. submitted to IEEE Trans. Medical Imaging, 2006.
# Michailovich O, Tanenbaum A. Fast approximation of smooth functions from samples of partial derivatives. Submitted for publication to IEEE Signal Processing, 2006.
# Zhu L, Yang Y, Haker S, and Tannenbaum A. An image morphing technique based on optimal mass preserving mapping. Submitted to IEEE Trans. Image Processing, 2006.
# Rathi Y, Vaswani N, Tannenbaum A, Yezzi Y. Tracking Deforming Objects using Particle Filtering for Geometric Active Contours. Submitted to IEEE PAMI, 2005.
# Rathi Y, Tannenbaum A. Kernel PCA for shape based segmentation of medical images. submitted to MICCAI, 2006.
# Gorczowski K, Gerig G, Fletcher T, Pizer SM, Styner M. Statistics of Pose and Shape in Multi-Object Complexes using Principal Geodesic Analysis. submitted to MICCAI, 2006.
# Goodlett C, Davis B, Jean R, Gilmore J, Gerig G. Improved Correspondence for DTI Population Studies via Unbiased Atlas Building. submitted to MICCAI, 2006.
# Corouge I, Fletcher PT, Sarang J, Gouttard S, Gerig G. Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis. submitted MedIA Journal, Jan. 2006
# Gribbin M, Clement M, Muller K, Poe M, Cascio C, Jomier M, Piven J, Gerig G. Statistical analysis of diffusion tensor image data based on first principles, submitted MICCAI'06, March 2006
# Flashman LA, Roth RM, Koven NS, McAllister TW, Vidaver RM, Pendergrass JC. Neural Correlates of Self-Evaluation in Individuals with Schizophrenia. in preparation.
# Basu S, Fletcher PT, Whitaker RT. Rician Noise Removal in Diffusion Tensor MRI, to appear MICCAI'06.
# Han X, Fischl B. Intensity Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms, submitted to IEEE Transactions on Medical Imaging.
# Yu P, Grant P, Qi Y, Han X, Ségonne F, Pienaar R, Busa E, Pacheco J, Makris N, Buckner R, Golland P, Fischl B. Cortical Surface Shape Analysis Based on Spherical Wavelets, submitted to IEEE Transactions on Medical Imaging
# Ségonne F, Pacheco J, Fischl B. Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops, submitted to IEEE Transactions on Medical Imaging
# Voineskos AN, Zai G, Bulgin N, Shaikh S, Lang D, Honer WG, Kennedy JL. MAG but not CNP Gene Associated with Total Brain White Matter. In Preparation. Presented in Part at World Congress of Psychiatric Genetics Annual Meeting. October, 2006.
# Voineskos AN, Bulgin N, Van Adrichem Q, Wong ACH, Lang D, Honer WG, Kennedy JL. MAG but not CNP Gene Associated with Schizophrenia. In Preparation.

Publications

2007-01-16T00:44:49Z

Delphine: /* Peer Reviewed Journal Papers */

The following publications gratefully acknowledge the support of NA-MIC. Please see [[Publications:NIH_Roadmap_acknowledgement|'''NA-MIC acknowledgement instructions''']] for instructions on how to acknowledge NA-MIC in your publications.

* '''Search Medline'''

# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=EB005149 Search Medline for NAMIC-enabled publications]

List of publications from other NCBCs:

# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=RR021813 Search Medline for CCB-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=lm008748 Search Medline for I2B2-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=gm072970 Search Medline for SIMBIOS-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=DA021519 Search Medline for NCIBI-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=CA121852 Search Medline for C2B2-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=HG004028 Search Medline for Bioontology-enabled publications]

 

* ** Note: Many technical journals are not listed in Medline. Medline therefore only holds a subset of NA-MIC related refereed publications.

== Peer Reviewed Journal Papers ==

# Nakamura M, McCarley RW, Kubicki M, Dickey CC, Niznikiewicz MA, Voglmaier MM, Seidman LJ, Maier SE, Westin CF, Kikinis R, Shenton ME. Fronto-temporal disconnectivity in schizotypal personality disorder: a diffusion tensor imaging study. Biol Psychiatry. 2005 Sep 15;58(6):468-78. [[Media:Nakamura_2005BiolPsych.pdf| PDF]]
# Tuch DS, Salat DH, Wisco JJ, Zaleta AK, Hevelone ND, Rosas HD. Choice reaction time performance correlates with diffusion anisotropy in white matter pathways supporting visuospatial attention. Proc Natl Acad Sci U S A. 2005 Aug 23;102(34):12212-7. [[Media:Tuch_PNAS_2005.pdf| PDF]]
# Tuch DS, Wisco JJ, Khachaturian MH, Ekstrom LB, Kotter R, Vanduffel W. Q-ball imaging of macaque white matter architecture. Philos Trans R Soc Lond B Biol Sci. 2005 May 29;360(1457):869-79. [[Media:Tuch_PhilosTransRBiolSoc_2005.pdf| PDF]]
# Niethammer M, Vela P, Tannenbaum A. On the evolution of closed curves by means of vector distance functions. Int. Journal Computer Vision, 2006. [[Media:Niethammer_etal_VISI849-04I.pdf| PDF]]
# Niethammer M, Tannenbaum A, Angenent S. Dynamic active contours. IEEE Trans. Automatic Control. 2006; 51:562-579. [[Media:Niethammer_paper1.pdf| PDF]]
# Turner JA, Smyth P, Macciardi F, Fallon JH, Kennedy JL, Potkin SG. Imaging phenotypes and genotypes in schizophrenia. Neuroinformatics. 2006;4(1):21-49. [[Media:Media-Turner_paper.pdf| PDF]]

'''''In Press'''''
# Nain D, Haker S, Bobick A, Tannenbaum A. "Multiscale 3D Shape Representation and Segmentation using Spherical Wavelets", in press, IEEE Transactions on Medical Imaging Special issue on Computational Anatomy.
# Liu T, Young G, Huang L, Chen N-K, Wong S. “76-space Analysis of Grey Matter Diffusivity: Methods and Applications,” in press, NeuroImage.
# O’Donnell L, Kubicki M, Shenton ME, Dreusicke MH, Grimson WEL, Westin CF. A method for clustering white matter fiber tracts. AJNR (In Press).
# Koo MS, Levitt JJ, McCarley RW, Seidman LJ, Dickey CC, Niznikiewicz MA, Voglmaier MM, Zamani P, Long KL, Kim SS, Shenton ME. Reduction of caudate volume in neuroleptic-naive female subjects with schizotypal personality disorder. Biol Psychiatry (In Press).
# Kuroki N, Kubicki M, Nestor PG, Salisbury DF, Park HJ, Levitt JJ, Woolston S, Frumin M, Niznikiewicz M, Westin CF, Maier SE, McCarley RW, Shenton ME. Fornix integrity and hippocampal volume in male schizophrenic patients. Biol Psychiatry (In Press).
# Onitsuka T, Niznikiewicz MA, Spencer KM, Frumin M, Kuroki N, Lucia LC, Shenton ME, McCarley RW. Schizophrenia is associated with functional and structural deficits in brain regions subserving face processing. Am J Psychiatry (In Press).
# Niethammer M, Tannenbaum A, Kalies W, Mischaikow K. Detecting simple points in higher dimensions. IEEE Image Processing, 2006. (In Press).
# Rathi Y, Dambreville S, Tannenbaum A. Comparative analysis of kernel methods for statistical shape learning. CVAMIA'06, 2006. (In Press).
# Roth RM, Koven, NS, Randolph JJ, Flashman LA, Pixley HS, Ricketts SM, Wishart HA, Saykin AJ. Event-Related fMRI study of Functional magnetic resonance imaging of executive control in bipolar disorder. NeuroReport, 2006 (In Press).
# Pohl KM, Fisher J, Grimson WEL, Kikinis R, Wells WM. [[Media:Pohl-ni-2006.pdf| A bayesian model for joint segmentation and registration.]] NeuroImage, 2006 (In Press).
# Fletcher PT, Joshi S. Riemannian Geometry for the Statistical Analysis of Diffusion Tensor Data. Signal Processing, 2006. (In Press).

== Peer Reviewed Conference Proceedings ==

'''Conferences included here represent the major high quality conferences in medical image analysis (MICCAI, IPMI, MMBIA, ISBI). These conferences only accept submission of full papers and guarantee a peer review process by at least three reviewers and an area chair. Acceptance rates are below 40% for MICCAI, IPMI and MMBIA and around 50% for ISBI.'''

# D. Nain, M. Styner, M. Niethammer, J. J. Levitt, M E Shenton, G Gerig, A. Bobick, A. Tannenbaum. Statistical Shape Analysis of Brain Structures using Spherical Wavelets. Accepted in The Fourth IEEE International Symposium on Biomedical Imaging (ISBI ’07), April 12-15, 2007, Washington DC, USA.
# Kim S, Smyth P. Hierarchical Dirichlet processes with random effects. Advances in Neural Information Processing Systems 19, to appear, 2006. [[Media:Nips_hMDP_RE.pdf| PDF ]]
# Kim S, Smyth P, Stern H. A nonparametric Bayesian approach to detecting spatial activation patterns in fMRI data. To appear in MICCAI, Oct 2-5, 2006.[[Media:InfMM_miccai.pdf| PDF ]]
# Nain D, Haker S, Bobick A, Tannenbaum A. Shape-driven surface segmentation using spherical wavelets. To appear in MICCAI, Oct 2-5, 2006.
# Styner M, Jomier M, Gerig G: Closed and Open Source Neuroimage Analysis Tools and Libraries at UNC. IEEE Symposium on Biomedical Imaging ISBI. 2006; 702-705. [[Media:ISBI06_Neurolib.pdf| PDF ]]
# Gerig G, Joshi S, Fletcher T, Gorczowski K, Xu S, Pizer SM, Styner M. Statistics of populations of images and its embedded objects: Driving applications in neuroimaging. IEEE Symposium on Biomedical Imaging ISBI. 2006; 1120-1123.[[Media:ISBI06-GerigShape.pdf| PDF]]
# Pieper S, Lorensen W, Schroeder W, Kikinis R. [[Media:Pieper-ISBI-2006-revised.pdf| The NA-MIC Kit: ITK, VTK, Pipelines, Grids and 3D Slicer as An Open Platform for the Medical Image Computing Community.]] IEEE Symposium on Biomedical Imaging ISBI. 2006; 698-701.
# Pichon E, Westin CF, and Tannenbaum A. A Hamilton-Jacobi-Bellman approach to high angular diffusion tractography. Proceedings of MICCAI, 2005. [[Media:Pichon-miccai05.pdf| PDF]]
# Yang Y, Zhu L, Haker S, Tannenbaum A. On the harmonic skeleton and vessel data. Proceeedings of MICCAI, 2005. [[Media:YangMICCAI2005.pdf| PDF]]
# Styner M, Gimpel Smith R, Cascio C, Oguz I, Jomier M. Corpus Callosum Subdivision based on a Probabilistic Model of Inter-hemispheric Connectivity. Medical Image Computing and Computer Assisted Interventions MICCAI. 2005 LNCS 3750;765-772. [[Media:MICCAI05CCSubdiv.pdf| PDF]]
# Liu T, Young G, Huang L, Chen N-K, Wong S. “76-space Analysis of Grey Matter Diffusivity: Methods and Applications,” MICCAI 2005.[[Media:MICCAI-2005--461-Liu.pdf| PDF]]
# Pichon E, Tannenbaum A. Curve segmentation using directional information, relation to pattern detection. Proc IEEE International Conference on Image Processing (ICIP), 2005
# Nain D, Haker S, Bobick A, Tannenbaum A. [[Media:Nain.miccai2005.pdf| Multiscale 3D Shape Analysis using Spherical Wavelets]]. Proc MICCAI, Oct 26-29 2005; p 459-467.
# Corouge I, Fletcher PT, Joshi S, Gilmore JH, Gerig G. [[Media:Corouge-miccai-2005.pdf| Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis.]] Proc. MICCAI, Oct 26-29 2005; LNCS 3749, pp. 131-139
# Ou W, Golland P. From Spatial Regularization to Anatomical Priors in fMRI Analysis. Proc IPMI, Jul 10-15 2005; LNCS 3565: p 88-100. [[Media:OuGolland_IPMI2005.pdf| PDF]]
# Pohl KM, Fisher J, Levitt JJ, Shenton ME, Kikinis R, Grimson WEL, Wells WM. [[Media:Pohl-miccai-2005.pdf| A Unifying Approach to Registration, Segmentation, and Intensity Correction,]] In Proc. MICCAI 2005: Eigth International Conference on Medical Image Computing and Computer Assisted Intervention, Palm Springs, CA, USA, Springer-Verlag, Part I, vol. 3749 of Lecture Notes in Computer Science, pp. 310-318, 2005
# Pohl KM, Bouix S, Shenton ME, Grimson WEL, Kikinis R. [[Media:Pohl-miccai-short-2005.pdf| Automatic Segmentation Using Non-Rigid Registration,]] In short communications of MICCAI 2005: Eighth International Conference on Medical Image Computing and Computer Assisted Intervention, Palm Springs, CA, USA, 2005
# Martin-Fernandez M, Bouix S, Ungar L, McCarley RW, Shenton ME. Two Methods for Validating Brain Tissue Classifiers. MICCAI 2005, Palm Springs, CA, USA: Duncan J and Gerig G (Eds.): Lecture Notes in Computer Science, volume 3749, pp 515-522, 2005. Springer-Verlag Berlin Heidelberg, 2005. [[Media:Martin-fernandezMICCAI05.pdf| PDF]]
# Kim S, Smyth P, Stern H, Turner J. Parametric response surface models for analysis of multi-site fMRI data. In Proc. MICCAI 2005: Eighth International Conference on Medical Image Computing and Computer Assisted Intervention, Palm Springs, CA, USA, Springer-Verlag, Part I, vol. 3749 of Lecture Notes in Computer Science, pp. 352-359, 2005. [[Media:Seyoung-official.pdf|PDF]]
# O'Donnell L, Westin C-F. White Matter Tract Clustering and Correspondence in Populations. MICCAI 2005, Palm Springs, CA, USA: Duncan J, Gerig G (Eds.): Lecture Notes in Computer Science, volume 3749, pp 140-147, 2005. Springer-Verlag Berlin Heidelberg, 2005. [[Media:OdonnellMICCAI05.pdf| PDF]]
# M. Maddah, A. Mewes, S. Haker, W. E. L. Grimson, and S. Warfield, [http://mit.edu/~mmaddah/www/Mahnaz_Miccai2005.pdf , Automated Atlas-Based Clustering of White Matter Fiber Tracts from DTMRI]. MICCAI05, Palm Spring, CA,: Lecture Notes in Computer Science, volume 3749, pp. 188-195, 2005.
# M. Maddah, W. E. L. Grimson, and S. Warfield, [http://mit.edu/~mmaddah/www/maddahISBI.pdf , Statistical Modeling and EM Clustering of White Matter Fiber Tracts], ISBI 2006: IEEE 2006 International Symposium on Biomedical Imaging, Arlington, VA, April 6-9, 2006

== Book Chapters ==

# Nain D, Tannenbaum A, Unal G, Yezzi A, Zeitouni O. On a stochastic model of geometric snakes. Mathematical Methods in Computer Vision: A Handbook, edited by Faugeras O, Paragios N, Springer-Verlag, 2005.
# Angenent S, Tannenbaum A, Yezzi A, Zeitouni O. Curve shortening and interacting particle systems. Book chapter in a volume edited by Hamid Krim, 2005.

== Others ==

=== Insight Journal ===

# Goodlett C, Corouge I, Jomier M, Gerig G. [http://hdl.handle.net/1926/39 A Quantitative DTI Fiber Tract Analysis Suite]. Insight Journal, 2005.
# Miller JV. [http://hdl.handle.net/1926/159 "Probability distributions for the Insight Toolkit."] Insight Journal, 2006.
# Gao Y, Melonakos J, Tannenbaum A. [http://hdl.handle.net/1926/225 "Conformal Flattening ITK Filter"] Insight Journal, 2006.
# Melonakos J, Krishnan K, Tannenbaum A. [[Media:Melonakos-ISC2006-bayesian.pdf| An ITK filter for Bayesian segmentation: itkBayesianClassifierImageFilter]]. Insight Journal, Jan 2006. http://hdl.handle.net/1926/160.
# Melonakos J, Al-Hakim R, Fallon J, Tannenbaum A. [[Media:Melonakos-ISC2005-bayesian.pdf| Knowledge-based segmentation of brain MRI scans using the Insight Toolkit]]. Insight Journal, Oct 2005. http://hdl.handle.net/1926/44.

=== Conferences and Workshops ===

# Rathi Y, Olver P, Sapiro G, Tannenbaum A. Affine Invariant Surface Evolutions for 3D Image Segmentation, SPIE 2006
# Rathi Y, Dambreville S, Tannenbaum A. Comparative Analyis of Kernel Methods for Statistical Shape Learning, 2nd Workshop on Computer Vision Approaches to Medical Image Analysis (in conjunction with ECCV) 2006.
# Eric Pichon, Delphine Nain, and Marc Niethammer. [[Media:Pichon-SPIEMI2006-laplace.pdf| A Laplace Equation Approach for Shape Comparison]]. Proc SPIE Medical Imaging, 2006.
# Al-Hakim R, Fallon J, Nain D, Melonakos J, Tannenbaum A. [[Media:Dlpfc-SPIE2006-full.pdf| A Dorsolateral Prefrontal Cortex Semi-Automatic Segmenter]]. Proc SPIE Medical Imaging, 2006.
# Pohl KM, Fisher J, Kikinis R, Grimson WEL, Wells WM. [[Media:Pohl-iccv-ws-2005.pdf| Shape Based Segmentation of Anatomical Structures in Magnetic Resonance Images,]] In Proc. ICCV 2005: Computer Vision for Biomedical Image Applications: Current Techniques and Future Trend, An International Conference on Computer Vision Workshop, Beijing, China, Springer-Verlag, vol. 3765 of Lecture Notes in Computer Science, 2005
# Zöllei L, Learned-Miller E, Grimson WEL, Wells WM III. Efficient Population Registration of 3D Data. Proc ICCV 2005, Computer Vision for Biomedical Image Applications; Beijing, China
# Angenent S, Pichon E, Tannenbaum A. Mathematical methods in medical imaging. Bulletin of American Mathematical Association, 2006.
# O'Donnell L, Westin C-F. A High-Dimensional Fiber Tract Atlas. accepted to ISMRM 2006.
# Zöllei L, Wells WM III. Multi-modal Image Registration Using Dirichlet-encoded Prior Information. oral presentation at WBIR06
# Fletcher PT, Whitaker RT. Riemannian Metrics on the Space of Solid Shapes. accepted to MICCAI'06 Workshop on Mathematical Foundations of Computational Anatomy (MFCA).
# Cates J, Meyer M, Fletcher PT, Whitaker R. Entropy-Based Particle Systems for Shape Correspondence. accepted to MICCAI'06 Workshop on Mathematical Foundations of Computational Anatomy (MFCA).

=== Submitted and in Preparation ===

# Flashman LA, Roth RM, Pixley HS, Cleavinger HB, Saykin AJ, McAllister TW, Vidaver RM. (submitted). Cavum septum pellucidum in schizophrenia: Clinical and neuropsychological correlates.
# Szymczak A, Tannenbaum A, Stillman A, Mischaikow K. Vessel cores from 3D imagery: a topological approach. submitted to IEEE Trans. Medical Imaging, 2006.
# Michailovich O, Tanenbaum A. Fast approximation of smooth functions from samples of partial derivatives. Submitted for publication to IEEE Signal Processing, 2006.
# Zhu L, Yang Y, Haker S, and Tannenbaum A. An image morphing technique based on optimal mass preserving mapping. Submitted to IEEE Trans. Image Processing, 2006.
# Rathi Y, Vaswani N, Tannenbaum A, Yezzi Y. Tracking Deforming Objects using Particle Filtering for Geometric Active Contours. Submitted to IEEE PAMI, 2005.
# Rathi Y, Tannenbaum A. Kernel PCA for shape based segmentation of medical images. submitted to MICCAI, 2006.
# Gorczowski K, Gerig G, Fletcher T, Pizer SM, Styner M. Statistics of Pose and Shape in Multi-Object Complexes using Principal Geodesic Analysis. submitted to MICCAI, 2006.
# Goodlett C, Davis B, Jean R, Gilmore J, Gerig G. Improved Correspondence for DTI Population Studies via Unbiased Atlas Building. submitted to MICCAI, 2006.
# Corouge I, Fletcher PT, Sarang J, Gouttard S, Gerig G. Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis. submitted MedIA Journal, Jan. 2006
# Gribbin M, Clement M, Muller K, Poe M, Cascio C, Jomier M, Piven J, Gerig G. Statistical analysis of diffusion tensor image data based on first principles, submitted MICCAI'06, March 2006
# Flashman LA, Roth RM, Koven NS, McAllister TW, Vidaver RM, Pendergrass JC. Neural Correlates of Self-Evaluation in Individuals with Schizophrenia. in preparation.
# Basu S, Fletcher PT, Whitaker RT. Rician Noise Removal in Diffusion Tensor MRI, to appear MICCAI'06.
# Han X, Fischl B. Intensity Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms, submitted to IEEE Transactions on Medical Imaging.
# Yu P, Grant P, Qi Y, Han X, Ségonne F, Pienaar R, Busa E, Pacheco J, Makris N, Buckner R, Golland P, Fischl B. Cortical Surface Shape Analysis Based on Spherical Wavelets, submitted to IEEE Transactions on Medical Imaging
# Ségonne F, Pacheco J, Fischl B. Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops, submitted to IEEE Transactions on Medical Imaging
# Voineskos AN, Zai G, Bulgin N, Shaikh S, Lang D, Honer WG, Kennedy JL. MAG but not CNP Gene Associated with Total Brain White Matter. In Preparation. Presented in Part at World Congress of Psychiatric Genetics Annual Meeting. October, 2006.
# Voineskos AN, Bulgin N, Van Adrichem Q, Wong ACH, Lang D, Honer WG, Kennedy JL. MAG but not CNP Gene Associated with Schizophrenia. In Preparation.

Publications

2007-01-16T00:42:06Z

Delphine: /* Peer Reviewed Conference Proceedings */

The following publications gratefully acknowledge the support of NA-MIC. Please see [[Publications:NIH_Roadmap_acknowledgement|'''NA-MIC acknowledgement instructions''']] for instructions on how to acknowledge NA-MIC in your publications.

* '''Search Medline'''

# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=EB005149 Search Medline for NAMIC-enabled publications]

List of publications from other NCBCs:

# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=RR021813 Search Medline for CCB-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=lm008748 Search Medline for I2B2-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=gm072970 Search Medline for SIMBIOS-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=DA021519 Search Medline for NCIBI-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=CA121852 Search Medline for C2B2-enabled publications]
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=HG004028 Search Medline for Bioontology-enabled publications]

 

* ** Note: Many technical journals are not listed in Medline. Medline therefore only holds a subset of NA-MIC related refereed publications.

== Peer Reviewed Journal Papers ==

# Nakamura M, McCarley RW, Kubicki M, Dickey CC, Niznikiewicz MA, Voglmaier MM, Seidman LJ, Maier SE, Westin CF, Kikinis R, Shenton ME. Fronto-temporal disconnectivity in schizotypal personality disorder: a diffusion tensor imaging study. Biol Psychiatry. 2005 Sep 15;58(6):468-78. [[Media:Nakamura_2005BiolPsych.pdf| PDF]]
# Tuch DS, Salat DH, Wisco JJ, Zaleta AK, Hevelone ND, Rosas HD. Choice reaction time performance correlates with diffusion anisotropy in white matter pathways supporting visuospatial attention. Proc Natl Acad Sci U S A. 2005 Aug 23;102(34):12212-7. [[Media:Tuch_PNAS_2005.pdf| PDF]]
# Tuch DS, Wisco JJ, Khachaturian MH, Ekstrom LB, Kotter R, Vanduffel W. Q-ball imaging of macaque white matter architecture. Philos Trans R Soc Lond B Biol Sci. 2005 May 29;360(1457):869-79. [[Media:Tuch_PhilosTransRBiolSoc_2005.pdf| PDF]]
# Niethammer M, Vela P, Tannenbaum A. On the evolution of closed curves by means of vector distance functions. Int. Journal Computer Vision, 2006. [[Media:Niethammer_etal_VISI849-04I.pdf| PDF]]
# Niethammer M, Tannenbaum A, Angenent S. Dynamic active contours. IEEE Trans. Automatic Control. 2006; 51:562-579. [[Media:Niethammer_paper1.pdf| PDF]]
# Turner JA, Smyth P, Macciardi F, Fallon JH, Kennedy JL, Potkin SG. Imaging phenotypes and genotypes in schizophrenia. Neuroinformatics. 2006;4(1):21-49. [[Media:Media-Turner_paper.pdf| PDF]]

'''''In Press'''''

# Liu T, Young G, Huang L, Chen N-K, Wong S. “76-space Analysis of Grey Matter Diffusivity: Methods and Applications,” in press, NeuroImage.
# O’Donnell L, Kubicki M, Shenton ME, Dreusicke MH, Grimson WEL, Westin CF. A method for clustering white matter fiber tracts. AJNR (In Press).
# Koo MS, Levitt JJ, McCarley RW, Seidman LJ, Dickey CC, Niznikiewicz MA, Voglmaier MM, Zamani P, Long KL, Kim SS, Shenton ME. Reduction of caudate volume in neuroleptic-naive female subjects with schizotypal personality disorder. Biol Psychiatry (In Press).
# Kuroki N, Kubicki M, Nestor PG, Salisbury DF, Park HJ, Levitt JJ, Woolston S, Frumin M, Niznikiewicz M, Westin CF, Maier SE, McCarley RW, Shenton ME. Fornix integrity and hippocampal volume in male schizophrenic patients. Biol Psychiatry (In Press).
# Onitsuka T, Niznikiewicz MA, Spencer KM, Frumin M, Kuroki N, Lucia LC, Shenton ME, McCarley RW. Schizophrenia is associated with functional and structural deficits in brain regions subserving face processing. Am J Psychiatry (In Press).
# Niethammer M, Tannenbaum A, Kalies W, Mischaikow K. Detecting simple points in higher dimensions. IEEE Image Processing, 2006. (In Press).
# Rathi Y, Dambreville S, Tannenbaum A. Comparative analysis of kernel methods for statistical shape learning. CVAMIA'06, 2006. (In Press).
# Roth RM, Koven, NS, Randolph JJ, Flashman LA, Pixley HS, Ricketts SM, Wishart HA, Saykin AJ. Event-Related fMRI study of Functional magnetic resonance imaging of executive control in bipolar disorder. NeuroReport, 2006 (In Press).
# Pohl KM, Fisher J, Grimson WEL, Kikinis R, Wells WM. [[Media:Pohl-ni-2006.pdf| A bayesian model for joint segmentation and registration.]] NeuroImage, 2006 (In Press).
# Fletcher PT, Joshi S. Riemannian Geometry for the Statistical Analysis of Diffusion Tensor Data. Signal Processing, 2006. (In Press).

== Peer Reviewed Conference Proceedings ==

'''Conferences included here represent the major high quality conferences in medical image analysis (MICCAI, IPMI, MMBIA, ISBI). These conferences only accept submission of full papers and guarantee a peer review process by at least three reviewers and an area chair. Acceptance rates are below 40% for MICCAI, IPMI and MMBIA and around 50% for ISBI.'''

# D. Nain, M. Styner, M. Niethammer, J. J. Levitt, M E Shenton, G Gerig, A. Bobick, A. Tannenbaum. Statistical Shape Analysis of Brain Structures using Spherical Wavelets. Accepted in The Fourth IEEE International Symposium on Biomedical Imaging (ISBI ’07), April 12-15, 2007, Washington DC, USA.
# Kim S, Smyth P. Hierarchical Dirichlet processes with random effects. Advances in Neural Information Processing Systems 19, to appear, 2006. [[Media:Nips_hMDP_RE.pdf| PDF ]]
# Kim S, Smyth P, Stern H. A nonparametric Bayesian approach to detecting spatial activation patterns in fMRI data. To appear in MICCAI, Oct 2-5, 2006.[[Media:InfMM_miccai.pdf| PDF ]]
# Nain D, Haker S, Bobick A, Tannenbaum A. Shape-driven surface segmentation using spherical wavelets. To appear in MICCAI, Oct 2-5, 2006.
# Styner M, Jomier M, Gerig G: Closed and Open Source Neuroimage Analysis Tools and Libraries at UNC. IEEE Symposium on Biomedical Imaging ISBI. 2006; 702-705. [[Media:ISBI06_Neurolib.pdf| PDF ]]
# Gerig G, Joshi S, Fletcher T, Gorczowski K, Xu S, Pizer SM, Styner M. Statistics of populations of images and its embedded objects: Driving applications in neuroimaging. IEEE Symposium on Biomedical Imaging ISBI. 2006; 1120-1123.[[Media:ISBI06-GerigShape.pdf| PDF]]
# Pieper S, Lorensen W, Schroeder W, Kikinis R. [[Media:Pieper-ISBI-2006-revised.pdf| The NA-MIC Kit: ITK, VTK, Pipelines, Grids and 3D Slicer as An Open Platform for the Medical Image Computing Community.]] IEEE Symposium on Biomedical Imaging ISBI. 2006; 698-701.
# Pichon E, Westin CF, and Tannenbaum A. A Hamilton-Jacobi-Bellman approach to high angular diffusion tractography. Proceedings of MICCAI, 2005. [[Media:Pichon-miccai05.pdf| PDF]]
# Yang Y, Zhu L, Haker S, Tannenbaum A. On the harmonic skeleton and vessel data. Proceeedings of MICCAI, 2005. [[Media:YangMICCAI2005.pdf| PDF]]
# Styner M, Gimpel Smith R, Cascio C, Oguz I, Jomier M. Corpus Callosum Subdivision based on a Probabilistic Model of Inter-hemispheric Connectivity. Medical Image Computing and Computer Assisted Interventions MICCAI. 2005 LNCS 3750;765-772. [[Media:MICCAI05CCSubdiv.pdf| PDF]]
# Liu T, Young G, Huang L, Chen N-K, Wong S. “76-space Analysis of Grey Matter Diffusivity: Methods and Applications,” MICCAI 2005.[[Media:MICCAI-2005--461-Liu.pdf| PDF]]
# Pichon E, Tannenbaum A. Curve segmentation using directional information, relation to pattern detection. Proc IEEE International Conference on Image Processing (ICIP), 2005
# Nain D, Haker S, Bobick A, Tannenbaum A. [[Media:Nain.miccai2005.pdf| Multiscale 3D Shape Analysis using Spherical Wavelets]]. Proc MICCAI, Oct 26-29 2005; p 459-467.
# Corouge I, Fletcher PT, Joshi S, Gilmore JH, Gerig G. [[Media:Corouge-miccai-2005.pdf| Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis.]] Proc. MICCAI, Oct 26-29 2005; LNCS 3749, pp. 131-139
# Ou W, Golland P. From Spatial Regularization to Anatomical Priors in fMRI Analysis. Proc IPMI, Jul 10-15 2005; LNCS 3565: p 88-100. [[Media:OuGolland_IPMI2005.pdf| PDF]]
# Pohl KM, Fisher J, Levitt JJ, Shenton ME, Kikinis R, Grimson WEL, Wells WM. [[Media:Pohl-miccai-2005.pdf| A Unifying Approach to Registration, Segmentation, and Intensity Correction,]] In Proc. MICCAI 2005: Eigth International Conference on Medical Image Computing and Computer Assisted Intervention, Palm Springs, CA, USA, Springer-Verlag, Part I, vol. 3749 of Lecture Notes in Computer Science, pp. 310-318, 2005
# Pohl KM, Bouix S, Shenton ME, Grimson WEL, Kikinis R. [[Media:Pohl-miccai-short-2005.pdf| Automatic Segmentation Using Non-Rigid Registration,]] In short communications of MICCAI 2005: Eighth International Conference on Medical Image Computing and Computer Assisted Intervention, Palm Springs, CA, USA, 2005
# Martin-Fernandez M, Bouix S, Ungar L, McCarley RW, Shenton ME. Two Methods for Validating Brain Tissue Classifiers. MICCAI 2005, Palm Springs, CA, USA: Duncan J and Gerig G (Eds.): Lecture Notes in Computer Science, volume 3749, pp 515-522, 2005. Springer-Verlag Berlin Heidelberg, 2005. [[Media:Martin-fernandezMICCAI05.pdf| PDF]]
# Kim S, Smyth P, Stern H, Turner J. Parametric response surface models for analysis of multi-site fMRI data. In Proc. MICCAI 2005: Eighth International Conference on Medical Image Computing and Computer Assisted Intervention, Palm Springs, CA, USA, Springer-Verlag, Part I, vol. 3749 of Lecture Notes in Computer Science, pp. 352-359, 2005. [[Media:Seyoung-official.pdf|PDF]]
# O'Donnell L, Westin C-F. White Matter Tract Clustering and Correspondence in Populations. MICCAI 2005, Palm Springs, CA, USA: Duncan J, Gerig G (Eds.): Lecture Notes in Computer Science, volume 3749, pp 140-147, 2005. Springer-Verlag Berlin Heidelberg, 2005. [[Media:OdonnellMICCAI05.pdf| PDF]]
# M. Maddah, A. Mewes, S. Haker, W. E. L. Grimson, and S. Warfield, [http://mit.edu/~mmaddah/www/Mahnaz_Miccai2005.pdf , Automated Atlas-Based Clustering of White Matter Fiber Tracts from DTMRI]. MICCAI05, Palm Spring, CA,: Lecture Notes in Computer Science, volume 3749, pp. 188-195, 2005.
# M. Maddah, W. E. L. Grimson, and S. Warfield, [http://mit.edu/~mmaddah/www/maddahISBI.pdf , Statistical Modeling and EM Clustering of White Matter Fiber Tracts], ISBI 2006: IEEE 2006 International Symposium on Biomedical Imaging, Arlington, VA, April 6-9, 2006

== Book Chapters ==

# Nain D, Tannenbaum A, Unal G, Yezzi A, Zeitouni O. On a stochastic model of geometric snakes. Mathematical Methods in Computer Vision: A Handbook, edited by Faugeras O, Paragios N, Springer-Verlag, 2005.
# Angenent S, Tannenbaum A, Yezzi A, Zeitouni O. Curve shortening and interacting particle systems. Book chapter in a volume edited by Hamid Krim, 2005.

== Others ==

=== Insight Journal ===

# Goodlett C, Corouge I, Jomier M, Gerig G. [http://hdl.handle.net/1926/39 A Quantitative DTI Fiber Tract Analysis Suite]. Insight Journal, 2005.
# Miller JV. [http://hdl.handle.net/1926/159 "Probability distributions for the Insight Toolkit."] Insight Journal, 2006.
# Gao Y, Melonakos J, Tannenbaum A. [http://hdl.handle.net/1926/225 "Conformal Flattening ITK Filter"] Insight Journal, 2006.
# Melonakos J, Krishnan K, Tannenbaum A. [[Media:Melonakos-ISC2006-bayesian.pdf| An ITK filter for Bayesian segmentation: itkBayesianClassifierImageFilter]]. Insight Journal, Jan 2006. http://hdl.handle.net/1926/160.
# Melonakos J, Al-Hakim R, Fallon J, Tannenbaum A. [[Media:Melonakos-ISC2005-bayesian.pdf| Knowledge-based segmentation of brain MRI scans using the Insight Toolkit]]. Insight Journal, Oct 2005. http://hdl.handle.net/1926/44.

=== Conferences and Workshops ===

# Rathi Y, Olver P, Sapiro G, Tannenbaum A. Affine Invariant Surface Evolutions for 3D Image Segmentation, SPIE 2006
# Rathi Y, Dambreville S, Tannenbaum A. Comparative Analyis of Kernel Methods for Statistical Shape Learning, 2nd Workshop on Computer Vision Approaches to Medical Image Analysis (in conjunction with ECCV) 2006.
# Eric Pichon, Delphine Nain, and Marc Niethammer. [[Media:Pichon-SPIEMI2006-laplace.pdf| A Laplace Equation Approach for Shape Comparison]]. Proc SPIE Medical Imaging, 2006.
# Al-Hakim R, Fallon J, Nain D, Melonakos J, Tannenbaum A. [[Media:Dlpfc-SPIE2006-full.pdf| A Dorsolateral Prefrontal Cortex Semi-Automatic Segmenter]]. Proc SPIE Medical Imaging, 2006.
# Pohl KM, Fisher J, Kikinis R, Grimson WEL, Wells WM. [[Media:Pohl-iccv-ws-2005.pdf| Shape Based Segmentation of Anatomical Structures in Magnetic Resonance Images,]] In Proc. ICCV 2005: Computer Vision for Biomedical Image Applications: Current Techniques and Future Trend, An International Conference on Computer Vision Workshop, Beijing, China, Springer-Verlag, vol. 3765 of Lecture Notes in Computer Science, 2005
# Zöllei L, Learned-Miller E, Grimson WEL, Wells WM III. Efficient Population Registration of 3D Data. Proc ICCV 2005, Computer Vision for Biomedical Image Applications; Beijing, China
# Angenent S, Pichon E, Tannenbaum A. Mathematical methods in medical imaging. Bulletin of American Mathematical Association, 2006.
# O'Donnell L, Westin C-F. A High-Dimensional Fiber Tract Atlas. accepted to ISMRM 2006.
# Zöllei L, Wells WM III. Multi-modal Image Registration Using Dirichlet-encoded Prior Information. oral presentation at WBIR06
# Fletcher PT, Whitaker RT. Riemannian Metrics on the Space of Solid Shapes. accepted to MICCAI'06 Workshop on Mathematical Foundations of Computational Anatomy (MFCA).
# Cates J, Meyer M, Fletcher PT, Whitaker R. Entropy-Based Particle Systems for Shape Correspondence. accepted to MICCAI'06 Workshop on Mathematical Foundations of Computational Anatomy (MFCA).

=== Submitted and in Preparation ===

# Flashman LA, Roth RM, Pixley HS, Cleavinger HB, Saykin AJ, McAllister TW, Vidaver RM. (submitted). Cavum septum pellucidum in schizophrenia: Clinical and neuropsychological correlates.
# Szymczak A, Tannenbaum A, Stillman A, Mischaikow K. Vessel cores from 3D imagery: a topological approach. submitted to IEEE Trans. Medical Imaging, 2006.
# Michailovich O, Tanenbaum A. Fast approximation of smooth functions from samples of partial derivatives. Submitted for publication to IEEE Signal Processing, 2006.
# Zhu L, Yang Y, Haker S, and Tannenbaum A. An image morphing technique based on optimal mass preserving mapping. Submitted to IEEE Trans. Image Processing, 2006.
# Rathi Y, Vaswani N, Tannenbaum A, Yezzi Y. Tracking Deforming Objects using Particle Filtering for Geometric Active Contours. Submitted to IEEE PAMI, 2005.
# Rathi Y, Tannenbaum A. Kernel PCA for shape based segmentation of medical images. submitted to MICCAI, 2006.
# Gorczowski K, Gerig G, Fletcher T, Pizer SM, Styner M. Statistics of Pose and Shape in Multi-Object Complexes using Principal Geodesic Analysis. submitted to MICCAI, 2006.
# Goodlett C, Davis B, Jean R, Gilmore J, Gerig G. Improved Correspondence for DTI Population Studies via Unbiased Atlas Building. submitted to MICCAI, 2006.
# Corouge I, Fletcher PT, Sarang J, Gouttard S, Gerig G. Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis. submitted MedIA Journal, Jan. 2006
# Gribbin M, Clement M, Muller K, Poe M, Cascio C, Jomier M, Piven J, Gerig G. Statistical analysis of diffusion tensor image data based on first principles, submitted MICCAI'06, March 2006
# Flashman LA, Roth RM, Koven NS, McAllister TW, Vidaver RM, Pendergrass JC. Neural Correlates of Self-Evaluation in Individuals with Schizophrenia. in preparation.
# Basu S, Fletcher PT, Whitaker RT. Rician Noise Removal in Diffusion Tensor MRI, to appear MICCAI'06.
# Han X, Fischl B. Intensity Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms, submitted to IEEE Transactions on Medical Imaging.
# Yu P, Grant P, Qi Y, Han X, Ségonne F, Pienaar R, Busa E, Pacheco J, Makris N, Buckner R, Golland P, Fischl B. Cortical Surface Shape Analysis Based on Spherical Wavelets, submitted to IEEE Transactions on Medical Imaging
# Ségonne F, Pacheco J, Fischl B. Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops, submitted to IEEE Transactions on Medical Imaging
# Voineskos AN, Zai G, Bulgin N, Shaikh S, Lang D, Honer WG, Kennedy JL. MAG but not CNP Gene Associated with Total Brain White Matter. In Preparation. Presented in Part at World Congress of Psychiatric Genetics Annual Meeting. October, 2006.
# Voineskos AN, Bulgin N, Van Adrichem Q, Wong ACH, Lang D, Honer WG, Kennedy JL. MAG but not CNP Gene Associated with Schizophrenia. In Preparation.

Algorithm:GATech

2007-01-16T00:41:08Z

Delphine: /* Multiscale Shape Analysis */

= Current Projects =

== Segmentation ==

=== [[Algorithm:GATech:Multiscale_Shape_Segmentation|Multiscale Shape Segmentation Techniques]] ===

To represent multiscale variations in a shape population in order to drive the segmentation of deep brain structures, such as the caudate nucleus or the hippocampus.

'''New: ''' Delphine Nain won the best student paper at [[MICCAI_2006|MICCAI 2006]] in the category "Segmentation and Registration" for her paper entitled "Shape-driven surface segmentation using spherical wavelets" by D. Nain, S. Haker, A. Bobick, A. Tannenbaum.

=== [[Algorithm:GATech:Rule_Based_Segmentation|Rule-Based Segmentation Techniques]] ===

In this work, we provide software to semi-automate the implementation of segmentation procedures based on expert neuroanatomist rules.

'''New: ''' Al-Hakim, et al. Parcellation of the Striatum. SPIE MI 2007.

=== [[Algorithm:GATech:KPCA_Segmentation|Kernel PCA for Segmentation]] ===

Segmentation performances using active contours can be drastically improved if the possible shapes of the object of interest are learnt. The goal of this work is to use Kernel PCA to learn shape priors. Kernel PCA allows for learning non linear dependencies in data sets, leading to more robust shape priors.

'''New: ''' S. Dambreville, Y. Rathi, and A. Tannenbaum. A Framework for Image Segmentation using Image Shape Models and Kernel PCA Shape Priors. PAMI. Submitted to PAMI.

=== [[Algorithm:GATech:Blood_Vessel_Segmentation|Blood Vessel Segmentation]] ===

The goal of this work is to develop blood vessel segmentation techniques for 3D MRI and CT data. The methods have been applied to coronary arteries and portal veins, with promising results.

'''New: '''Y. Yang, S. George, D. Martin, A. Tannenbaum, and D. Giddens. 3D Modeling of Patient-Specific Geometries of Portal Veins Using MR Images. In Proceedings IEEE EMBS, 2006

=== [[Algorithm:GATech:Knowledge_Based_Bayesian_Segmentation|Knowledge-Based Bayesian Segmentation]] ===

This ITK filter is a segmentation algorithm that utilizes Bayes's Rule along with an affine-invariant anisotropic smoothing filter.

'''New: ''' J. Melonakos, K. Krishnan, and A. Tannenbaum. An ITK Filter for Bayesian Segmentation: itkBayesianClassifierImageFilter. Insight Journal, 2006.

=== [[Algorithm:GATech:Stochastic_Methods_Segmentation|Stochastic Methods for Segmentation]] ===

New stochastic methods for implementing curvature driven flows for various medical tasks such as segmentation.

'''New: ''' Currently under investigation.

== Registration ==

=== [[Algorithm:GATech:Conformal_Flattening_Registration|Conformal Flattening]] ===

The goal of this project is for better visualizing and computation of neural activity from fMRI brain imagery. Also, with this technique, shapes can be mapped to shperes for shape analysis, registration or other purposes. Our technique is based on conformal mappings which map genus-zero surface: in fmri case cortical or other surfaces, onto a sphere in an angle preserving manner.

'''New: ''' Y. Gao, J. Melonakos, and A. Tannenbaum. Conformal Flattening ITK Filter. ISC/NA-MIC Workshop on Open Science at MICCAI 2006.

=== [[Algorithm:GATech:Optimal_Mass_Transport_Registration|Optimal Mass Transport Registration]] ===

The goal of this project is to implement a computationaly efficient Elastic/Non-rigid Registration algorithm based on the Monge-Kantorovich theory of optimal mass transport for 3D Medical Imagery. Our technique is based on Multigrid and Multiresolution techniques. This method is particularly useful because it is parameter free and utilizes all of the grayscale data in the image pairs in a symmetric fashion and no landmarks need to be specified for correspondence.

'''New: ''' Tauseef ur Rehman, A. Tannenbaum. Multigrid Optimal Mass Transport for Image Registration and Morphing. Accepted for SPIE Conference on Computational Imaging, Jan 2007.

== DWI Processing ==

=== [[Algorithm:GATech:Finsler_Active_Contour_DWI|Finsler Active Contour DWI Tractography]] ===

In this work, we provide an energy minimization framework which allows one to find optimal curves in direction-dependent data (i.e. where the cost associated with the curve depends both upon its position and orientation)

'''New: ''' E. Pichon, J. Melonakos, S. Angenet, A. Tannenbaum. Publication currently under review.

== Shape Analysis ==

=== [[Algorithm:GATech:Multiscale_Shape_Analysis|Multiscale Shape Analysis]] ===

We present a novel method of statistical surface-based morphometry based on the use of non-parametric permutation tests and a spherical wavelet (SWC) shape representation.

'''New: ''' D. Nain, M. Styner, M. Niethammer, J. J. Levitt, M E Shenton, G Gerig, A. Bobick, A. Tannenbaum. Statistical Shape Analysis of Brain Structures using Spherical Wavelets. Accepted in The Fourth IEEE International Symposium on Biomedical Imaging (ISBI ’07) that will be held April 12-15, 2007 in Metro Washington DC, USA.

=== [[Algorithm:GATech:Centerline_Generation_for_Vessels|Centerline Generation for Vessels]] ===

The goal of this work is to generate centerlines from segmented 3D surfaces of blood vessels using a harmonic skeletonization technique. The generated centerlines are used as a guide to visualize and evaluate stenoses in human coronary arteries.

=== [[Algorithm:GATech:KPCA_LLE_KLLE_Shape_Analysis|KPCA, LLE, KLLE Shape Analysis]] ===

The goal of this work is to study and compare shape learning techniques. The techniques considered are Linear Principal Components Analysis (PCA), Kernel PCA, Locally Linear Embedding (LLE) and Kernel LLE.

 

= Completed Projects =

== Segmentation ==

=== [[Algorithm:GATech:Fast_Marching_Slicer_2|Fast Marching Slicer 2 Module]] ===

The Fast Marching Algorithm was added as a module to Slicer 2.

=== [[Algorithm:GATech:Statistical_Segmentation_Slicer_2|Statistical/PDE Methods for Segmentation]] ===

This flow was added to Slicer 2.

=== [[Algorithm:GATech:Image_Smooth_Slicer_2|Image Smooth Slicer 2 Module]] ===

2D and 3D smoothing of images.

=== [[Algorithm:Affine_Segment_Slicer_2|Affine Segment Slicer 2 Module]] ===

This module can be used to perform edge based segmentation.

Projects:SphericalWaveletsInITK

2007-01-09T19:12:19Z

Delphine: /* Description */

== Description ==

For a general description of how we are using spherical wavelets for shape analysis, see [[Algorithm:GATech:Multiscale_Shape_Analysis|Multiscale Shape Analysis]]

This page outlines the steps we will take to code the Spherical Wavelet transform in ITK.

* The best place to learn about the spherical wavelet transform that we will implement is in this paper, that also has pseudo-code.

: Spherical Wavelets: Texture Processing (1995) Peter Schröder, Wim Sweldens
: http://citeseer.ist.psu.edu/oder95spherical.html

In this paper, it is shown how to do decompose a scalar signal defined on a spherical mesh into spherical wavelet coefficients (analysis step, also called forward transform), and vice-versa (synthesis step, also called inverse transform).

* With the goal of analyzing the scalar function defined on a spherical topological surface, the spherical parametrization is needed as the first step. Then, we can deem the function to be defined on a sphere. (If the function is a vector one, we can apply the analysis component by component. Thus the scalar function is used for simplicity in the future.)

* For our specific case of SHAPE representation, the function we are going to analyze are the x, y and z coordinates of the original triangulated surface.

* The numerical computation of spherical wavelet analysis requires the scalar function to be defined on a special triangulated sphere, the one generated by a recursive subdivision process. Also for a better performance, the base shape of the triangulation is selected as an icosahedron. The scalar function defined on the original spherical mesh is then interpolated onto the mesh generated by the recursive subdivision using bi-linear interpolation.

* The forward wavelet transformation is carried out on the configuration of the previous step and a set of wavelet coefficients are obtained, called Gamma coefficients. The backward transformation can recover the Gamma coefficients into an approximation of the original scalar function.

== Implementation ==

* Before the spherical wavelet transformation, the scalar function is interpolated onto a sphere which is generated from recursively subdividing an icosahedron and which has the least number of vertexes more than that of the original mesh.

* The whole process is done in one ITK filter, itkSWaveletFilter inherited from itkMeshSource class.

* The processes going within the class are:
# The hierarchy of the recursive subdivision is built from the icosahedron. The parameters needed for wavelet decomposition are calculated and stored in the internally. The level of the subdivision is chosen so that the finest sphere in the subdivision coincides with the one in the previous interpolation step.
# The scalar function is set using the API SetScalarFunction().
# The wavelet coefficients are calculated from the finest level and downward. It's and implementation of the lifting scheme of the second generation of wavelet transformation.
# The coefficients of all levels are stored in one structure of vector and can be exported to a file if needed.
# If needed, the reconstruction of function can be carried out from the coefficients. The difference between the reconstructed function and the original function is around 10^{-16}.

For a preliminary API, see [[NA-MIC/Projects/Structural/Shape_Analysis/ITK_Spherical_Wavelets_API|ITK Spherical Wavelets API]]

== Current Status ==

* Basically it's all set. All thing we need are stored internally.
* So the only thing needs to be done is to choose what data to output and how to output them to fit in the whole process of shape analysis pipeline.

== Next Steps ==

* We will discuss the filter interfaces to fit this into the whole procedure of shape analysis.

== Members ==

* Yi Gao (Gatech)
* Delphine Nain (Gatech)
* Xavier LeFaucheur (Gatech)
* John Melonakos (Gatech)
* Jim Miller (GE)
* Luis Ibanez (Kitware)
* Martin Styner (UNC)

== Links ==

* [[NA-MIC/Projects/Structural/Shape_Analysis/3D_Shape_Analysis_Using_Spherical_Wavelets|3D Shape Analysis Using Spherical Wavelets]]
* [[NA-MIC/Projects/Structural/Shape_Analysis/ITK_Spherical_Wavelets_API|ITK Spherical Wavelets API]]

File:2007 Project Half Week ShapeAnalysis WithSphericalWavelets.ppt

2007-01-08T21:53:21Z

Delphine:

Projects:SphericalWaveletsInITK

2007-01-08T21:33:18Z

Delphine: /* Implementation */

== Description ==

For a general description of how we are using spherical wavelets for shape analysis, see [[NA-MIC/Projects/Structural/Shape_Analysis/3D_Shape_Analysis_Using_Spherical_Wavelets|3D Shape Analysis Using Spherical Wavelets]]

This page outlines the steps we will take to code the Spherical Wavelet transform in ITK.

* The best place to learn about the spherical wavelet transform that we will implement is in this paper, that also has pseudo-code.

: Spherical Wavelets: Texture Processing (1995) Peter Schröder, Wim Sweldens
: http://citeseer.ist.psu.edu/oder95spherical.html

In this paper, it is shown how to do decompose a scalar signal defined on a spherical mesh into spherical wavelet coefficients (analysis step, also called forward transform), and vice-versa (synthesis step, also called inverse transform).

* With the goal of analyzing the scalar function defined on a spherical topological surface, the spherical parametrization is needed as the first step. Then, we can deem the function to be defined on a sphere. (If the function is a vector one, we can apply the analysis component by component. Thus the scalar function is used for simplicity in the future.)

* For our specific case of SHAPE representation, the function we are going to analyze are the x, y and z coordinates of the original triangulated surface.

* The numerical computation of spherical wavelet analysis requires the scalar function to be defined on a special triangulated sphere, the one generated by a recursive subdivision process. Also for a better performance, the base shape of the triangulation is selected as an icosahedron. The scalar function defined on the original spherical mesh is then interpolated onto the mesh generated by the recursive subdivision using bi-linear interpolation.

* The forward wavelet transformation is carried out on the configuration of the previous step and a set of wavelet coefficients are obtained, called Gamma coefficients. The backward transformation can recover the Gamma coefficients into an approximation of the original scalar function.

== Implementation ==

* Before the spherical wavelet transformation, the scalar function is interpolated onto a sphere which is generated from recursively subdividing an icosahedron and which has the least number of vertexes more than that of the original mesh.

* The whole process is done in one ITK filter, itkSWaveletFilter inherited from itkMeshSource class.

* The processes going within the class are:
# The hierarchy of the recursive subdivision is built from the icosahedron. The parameters needed for wavelet decomposition are calculated and stored in the internally. The level of the subdivision is chosen so that the finest sphere in the subdivision coincides with the one in the previous interpolation step.
# The scalar function is set using the API SetScalarFunction().
# The wavelet coefficients are calculated from the finest level and downward. It's and implementation of the lifting scheme of the second generation of wavelet transformation.
# The coefficients of all levels are stored in one structure of vector and can be exported to a file if needed.
# If needed, the reconstruction of function can be carried out from the coefficients. The difference between the reconstructed function and the original function is around 10^{-16}.

For a preliminary API, see [[NA-MIC/Projects/Structural/Shape_Analysis/ITK_Spherical_Wavelets_API|ITK Spherical Wavelets API]]

== Current Status ==

* Basically it's all set. All thing we need are stored internally.
* So the only thing needs to be done is to choose what data to output and how to output them to fit in the whole process of shape analysis pipeline.

== Next Steps ==

* We will discuss the filter interfaces to fit this into the whole procedure of shape analysis.

== Members ==

* Yi Gao (Gatech)
* Delphine Nain (Gatech)
* Xavier LeFaucheur (Gatech)
* John Melonakos (Gatech)
* Jim Miller (GE)
* Luis Ibanez (Kitware)
* Martin Styner (UNC)

== Links ==

* [[NA-MIC/Projects/Structural/Shape_Analysis/3D_Shape_Analysis_Using_Spherical_Wavelets|3D Shape Analysis Using Spherical Wavelets]]
* [[NA-MIC/Projects/Structural/Shape_Analysis/ITK_Spherical_Wavelets_API|ITK Spherical Wavelets API]]

2007 Project Half Week

2007-01-04T23:03:00Z

Delphine: /* Structural Analysis */

Back to [[AHM_2007|AHM_2007]]

== Results ==
Results of this event will be summarized here after it is completed.

==Please note==
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

== Projects ==
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page.

===Structural Analysis===
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
# Scripts to run and visualize [[Algorithm:GATech:Multiscale_Shape_Analysis|UNC shape analysis with Spherical Wavelet Features]] (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] ‎
#SVM Shape Analysis (Brad, Polina, Martin)
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration (Stephen, Jim, Ross)]]
## Driving problem: Congealing with B-spline (Lilla, Stephen)
## Driving problem: Non-rigid registration of anatomical MRI (Kilian, Stephen)
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration.ppt| 4-block PPT Jan 2007]]

===Diffusion Image Analysis===
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]

===NA-MIC Kit===
#Slicer3 Infrastructure Projects
##'''[[Slicer3:Architecture/Features|Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata)
##'''[[Slicer3:Data_Model|Data Model / libMRML]]''' ('''Alex''', Steve)
##'''[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
##'''[[Slicer3:Interface_Design|Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
###See [[Slicer3:UIEngineering|Slicer3:UIEngineering]]
##'''[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
###[[Slicer3:DTMRI|DTMRI]]<nowiki>: </nowiki>'''Raul''', [http://lmi.bwh.harvard.edu LMI]
###[[Slicer3:DTMRI|Tractography]]<nowiki>: </nowiki>'''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
###[[Slicer3:Editor|Editor]]<nowiki>: </nowiki>'''Steve'''
###[[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]<nowiki>: </nowiki>'''Nicole'''
###[[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]<nowiki>: </nowiki>'''Haiying'''
###[[Slicer3:EM|EMSegment Interface]]<nowiki>: </nowiki>'''Brad Davis'''
###[[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]<nowiki>: </nowiki>'''Steve Pieper'''
##'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie)
##Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[Image:2007 AHM Programming Half Week Slicer3 Launch.ppt]]
##'''[[Slicer3:Pipeline_Integration|Pipeline Integration]]''' ('''Jags''')
##'''[[Slicer3:Grid_Interface|Grid Integration]]''' ('''Jeff Grethe''', Neil)
##'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''')
#[[Slicer3:Grid_Interface|Grid Execution]] (Neil, Bill, Jim) [[2007_Project_Half_Week_GridExecution.ppt]]
#Tractography in Slicer3 (Lauren, Raul)
#Model Hierarchies (Alex, Lauren, Kilian, Brad, Ron) -- generalize concepts from DTI and EM group nodes to support atlas hierachies like in slicer2.

===External Collaborations===
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT 2007]]
#Developing IGT workflow for Slicer3 (Simon DiMaio, Haiying Liu, Noby Hata, Stephen Aylward) [[IGT|IGT Project page in NA-MIC wiki]]
#Radiology Workstation Module for Slicer3 (Pat, Steve)
#vmtk module for Slicer(Luca Antiga, Jim Miller)
#Hexahedral Voxel Meshing Slicer Module [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]] (Nicole Grosland, Vincent Magnotta, Curt Lisle, Ritesh Bafna, Steve Pieper) [[Media:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 4 block PPT 2007]]

----
This following is a list of projects carried out at the last project week (summer 2006). For new attendees, these projects can be used as templates. For attendees involved in the last project week, please move projects from the list below to the list above if you intend to continue these projects. And please do add a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT for 2007]].

=== 2006 Structural Analysis ===

# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Xavier Le Faucheur, GT, Delphine Nain, GT, John Melonakos GT/GE, Jim Miller GE, Luis Ibanez, Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT 2006]]
# [[NA-MIC/Projects/Structural/Shape_Analysis/ShapeStatisticsWithPermTestCorrectionAndFDR|ITK statistical analysis using non-parametric permutation analysis and false discovery rate]] (Martin Styner, UNC): [[Media:2006_06_PW_StatAnal.ppt| 4 block PPT 2006 ]]
# [[NA-MIC/Projects/Structural/Shape_Analysis/Correspondence|Local curvature based correspondence in ITK]] (Ipek Oguz, Martin Styner, UNC): [[Media:2006_MIT_Project_Week_LocalCurvatureBasedCorrespondence.ppt| 4 block PPT 2006]]
# [[NA-MIC/Projects/Structural/Shape_Analysis/FemaleSPDCaudates|Shape analysis of female SPD dataset]] (Jim Levitt, PNL, Marc Niethammer, PNL, Sylvain Bouix, PNL, Martin Styner, UNC): [[Media:2006_06_PW_female_SPD.ppt| 4-block PPT 2006]]
# [[NA-MIC/Projects/Structural/Mesh/Mesh_Untangling|Mesh Untangling]] (Gheorghe Postelnicu, MGH, Bill Lorensen GE): [[Media:2006_Summer_Project_Week_Mesh_Untangling.ppt|4 block PPT 2006]]
# [[NA-MIC/Projects/Structural/Registration/Histology_MR_Registration|MR Histology Registration]] (Gheorghe Postelnicu MGH, Bill Lorensen GE): [[Media:2006_Summer_Project_Week_MGH_Histology_MR_Registration.ppt|4 block PPT 2006]]

=== 2006 Diffusion Image Analysis ===

# [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|ITK DTI Image Processing Modules]] (Casey Goodlett UNC, Tom Fletcher Utah, Bill Lorensen GE, John Melonakos GT/GE): [[Media:2006_Summer_Project_Week_DTI_Processing.ppt|4-block PPT 2006]]
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Fiber_Tools_Slicer_Integration|Fiber Tools / Slicer 3 Integration]] (Casey Goodlett UNC, Bill Lorensen GE): [[Media:2006_Summer_Project_Week_FiberTracking_Slicer_Integration.ppt|4-block PPT 2006]]
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Stochastic_Fiber_Tracing_Applications|Stochastic Fiber Tracing Applications]] (C-F Westin, Marek Kubicki, Raul San-Jose, AW de Vries, All LMI):[[Media:2006_Summer_Project_Week_stochastictracking.ppt| 4-block PPT 2006]]
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Slicer_Fiber_Anatomical_Labeling|Slicer Fiber (Model) Labeling Interface]] (Lauren O'Donnell MIT, Marek Kubicki BWH) :[[Media:2006_Summer_Project_Week_ModelLabel.ppt| 4-block PPT 2006]]

=== 2006 FMRI Image Analysis ===

# [[NA-MIC/Projects/Structural/Conformal_Flattening_in_ITK|Conformal Flattening in ITK]](Yi Gao GT, John Melonakos GT/GE, Jim Miller GE, Luis Ibanez Kitware, Marc Niethammer BWH): [[Media:2006_Summer_Project_Week_ConformalFlattening.ppt| 4-block PPT 2006]]
# [[NA-MIC/Projects/fMRI_Analysis/Spatial_Regularization_for_fMRI_Detection|Spatial Regularization in fMRI Analysis]](Wanmei Ou, Polina Golland, Sandy Wells, and Carsten) [[Media:2006_Summer_Project_Week_fMRIMRF.ppt| 4-block PPT 2006]]

=== 2006 NA-MIC Kit ===

# [[2006_Project_Week_MIT_SlicerUI|Slicer3 Interface]] (Wendy Plesniak, Sebastien Barre, Steve Pieper, Mathieu Malaterre, Randy Gollub, Michael Halle), [[Media:2006_Summer_Project_Week_Slicer3UI.ppt|4-block PPT 2006]]
# [[2006_Project_Week_MIT_Migrating_Slicer2.x_Modules_to_Slicer3|Migrating Slicer2.x Modules to Slicer3]] (Nicole Aucoin, Mathieu Malaterre, Katie Hayes, Bill Lorensen): [[Media:2006_Summer_Project_Week_Migrating_Slicer2x_Modules_to_Slicer3.ppt|4-block PPT 2006]]
# [[2006_Project_Week_Kitware_Slicer3_Packaging|Slicer3 Packaging]] (Andy Cedilnik, Steve Pieper) [[Media:2006_Summer_Project_Week_Slicer3_Packaging.ppt|4-block PPT 2006]]
# [[2006_Project_Week_MIT_Grid_Integration|Slicer3 Grid Integration]] (Jeff Grethe, Brendan Faherty, Steve Pieper, Katie Hayes), [[Media:2006_Summer_Project_Week_Grid_Interface_for_Slicer3.ppt|4-block PPT 2006]]
# [[2006_Project_Week_MIT_LONIPipelineIntegration|Slicer3 Pipeline Integration ]] (Jagadeeswaran Rajendiran, Martin Styner, Steve Pieper), [[Media:2006_Summer_Project_Week_Jagadeeswaran_June30.ppt|4 block PPT 2006]]
# [[2006_Project_MGH_File_Format_Converter|2006 Project MGH File Format Converter]](Gheorghe Postelnicu, Bill Lorensen) [[Media:2006_Summer_Project_MIT_MGH_IO.ppt|4-block PPT 2006]]
# Volumetric Meshing (Kiran Shivanna, Vincent Magnotta, Nicole Grosland):[[Media:2006_Summer_Project_Week_Volumetric_Meshing.ppt|4-block PPT 2006]]
# Dicom Query/Retrieve (Eduardo Suárez, Rafael Nebot, Steve Pieper, Jim Miller):[[Media:2006_Summer_Project_Week_Slicer_Query_Retrieve.ppt|4-block PPT 2006]]
# A Translation Station for Imaging (Pat Mongkolwat, Alex Kogan, Tom Lechner, Steve Pieper, Wendy Plesniak):[[Media:2006_Project_Week_MIT_IntegrateSlicerWith_A_PACS_Workstation.ppt|4-block PPT 2006]]
# [[NA-MIC/Projects/Slicer3_for_IGT/Converting_vtkFMRIEngine_and_vtkMRAblation_to_Slicer3_modules|Converting vtkFMRIEngine and vtkMRAblation to Slicer3 modules]] (Noby Hata, Haiying Liu, Steve Pieper, Jim Miller): [[Media:2006_Summer_Project_Week_Slicer3_IGT.ppt| 4-block ppt 2006]]

=== 2006 NA-MIC Kit Support for Non-Medical Data ===

# ITK IO support for reading astronomy data and coordinates from FITS files (Douglas Alan IIC, Michael Halle BWH/IIC, Luis Ibanez Kitware)[[Media:2006_Summer_Project_Week_Astronomy_FITS_Reader_Prelim_Results.ppt| 4-block PPT 2006]]

== Logistics ==

'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)

'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].

2007 Project Half Week

2007-01-04T23:01:22Z

Delphine: /* Structural Analysis */

Back to [[AHM_2007|AHM_2007]]

== Results ==
Results of this event will be summarized here after it is completed.

==Please note==
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

== Projects ==
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page.

===Structural Analysis===
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
# Scripts to run and visualize UNC shape analysis with Spherical Wavelet Features (Delphine Nain, Yi Gao (GaTech), Martin Styner (UNC)): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] ‎
#SVM Shape Analysis (Brad, Polina, Martin)
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration (Stephen, Jim, Ross)]]
## Driving problem: Congealing with B-spline (Lilla, Stephen)
## Driving problem: Non-rigid registration of anatomical MRI (Kilian, Stephen)
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration.ppt| 4-block PPT Jan 2007]]

===Diffusion Image Analysis===
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]

===NA-MIC Kit===
#Slicer3 Infrastructure Projects
##'''[[Slicer3:Architecture/Features|Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata)
##'''[[Slicer3:Data_Model|Data Model / libMRML]]''' ('''Alex''', Steve)
##'''[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
##'''[[Slicer3:Interface_Design|Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
###See [[Slicer3:UIEngineering|Slicer3:UIEngineering]]
##'''[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
###[[Slicer3:DTMRI|DTMRI]]<nowiki>: </nowiki>'''Raul''', [http://lmi.bwh.harvard.edu LMI]
###[[Slicer3:DTMRI|Tractography]]<nowiki>: </nowiki>'''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
###[[Slicer3:Editor|Editor]]<nowiki>: </nowiki>'''Steve'''
###[[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]<nowiki>: </nowiki>'''Nicole'''
###[[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]<nowiki>: </nowiki>'''Haiying'''
###[[Slicer3:EM|EMSegment Interface]]<nowiki>: </nowiki>'''Brad Davis'''
###[[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]<nowiki>: </nowiki>'''Steve Pieper'''
##'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie)
##Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[Image:2007 AHM Programming Half Week Slicer3 Launch.ppt]]
##'''[[Slicer3:Pipeline_Integration|Pipeline Integration]]''' ('''Jags''')
##'''[[Slicer3:Grid_Interface|Grid Integration]]''' ('''Jeff Grethe''', Neil)
##'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''')
#[[Slicer3:Grid_Interface|Grid Execution]] (Neil, Bill, Jim) [[2007_Project_Half_Week_GridExecution.ppt]]
#Tractography in Slicer3 (Lauren, Raul)
#Model Hierarchies (Alex, Lauren, Kilian, Brad, Ron) -- generalize concepts from DTI and EM group nodes to support atlas hierachies like in slicer2.

===External Collaborations===
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT 2007]]
#Developing IGT workflow for Slicer3 (Simon DiMaio, Haiying Liu, Noby Hata, Stephen Aylward) [[IGT|IGT Project page in NA-MIC wiki]]
#Radiology Workstation Module for Slicer3 (Pat, Steve)
#vmtk module for Slicer(Luca Antiga, Jim Miller)
#Hexahedral Voxel Meshing Slicer Module [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]] (Nicole Grosland, Vincent Magnotta, Curt Lisle, Ritesh Bafna, Steve Pieper) [[Media:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 4 block PPT 2007]]

----
This following is a list of projects carried out at the last project week (summer 2006). For new attendees, these projects can be used as templates. For attendees involved in the last project week, please move projects from the list below to the list above if you intend to continue these projects. And please do add a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT for 2007]].

=== 2006 Structural Analysis ===

# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Xavier Le Faucheur, GT, Delphine Nain, GT, John Melonakos GT/GE, Jim Miller GE, Luis Ibanez, Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT 2006]]
# [[NA-MIC/Projects/Structural/Shape_Analysis/ShapeStatisticsWithPermTestCorrectionAndFDR|ITK statistical analysis using non-parametric permutation analysis and false discovery rate]] (Martin Styner, UNC): [[Media:2006_06_PW_StatAnal.ppt| 4 block PPT 2006 ]]
# [[NA-MIC/Projects/Structural/Shape_Analysis/Correspondence|Local curvature based correspondence in ITK]] (Ipek Oguz, Martin Styner, UNC): [[Media:2006_MIT_Project_Week_LocalCurvatureBasedCorrespondence.ppt| 4 block PPT 2006]]
# [[NA-MIC/Projects/Structural/Shape_Analysis/FemaleSPDCaudates|Shape analysis of female SPD dataset]] (Jim Levitt, PNL, Marc Niethammer, PNL, Sylvain Bouix, PNL, Martin Styner, UNC): [[Media:2006_06_PW_female_SPD.ppt| 4-block PPT 2006]]
# [[NA-MIC/Projects/Structural/Mesh/Mesh_Untangling|Mesh Untangling]] (Gheorghe Postelnicu, MGH, Bill Lorensen GE): [[Media:2006_Summer_Project_Week_Mesh_Untangling.ppt|4 block PPT 2006]]
# [[NA-MIC/Projects/Structural/Registration/Histology_MR_Registration|MR Histology Registration]] (Gheorghe Postelnicu MGH, Bill Lorensen GE): [[Media:2006_Summer_Project_Week_MGH_Histology_MR_Registration.ppt|4 block PPT 2006]]

=== 2006 Diffusion Image Analysis ===

# [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|ITK DTI Image Processing Modules]] (Casey Goodlett UNC, Tom Fletcher Utah, Bill Lorensen GE, John Melonakos GT/GE): [[Media:2006_Summer_Project_Week_DTI_Processing.ppt|4-block PPT 2006]]
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Fiber_Tools_Slicer_Integration|Fiber Tools / Slicer 3 Integration]] (Casey Goodlett UNC, Bill Lorensen GE): [[Media:2006_Summer_Project_Week_FiberTracking_Slicer_Integration.ppt|4-block PPT 2006]]
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Stochastic_Fiber_Tracing_Applications|Stochastic Fiber Tracing Applications]] (C-F Westin, Marek Kubicki, Raul San-Jose, AW de Vries, All LMI):[[Media:2006_Summer_Project_Week_stochastictracking.ppt| 4-block PPT 2006]]
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Slicer_Fiber_Anatomical_Labeling|Slicer Fiber (Model) Labeling Interface]] (Lauren O'Donnell MIT, Marek Kubicki BWH) :[[Media:2006_Summer_Project_Week_ModelLabel.ppt| 4-block PPT 2006]]

=== 2006 FMRI Image Analysis ===

# [[NA-MIC/Projects/Structural/Conformal_Flattening_in_ITK|Conformal Flattening in ITK]](Yi Gao GT, John Melonakos GT/GE, Jim Miller GE, Luis Ibanez Kitware, Marc Niethammer BWH): [[Media:2006_Summer_Project_Week_ConformalFlattening.ppt| 4-block PPT 2006]]
# [[NA-MIC/Projects/fMRI_Analysis/Spatial_Regularization_for_fMRI_Detection|Spatial Regularization in fMRI Analysis]](Wanmei Ou, Polina Golland, Sandy Wells, and Carsten) [[Media:2006_Summer_Project_Week_fMRIMRF.ppt| 4-block PPT 2006]]

=== 2006 NA-MIC Kit ===

# [[2006_Project_Week_MIT_SlicerUI|Slicer3 Interface]] (Wendy Plesniak, Sebastien Barre, Steve Pieper, Mathieu Malaterre, Randy Gollub, Michael Halle), [[Media:2006_Summer_Project_Week_Slicer3UI.ppt|4-block PPT 2006]]
# [[2006_Project_Week_MIT_Migrating_Slicer2.x_Modules_to_Slicer3|Migrating Slicer2.x Modules to Slicer3]] (Nicole Aucoin, Mathieu Malaterre, Katie Hayes, Bill Lorensen): [[Media:2006_Summer_Project_Week_Migrating_Slicer2x_Modules_to_Slicer3.ppt|4-block PPT 2006]]
# [[2006_Project_Week_Kitware_Slicer3_Packaging|Slicer3 Packaging]] (Andy Cedilnik, Steve Pieper) [[Media:2006_Summer_Project_Week_Slicer3_Packaging.ppt|4-block PPT 2006]]
# [[2006_Project_Week_MIT_Grid_Integration|Slicer3 Grid Integration]] (Jeff Grethe, Brendan Faherty, Steve Pieper, Katie Hayes), [[Media:2006_Summer_Project_Week_Grid_Interface_for_Slicer3.ppt|4-block PPT 2006]]
# [[2006_Project_Week_MIT_LONIPipelineIntegration|Slicer3 Pipeline Integration ]] (Jagadeeswaran Rajendiran, Martin Styner, Steve Pieper), [[Media:2006_Summer_Project_Week_Jagadeeswaran_June30.ppt|4 block PPT 2006]]
# [[2006_Project_MGH_File_Format_Converter|2006 Project MGH File Format Converter]](Gheorghe Postelnicu, Bill Lorensen) [[Media:2006_Summer_Project_MIT_MGH_IO.ppt|4-block PPT 2006]]
# Volumetric Meshing (Kiran Shivanna, Vincent Magnotta, Nicole Grosland):[[Media:2006_Summer_Project_Week_Volumetric_Meshing.ppt|4-block PPT 2006]]
# Dicom Query/Retrieve (Eduardo Suárez, Rafael Nebot, Steve Pieper, Jim Miller):[[Media:2006_Summer_Project_Week_Slicer_Query_Retrieve.ppt|4-block PPT 2006]]
# A Translation Station for Imaging (Pat Mongkolwat, Alex Kogan, Tom Lechner, Steve Pieper, Wendy Plesniak):[[Media:2006_Project_Week_MIT_IntegrateSlicerWith_A_PACS_Workstation.ppt|4-block PPT 2006]]
# [[NA-MIC/Projects/Slicer3_for_IGT/Converting_vtkFMRIEngine_and_vtkMRAblation_to_Slicer3_modules|Converting vtkFMRIEngine and vtkMRAblation to Slicer3 modules]] (Noby Hata, Haiying Liu, Steve Pieper, Jim Miller): [[Media:2006_Summer_Project_Week_Slicer3_IGT.ppt| 4-block ppt 2006]]

=== 2006 NA-MIC Kit Support for Non-Medical Data ===

# ITK IO support for reading astronomy data and coordinates from FITS files (Douglas Alan IIC, Michael Halle BWH/IIC, Luis Ibanez Kitware)[[Media:2006_Summer_Project_Week_Astronomy_FITS_Reader_Prelim_Results.ppt| 4-block PPT 2006]]

== Logistics ==

'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)

'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].

2007 Project Half Week

2007-01-04T22:55:52Z

Delphine: /* Structural Analysis */

Back to [[AHM_2007|AHM_2007]]

== Results ==
Results of this event will be summarized here after it is completed.

==Please note==
* Everyone should '''bring a laptop'''. We will have three or four projectors.
* About half the time will be spent working on projects and the other half in project related discussions.

== Projects ==
This is the list of projects discussed in the preparation tcons on [[Engineering:TCON_12_07_2006|December 7]] and [[Engineering:TCON_12_14_2006|December 14, 2006]]. Each project lead (first name in the list) needs to complete a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT]], and upload and link it to this page.

===Structural Analysis===
# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Delphine Nain - GT, Yi Gao - GT, Jim Miller - GE, Luis Ibanez - Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT Summer 2006]],[[Media:2007_Project_Half_Week_SphericalWaveletInITK.ppt| 4-block PPT Jan 2007]]
#scripts to run UNC shape analysis (delphine, Martin): [[Media:2007_Project_Half_Week_ShapeAnalysis_WithSphericalWavelets.ppt| 4-block PPT Jan 2007]]
#EMSegmenter Software Development (Kilian, Brad) [[Media:2007_Project_Half_Week_EMSegment.ppt | 4-block PPT Jan 2007]] ‎
#SVM Shape Analysis (Brad, Polina, Martin)
#[[Non_Rigid_Registration|Parallelization of ITK for deformable registration (Stephen, Jim, Ross)]]
## Driving problem: Congealing with B-spline (Lilla, Stephen)
## Driving problem: Non-rigid registration of anatomical MRI (Kilian, Stephen)
# Integrating KWMeshVisu into Slicer (Ipek, Martin, Sebastien), [[Media:2006_AHM_Programming_Half_week_MeshVisu.ppt|4-block PPT Jan 2006]], [[Media:2007_AHM_Programming_Half_week_MeshVisu.ppt |4-block PPT Jan 2007 ]]
#Group-wise Registration of Medical Images(Serdar, Polina, Mert, Sandy ), [[Media:2007_Project_Half_Week_GroupWiseRegistration.ppt| 4-block PPT Jan 2007]]

===Diffusion Image Analysis===
#Finsler Tractography (John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerTractography.ppt| 4-block PPT Jan 2007]]
#Finsler Levelsets (Vandana Mohan - GT, John Melonakos - GT, Luis Ibanez - Kitware): [[Media:2007_Project_Half_Week_FinslerLevelsets.ppt| 4-block PPT Jan 2007]]
#Tensor estimation and Monte-Carlo simulation (Casey Goodlett - UNC, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_TensorEstimation.ppt | 4-block PPT Jan 2007]]
#Rician Noise Remvoal in Diffusion Tensor MRI (McKay Davis - Utah, Tom Fletcher - Utah): [[Media:2007_Project_Half_Week_RicianNoiseDTI.ppt | 4-block PPT Jan 2007]]
#ITK implementation of POIStat, and Integration into Slicer3 (Dennis, Steve), [[Media:2007_Project_Half_Week_PoistatsSlicerItkIntegration.ppt| 4-block PPT Jan 2007]]
#Image Format issues in application of POIStats to Dartmouth data (Dennis, Steve, Luis, John West, Andy Saykin), [[Media:2007_Project_Half_Week_PoistatsImageFormatDartmouth.ppt| 4-block PPT Jan 2007]]

===NA-MIC Kit===
#Slicer3 Infrastructure Projects
##'''[[Slicer3:Architecture/Features|Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata)
##'''[[Slicer3:Data_Model|Data Model / libMRML]]''' ('''Alex''', Steve)
##'''[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)
##'''[[Slicer3:Interface_Design|Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan) [[Media:2007_Project_Half_Week_SlicerUI.ppt| 4-block PPT Jan 2007]]
###See [[Slicer3:EventBindings|Slicer3:EventBindings]].
##'''[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)
###[[Slicer3:DTMRI|DTMRI]]<nowiki>: </nowiki>'''Raul''', [http://lmi.bwh.harvard.edu LMI]
###[[Slicer3:DTMRI|Tractography]]<nowiki>: </nowiki>'''Lauren''' [[Media:2007_Project_Half_Week_Tractography.ppt| 4-block PPT Jan 2007]]
###[[Slicer3:Editor|Editor]]<nowiki>: </nowiki>'''Steve'''
###[[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]<nowiki>: </nowiki>'''Nicole'''
###[[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]<nowiki>: </nowiki>'''Haiying'''
###[[Slicer3:EM|EMSegment Interface]]<nowiki>: </nowiki>'''Brad Davis'''
###[[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]<nowiki>: </nowiki>'''Steve Pieper'''
##'''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie)
##Slicer3 launch and deployment issues (Steve, Jim, Bill, Will, Sebastien, Andy) [[Image:2007 AHM Programming Half Week Slicer3 Launch.ppt]]
##'''[[Slicer3:Pipeline_Integration|Pipeline Integration]]''' ('''Jags''')
##'''[[Slicer3:Grid_Interface|Grid Integration]]''' ('''Jeff Grethe''', Neil)
##'''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''')
#[[Slicer3:Grid_Interface|Grid Execution]] (Neil, Bill, Jim) [[2007_Project_Half_Week_GridExecution.ppt]]
#Tractography in Slicer3 (Lauren, Raul)
#Model Hierarchies (Alex, Lauren, Kilian, Brad, Ron) -- generalize concepts from DTI and EM group nodes to support atlas hierachies like in slicer2.

===External Collaborations===
#Converting ITK Pipeline for Archip's, HPC based, deformable registration to Slicer3 Module (Daniel Goldberg, Jim Miller, Bill Lorensen) [[Media:2007_Project_Half_Week_ConvertingITKPipelineDeformableRegistrationtoSlicer3.ppt|4 block PPT 2007]]
#Developing IGT workflow for Slicer3 (Simon DiMaio, Haiying Liu, Noby Hata, Stephen Aylward) [[IGT|IGT Project page in NA-MIC wiki]]
#Radiology Workstation Module for Slicer3 (Pat, Steve)
#vmtk module for Slicer(Luca Antiga, Jim Miller)
#Hexahedral Voxel Meshing Slicer Module [[NA-MIC_Collaborations#PAR-05-063_Automated_FE_Mesh_Development | for collaboration grant]] (Nicole Grosland, Vincent Magnotta, Curt Lisle, Ritesh Bafna, Steve Pieper) [[Media:2007_AHM_Programming_Half Week_VoxelMeshing.ppt|Voxel Meshing 4 block PPT 2007]]

----
This following is a list of projects carried out at the last project week (summer 2006). For new attendees, these projects can be used as templates. For attendees involved in the last project week, please move projects from the list below to the list above if you intend to continue these projects. And please do add a [[Media:2007_Project_Half_Week_Template.ppt|new 4-block PPT for 2007]].

=== 2006 Structural Analysis ===

# [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]] (Xavier Le Faucheur, GT, Delphine Nain, GT, John Melonakos GT/GE, Jim Miller GE, Luis Ibanez, Kitware): [[Media:2006_Project_Week_MIT_SphericalWaveletInITK.ppt| 4-block PPT 2006]]
# [[NA-MIC/Projects/Structural/Shape_Analysis/ShapeStatisticsWithPermTestCorrectionAndFDR|ITK statistical analysis using non-parametric permutation analysis and false discovery rate]] (Martin Styner, UNC): [[Media:2006_06_PW_StatAnal.ppt| 4 block PPT 2006 ]]
# [[NA-MIC/Projects/Structural/Shape_Analysis/Correspondence|Local curvature based correspondence in ITK]] (Ipek Oguz, Martin Styner, UNC): [[Media:2006_MIT_Project_Week_LocalCurvatureBasedCorrespondence.ppt| 4 block PPT 2006]]
# [[NA-MIC/Projects/Structural/Shape_Analysis/FemaleSPDCaudates|Shape analysis of female SPD dataset]] (Jim Levitt, PNL, Marc Niethammer, PNL, Sylvain Bouix, PNL, Martin Styner, UNC): [[Media:2006_06_PW_female_SPD.ppt| 4-block PPT 2006]]
# [[NA-MIC/Projects/Structural/Mesh/Mesh_Untangling|Mesh Untangling]] (Gheorghe Postelnicu, MGH, Bill Lorensen GE): [[Media:2006_Summer_Project_Week_Mesh_Untangling.ppt|4 block PPT 2006]]
# [[NA-MIC/Projects/Structural/Registration/Histology_MR_Registration|MR Histology Registration]] (Gheorghe Postelnicu MGH, Bill Lorensen GE): [[Media:2006_Summer_Project_Week_MGH_Histology_MR_Registration.ppt|4 block PPT 2006]]

=== 2006 Diffusion Image Analysis ===

# [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|ITK DTI Image Processing Modules]] (Casey Goodlett UNC, Tom Fletcher Utah, Bill Lorensen GE, John Melonakos GT/GE): [[Media:2006_Summer_Project_Week_DTI_Processing.ppt|4-block PPT 2006]]
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Fiber_Tools_Slicer_Integration|Fiber Tools / Slicer 3 Integration]] (Casey Goodlett UNC, Bill Lorensen GE): [[Media:2006_Summer_Project_Week_FiberTracking_Slicer_Integration.ppt|4-block PPT 2006]]
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Stochastic_Fiber_Tracing_Applications|Stochastic Fiber Tracing Applications]] (C-F Westin, Marek Kubicki, Raul San-Jose, AW de Vries, All LMI):[[Media:2006_Summer_Project_Week_stochastictracking.ppt| 4-block PPT 2006]]
# [[NA-MIC/Projects/Diffusion_Image_Analysis/Slicer_Fiber_Anatomical_Labeling|Slicer Fiber (Model) Labeling Interface]] (Lauren O'Donnell MIT, Marek Kubicki BWH) :[[Media:2006_Summer_Project_Week_ModelLabel.ppt| 4-block PPT 2006]]

=== 2006 FMRI Image Analysis ===

# [[NA-MIC/Projects/Structural/Conformal_Flattening_in_ITK|Conformal Flattening in ITK]](Yi Gao GT, John Melonakos GT/GE, Jim Miller GE, Luis Ibanez Kitware, Marc Niethammer BWH): [[Media:2006_Summer_Project_Week_ConformalFlattening.ppt| 4-block PPT 2006]]
# [[NA-MIC/Projects/fMRI_Analysis/Spatial_Regularization_for_fMRI_Detection|Spatial Regularization in fMRI Analysis]](Wanmei Ou, Polina Golland, Sandy Wells, and Carsten) [[Media:2006_Summer_Project_Week_fMRIMRF.ppt| 4-block PPT 2006]]

=== 2006 NA-MIC Kit ===

# [[2006_Project_Week_MIT_SlicerUI|Slicer3 Interface]] (Wendy Plesniak, Sebastien Barre, Steve Pieper, Mathieu Malaterre, Randy Gollub, Michael Halle), [[Media:2006_Summer_Project_Week_Slicer3UI.ppt|4-block PPT 2006]]
# [[2006_Project_Week_MIT_Migrating_Slicer2.x_Modules_to_Slicer3|Migrating Slicer2.x Modules to Slicer3]] (Nicole Aucoin, Mathieu Malaterre, Katie Hayes, Bill Lorensen): [[Media:2006_Summer_Project_Week_Migrating_Slicer2x_Modules_to_Slicer3.ppt|4-block PPT 2006]]
# [[2006_Project_Week_Kitware_Slicer3_Packaging|Slicer3 Packaging]] (Andy Cedilnik, Steve Pieper) [[Media:2006_Summer_Project_Week_Slicer3_Packaging.ppt|4-block PPT 2006]]
# [[2006_Project_Week_MIT_Grid_Integration|Slicer3 Grid Integration]] (Jeff Grethe, Brendan Faherty, Steve Pieper, Katie Hayes), [[Media:2006_Summer_Project_Week_Grid_Interface_for_Slicer3.ppt|4-block PPT 2006]]
# [[2006_Project_Week_MIT_LONIPipelineIntegration|Slicer3 Pipeline Integration ]] (Jagadeeswaran Rajendiran, Martin Styner, Steve Pieper), [[Media:2006_Summer_Project_Week_Jagadeeswaran_June30.ppt|4 block PPT 2006]]
# [[2006_Project_MGH_File_Format_Converter|2006 Project MGH File Format Converter]](Gheorghe Postelnicu, Bill Lorensen) [[Media:2006_Summer_Project_MIT_MGH_IO.ppt|4-block PPT 2006]]
# Volumetric Meshing (Kiran Shivanna, Vincent Magnotta, Nicole Grosland):[[Media:2006_Summer_Project_Week_Volumetric_Meshing.ppt|4-block PPT 2006]]
# Dicom Query/Retrieve (Eduardo Suárez, Rafael Nebot, Steve Pieper, Jim Miller):[[Media:2006_Summer_Project_Week_Slicer_Query_Retrieve.ppt|4-block PPT 2006]]
# A Translation Station for Imaging (Pat Mongkolwat, Alex Kogan, Tom Lechner, Steve Pieper, Wendy Plesniak):[[Media:2006_Project_Week_MIT_IntegrateSlicerWith_A_PACS_Workstation.ppt|4-block PPT 2006]]
# [[NA-MIC/Projects/Slicer3_for_IGT/Converting_vtkFMRIEngine_and_vtkMRAblation_to_Slicer3_modules|Converting vtkFMRIEngine and vtkMRAblation to Slicer3 modules]] (Noby Hata, Haiying Liu, Steve Pieper, Jim Miller): [[Media:2006_Summer_Project_Week_Slicer3_IGT.ppt| 4-block ppt 2006]]

=== 2006 NA-MIC Kit Support for Non-Medical Data ===

# ITK IO support for reading astronomy data and coordinates from FITS files (Douglas Alan IIC, Michael Halle BWH/IIC, Luis Ibanez Kitware)[[Media:2006_Summer_Project_Week_Astronomy_FITS_Reader_Prelim_Results.ppt| 4-block PPT 2006]]

== Logistics ==

'''Dates:''' January 10 & 12, 2007 (There will be no project-week related events scheduled for Thursday, January 11th, the day of the AHM.)

'''Registration Fee:''' Registration fee is $215 for this event, and includes registration for the NA-MIC AHM. Separate registration, either for the AHM, or the project event are not available. To register and reserve hotel rooms, please [[AHM_2007#Registration_and_Hotel_Logistics|follow this link]].

== Background and Preparation ==

We continue to call this event "Project Week" or "Project Half Week", depending on how its duration, rather than by its original name of "Programming Week". Along with programming, a fair amount of algorithm design, and clinical application brainstorming also takes places and the name change reflects the broader scope of the event. What does this means for participants: if you are participating in a NA-MIC project or collaboration by providing algorithmic or clinical input, you are very welcome to attend. As always, participation is entirely voluntary.

=== Goals ===

The main goal of this week is to move forward the deliverables of NA-MIC. All NA-MIC participants and their collaborators are welcome.

* Members of all cores are welcome. This event involves programming, algorithm design, and clinical application development/testing.
* The event is open to people outside NA-MIC, subject to availability.
* You '''do''' need to be actively working on a NA-MIC related project in order to make this investment worthwhile for everyone.
* Participation in this event is voluntary -- if you don't think this will help you move forward in your work, there is no obligation to attend.
* Ideal candidates are those who want to contribute to the NA-MIC Kit, and those who can help make it happen.
* This is not an introduction to the components of the NA-MIC Kit.
* Submit any projects that you would like to work on during this week, and what type of help you might need for it.

=== Preparation for the workshop ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-programming-week na-mic-programming-week mailing list]
# [[Engineering:TCON_12_07_2006|December 7: Kickoff TCON]]
# December 14: Create a Wiki page per project (the participants must do this, hopefully jointly)
# [[Engineering:TCON_12_14_2006|December 14: TCON#2 to discuss projects and verify teams]]
# December: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Andy)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Andy)
# [[Engineering:TCON_2007#2007-Jan-04|January 4, 2007: TCON#3 last preparation tcon]]
# By January 9th: Complete the top half of [[Media:2007_Project_Half_Week_Template.ppt|this powerpoint template]] for each project. Upload and link to the right place.
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== A History in Wiki Links ==

A history of all the programming/project events in NA-MIC is available by following [[Engineering:Programming_Events|this link]].

Projects:MultiscaleShapeSegmentation

2006-12-22T17:26:08Z

Delphine: /* Shape Representation and Prior */

== Objective ==
To represent multiscale variations in a shape population in order to drive the segmentation of deep brain structures, such as the caudate nucleus or the hippocampus.

== Overview ==

=== Shape Representation and Prior ===
The overview of our shape representation is given in Figure 1. Our technique defines a multiscale parametric model of surfaces belonging to the same population using a compact set of spherical wavelets targeted to that population (Figure 2). We further refine the shape representation by separating into groups wavelet coefficients that describe independent global and/or local biological variations in the population, using spectral graph partitioning. We then learn a prior probability distribution induced over each group to explicitly encode these variations at different scales and spatial locations (Figure 4) [1].

[[Image:Gatech_SW_representation.png|thumb|200px|Figure 1: Steps of the Shape Representation using Spherical Wavelets]]
[[Image:Gatech_SW_mscale_shape.png|thumb|200px|Figure 2: A shape is represented using spherical wavelet coefficients]]

=== Segmentation ===
Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior for segmentation. Additionally, the optimization method can be applied in a coarse-to-fine manner.

=== Results ===
We applied our algorithm to the caudate nucleus, a brain structure of interest in the study of schizophrenia [2]. Our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model (ASM) algorithm, by capturing finer shape details.

== References ==
* [1] Nain D, Haker S, Bobick A, Tannenbaum A. Multiscale 3D Shape Analysis using Spherical Wavelets. Proc MICCAI, Oct 26-29 2005; p 459-467 [1]
* [2] Nain D, Haker S, Bobick A, Tannenbaum A. Shape-driven 3D Segmentation using Spherical Wavelets. Proc MICCAI, Oct 2-5, 2006. PDF of paper

== Key Investigators ==
* Core 1:
** Georgia Tech: Delphine Nain, Aaron Bobick, Allen Tannenbaum
** Harvard SPL: Steven Haker

== Collaborators ==

* Core 1: Martin Styner (UNC)
* Core 2: Jim Miller (GE), Luis Ibanez (Kitware)
* Core 3: James Levitt, Marc Niethammer, Sylvain Bouix, Martha Shenton (Harvard PNL)

== Links: ==
* Paper presented in [[MICCAI_2006|MICCAI 2006, Copenhagen, October 2 - 4, 2006 ]]
* Code: [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]]
* [[Algorithm:GATech|Georgia Tech Summary Page]]
* [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

Projects:MultiscaleShapeSegmentation

2006-12-22T17:25:36Z

Delphine: /* Shape Representation and Prior */

== Objective ==
To represent multiscale variations in a shape population in order to drive the segmentation of deep brain structures, such as the caudate nucleus or the hippocampus.

== Overview ==

=== Shape Representation and Prior ===
The overview of our shape representation is given in Figure 1. Our technique defines a multiscale parametric model of surfaces belonging to the same population using a compact set of spherical wavelets targeted to that population (Figure 2). We further refine the shape representation by separating into groups wavelet coefficients that describe independent global and/or local biological variations in the population, using spectral graph partitioning. We then learn a prior probability distribution induced over each group to explicitly encode these variations at different scales and spatial locations (Figure 4) [1].

[[Image:Gatech_SW_representation.png|thumb|right|200px|Figure 1: Steps of the Shape Representation using Spherical Wavelets]]
[[Image:Gatech_SW_mscale_shape.png|thumb|right|200px|Figure 2: A shape is represented using spherical wavelet coefficients]]

=== Segmentation ===
Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior for segmentation. Additionally, the optimization method can be applied in a coarse-to-fine manner.

=== Results ===
We applied our algorithm to the caudate nucleus, a brain structure of interest in the study of schizophrenia [2]. Our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model (ASM) algorithm, by capturing finer shape details.

== References ==
* [1] Nain D, Haker S, Bobick A, Tannenbaum A. Multiscale 3D Shape Analysis using Spherical Wavelets. Proc MICCAI, Oct 26-29 2005; p 459-467 [1]
* [2] Nain D, Haker S, Bobick A, Tannenbaum A. Shape-driven 3D Segmentation using Spherical Wavelets. Proc MICCAI, Oct 2-5, 2006. PDF of paper

== Key Investigators ==
* Core 1:
** Georgia Tech: Delphine Nain, Aaron Bobick, Allen Tannenbaum
** Harvard SPL: Steven Haker

== Collaborators ==

* Core 1: Martin Styner (UNC)
* Core 2: Jim Miller (GE), Luis Ibanez (Kitware)
* Core 3: James Levitt, Marc Niethammer, Sylvain Bouix, Martha Shenton (Harvard PNL)

== Links: ==
* Paper presented in [[MICCAI_2006|MICCAI 2006, Copenhagen, October 2 - 4, 2006 ]]
* Code: [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]]
* [[Algorithm:GATech|Georgia Tech Summary Page]]
* [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

Projects:MultiscaleShapeSegmentation

2006-12-22T17:24:51Z

Delphine: /* Shape Representation and Prior */

== Objective ==
To represent multiscale variations in a shape population in order to drive the segmentation of deep brain structures, such as the caudate nucleus or the hippocampus.

== Overview ==

=== Shape Representation and Prior ===
The overview of our shape representation is given in Figure 1. Our technique defines a multiscale parametric model of surfaces belonging to the same population using a compact set of spherical wavelets targeted to that population (Figure 2). We further refine the shape representation by separating into groups wavelet coefficients that describe independent global and/or local biological variations in the population, using spectral graph partitioning. We then learn a prior probability distribution induced over each group to explicitly encode these variations at different scales and spatial locations (Figure 4) [1].

[[Image:Gatech_SW_Representation.png|thumb|right|200px|Figure 1: Steps of the Shape Representation using Spherical Wavelets]]
[[Image:Gatech_SW_mscale_shape.png|thumb|right|200px|Figure 2: A shape is represented using spherical wavelet coefficients]]

=== Segmentation ===
Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior for segmentation. Additionally, the optimization method can be applied in a coarse-to-fine manner.

=== Results ===
We applied our algorithm to the caudate nucleus, a brain structure of interest in the study of schizophrenia [2]. Our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model (ASM) algorithm, by capturing finer shape details.

== References ==
* [1] Nain D, Haker S, Bobick A, Tannenbaum A. Multiscale 3D Shape Analysis using Spherical Wavelets. Proc MICCAI, Oct 26-29 2005; p 459-467 [1]
* [2] Nain D, Haker S, Bobick A, Tannenbaum A. Shape-driven 3D Segmentation using Spherical Wavelets. Proc MICCAI, Oct 2-5, 2006. PDF of paper

== Key Investigators ==
* Core 1:
** Georgia Tech: Delphine Nain, Aaron Bobick, Allen Tannenbaum
** Harvard SPL: Steven Haker

== Collaborators ==

* Core 1: Martin Styner (UNC)
* Core 2: Jim Miller (GE), Luis Ibanez (Kitware)
* Core 3: James Levitt, Marc Niethammer, Sylvain Bouix, Martha Shenton (Harvard PNL)

== Links: ==
* Paper presented in [[MICCAI_2006|MICCAI 2006, Copenhagen, October 2 - 4, 2006 ]]
* Code: [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]]
* [[Algorithm:GATech|Georgia Tech Summary Page]]
* [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

Projects:MultiscaleShapeSegmentation

2006-12-22T17:17:50Z

Delphine: /* Links: */

== Objective ==
To represent multiscale variations in a shape population in order to drive the segmentation of deep brain structures, such as the caudate nucleus or the hippocampus.

== Overview ==

=== Shape Representation and Prior ===
The overview of our shape representation is given in Figure 1. Our technique defines a multiscale parametric model of surfaces belonging to the same population using a compact set of spherical wavelets targeted to that population (Figure 2). We further refine the shape representation by separating into groups wavelet coefficients that describe independent global and/or local biological variations in the population, using spectral graph partitioning. We then learn a prior probability distribution induced over each group to explicitly encode these variations at different scales and spatial locations (Figure 4) [1].

=== Segmentation ===
Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior for segmentation. Additionally, the optimization method can be applied in a coarse-to-fine manner.

=== Results ===
We applied our algorithm to the caudate nucleus, a brain structure of interest in the study of schizophrenia [2]. Our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model (ASM) algorithm, by capturing finer shape details.

== References ==
* [1] Nain D, Haker S, Bobick A, Tannenbaum A. Multiscale 3D Shape Analysis using Spherical Wavelets. Proc MICCAI, Oct 26-29 2005; p 459-467 [1]
* [2] Nain D, Haker S, Bobick A, Tannenbaum A. Shape-driven 3D Segmentation using Spherical Wavelets. Proc MICCAI, Oct 2-5, 2006. PDF of paper

== Key Investigators ==
* Core 1:
** Georgia Tech: Delphine Nain, Aaron Bobick, Allen Tannenbaum
** Harvard SPL: Steven Haker

== Collaborators ==

* Core 1: Martin Styner (UNC)
* Core 2: Jim Miller (GE), Luis Ibanez (Kitware)
* Core 3: James Levitt, Marc Niethammer, Sylvain Bouix, Martha Shenton (Harvard PNL)

== Links: ==
* Paper presented in [[MICCAI_2006|MICCAI 2006, Copenhagen, October 2 - 4, 2006 ]]
* Code: [[NA-MIC/Projects/Structural/Shape_Analysis/Spherical_Wavelets_in_ITK|ITK Spherical Wavelet Transform Filter]]
* [[Algorithm:GATech|Georgia Tech Summary Page]]
* [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

Projects:MultiscaleShapeSegmentation

2006-12-22T17:12:12Z

Delphine: /* Links: */

== Objective ==
To represent multiscale variations in a shape population in order to drive the segmentation of deep brain structures, such as the caudate nucleus or the hippocampus.

== Overview ==

=== Shape Representation and Prior ===
The overview of our shape representation is given in Figure 1. Our technique defines a multiscale parametric model of surfaces belonging to the same population using a compact set of spherical wavelets targeted to that population (Figure 2). We further refine the shape representation by separating into groups wavelet coefficients that describe independent global and/or local biological variations in the population, using spectral graph partitioning. We then learn a prior probability distribution induced over each group to explicitly encode these variations at different scales and spatial locations (Figure 4) [1].

=== Segmentation ===
Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior for segmentation. Additionally, the optimization method can be applied in a coarse-to-fine manner.

=== Results ===
We applied our algorithm to the caudate nucleus, a brain structure of interest in the study of schizophrenia [2]. Our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model (ASM) algorithm, by capturing finer shape details.

== References ==
* [1] Nain D, Haker S, Bobick A, Tannenbaum A. Multiscale 3D Shape Analysis using Spherical Wavelets. Proc MICCAI, Oct 26-29 2005; p 459-467 [1]
* [2] Nain D, Haker S, Bobick A, Tannenbaum A. Shape-driven 3D Segmentation using Spherical Wavelets. Proc MICCAI, Oct 2-5, 2006. PDF of paper

== Key Investigators ==
* Core 1:
** Georgia Tech: Delphine Nain, Aaron Bobick, Allen Tannenbaum
** Harvard SPL: Steven Haker

== Collaborators ==

* Core 1: Martin Styner (UNC)
* Core 2: Jim Miller (GE), Luis Ibanez (Kitware)
* Core 3: James Levitt, Marc Niethammer, Sylvain Bouix, Martha Shenton (Harvard PNL)

== Links: ==
* Paper presented in [[MICCAI_2006|MICCAI 2006, Copenhagen, October 2 - 4, 2006 ]]
* Code: ITK Spherical Wavelet Transform Filter
* [[Algorithm:GATech|Georgia Tech Summary Page]]
* [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

Projects:MultiscaleShapeSegmentation

2006-12-22T17:09:31Z

Delphine: /* Links: */

== Objective ==
To represent multiscale variations in a shape population in order to drive the segmentation of deep brain structures, such as the caudate nucleus or the hippocampus.

== Overview ==

=== Shape Representation and Prior ===
The overview of our shape representation is given in Figure 1. Our technique defines a multiscale parametric model of surfaces belonging to the same population using a compact set of spherical wavelets targeted to that population (Figure 2). We further refine the shape representation by separating into groups wavelet coefficients that describe independent global and/or local biological variations in the population, using spectral graph partitioning. We then learn a prior probability distribution induced over each group to explicitly encode these variations at different scales and spatial locations (Figure 4) [1].

=== Segmentation ===
Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior for segmentation. Additionally, the optimization method can be applied in a coarse-to-fine manner.

=== Results ===
We applied our algorithm to the caudate nucleus, a brain structure of interest in the study of schizophrenia [2]. Our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model (ASM) algorithm, by capturing finer shape details.

== References ==
* [1] Nain D, Haker S, Bobick A, Tannenbaum A. Multiscale 3D Shape Analysis using Spherical Wavelets. Proc MICCAI, Oct 26-29 2005; p 459-467 [1]
* [2] Nain D, Haker S, Bobick A, Tannenbaum A. Shape-driven 3D Segmentation using Spherical Wavelets. Proc MICCAI, Oct 2-5, 2006. PDF of paper

== Key Investigators ==
* Core 1:
** Georgia Tech: Delphine Nain, Aaron Bobick, Allen Tannenbaum
** Harvard SPL: Steven Haker

== Collaborators ==

* Core 1: Martin Styner (UNC)
* Core 2: Jim Miller (GE), Luis Ibanez (Kitware)
* Core 3: James Levitt, Marc Niethammer, Sylvain Bouix, Martha Shenton (Harvard PNL)

== Links: ==
* Paper presented in MICCAI 2006, Copenhagen, October 2 - 4, 2006
* Code: ITK Spherical Wavelet Transform Filter
* [[Algorithm:GATech|Georgia Tech Summary Page]]
* [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

Projects:MultiscaleShapeSegmentation

2006-12-22T17:08:52Z

Delphine:

== Objective ==
To represent multiscale variations in a shape population in order to drive the segmentation of deep brain structures, such as the caudate nucleus or the hippocampus.

== Overview ==

=== Shape Representation and Prior ===
The overview of our shape representation is given in Figure 1. Our technique defines a multiscale parametric model of surfaces belonging to the same population using a compact set of spherical wavelets targeted to that population (Figure 2). We further refine the shape representation by separating into groups wavelet coefficients that describe independent global and/or local biological variations in the population, using spectral graph partitioning. We then learn a prior probability distribution induced over each group to explicitly encode these variations at different scales and spatial locations (Figure 4) [1].

=== Segmentation ===
Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior for segmentation. Additionally, the optimization method can be applied in a coarse-to-fine manner.

=== Results ===
We applied our algorithm to the caudate nucleus, a brain structure of interest in the study of schizophrenia [2]. Our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model (ASM) algorithm, by capturing finer shape details.

== References ==
* [1] Nain D, Haker S, Bobick A, Tannenbaum A. Multiscale 3D Shape Analysis using Spherical Wavelets. Proc MICCAI, Oct 26-29 2005; p 459-467 [1]
* [2] Nain D, Haker S, Bobick A, Tannenbaum A. Shape-driven 3D Segmentation using Spherical Wavelets. Proc MICCAI, Oct 2-5, 2006. PDF of paper

== Key Investigators ==
* Core 1:
** Georgia Tech: Delphine Nain, Aaron Bobick, Allen Tannenbaum
** Harvard SPL: Steven Haker

== Collaborators ==

* Core 1: Martin Styner (UNC)
* Core 2: Jim Miller (GE), Luis Ibanez (Kitware)
* Core 3: James Levitt, Marc Niethammer, Sylvain Bouix, Martha Shenton (Harvard PNL)

== Links: ==

* [[Algorithm:GATech|Georgia Tech Summary Page]]
* [[NA-MIC_Collaborations|NA-MIC_Collaborations]]

Algorithm:GATech

2006-12-22T16:56:55Z

Delphine: /* Multiscale Shape Analysis */

= Current Projects =

== Segmentation ==

=== [[Algorithm:GATech:Multiscale_Shape_Segmentation|Multiscale Shape Segmentation Techniques]] ===

To represent multiscale variations in a shape population in order to drive the segmentation of deep brain structures, such as the caudate nucleus or the hippocampus.

'''New: ''' Delphine Nain won the best student paper at [[MICCAI_2006|MICCAI 2006]] in the category "Segmentation and Registration" for her paper entitled "Shape-driven surface segmentation using spherical wavelets" by D. Nain, S. Haker, A. Bobick, A. Tannenbaum.

=== [[Algorithm:GATech:Rule_Based_Segmentation|Rule-Based Segmentation Techniques]] ===

In this work, we provide software to semi-automate the implementation of segmentation procedures based on expert neuroanatomist rules.

'''New: ''' Al-Hakim, et al. Parcellation of the Striatum. SPIE MI 2007.

=== [[Algorithm:GATech:KPCA_Segmentation|Kernel PCA for Segmentation]] ===

Segmentation performances using active contours can be drastically improved if the possible shapes of the object of interest are learnt. The goal of this work is to use Kernel PCA to learn shape priors. Kernel PCA allows for learning non linear dependencies in data sets, leading to more robust shape priors.

'''New: ''' S. Dambreville, Y. Rathi, and A. Tannenbaum. A Framework for Image Segmentation using Image Shape Models and Kernel PCA Shape Priors. PAMI. Submitted to PAMI.

=== [[Algorithm:GATech:Blood_Vessel_Segmentation|Blood Vessel Segmentation]] ===

The goal of this work is to develop blood vessel segmentation techniques for 3D MRI and CT data. The methods have been applied to coronary arteries and portal veins, with promising results.

'''New: '''Y. Yang, S. George, D. Martin, A. Tannenbaum, and D. Giddens. 3D Modeling of Patient-Specific Geometries of Portal Veins Using MR Images. In Proceedings IEEE EMBS, 2006

=== [[Algorithm:GATech:Knowledge_Based_Bayesian_Segmentation|Knowledge-Based Bayesian Segmentation]] ===

This ITK filter is a segmentation algorithm that utilizes Bayes's Rule along with an affine-invariant anisotropic smoothing filter.

'''New: ''' J. Melonakos, K. Krishnan, and A. Tannenbaum. An ITK Filter for Bayesian Segmentation: itkBayesianClassifierImageFilter. Insight Journal, 2006.

=== [[Algorithm:GATech:Stochastic_Methods_Segmentation|Stochastic Methods for Segmentation]] ===

New stochastic methods for implementing curvature driven flows for various medical tasks such as segmentation.

'''New: ''' Currently under investigation.

== Registration ==

=== [[Algorithm:GATech:Conformal_Flattening_Registration|Conformal Flattening]] ===

The goal of this project is for better visualizing and computation of neural activity from fMRI brain imagery. Also, with this technique, shapes can be mapped to shperes for shape analysis, registration or other purposes. Our technique is based on conformal mappings which map genus-zero surface: in fmri case cortical or other surfaces, onto a sphere in an angle preserving manner.

'''New: ''' Y. Gao, J. Melonakos, and A. Tannenbaum. Conformal Flattening ITK Filter. ISC/NA-MIC Workshop on Open Science at MICCAI 2006.

=== [[Algorithm:GATech:Optimal_Mass_Transport_Registration|Optimal Mass Transport Registration]] ===

The goal of this project is to implement a computationaly efficient Elastic/Non-rigid Registration algorithm based on the Monge-Kantorovich theory of optimal mass transport for 3D Medical Imagery. Our technique is based on Multigrid and Multiresolution techniques. This method is particularly useful because it is parameter free and utilizes all of the grayscale data in the image pairs in a symmetric fashion and no landmarks need to be specified for correspondence.

'''New: ''' Tauseef ur Rehman, A. Tannenbaum. Multigrid Optimal Mass Transport for Image Registration and Morphing. Accepted for SPIE Conference on Computational Imaging, Jan 2007.

== DWI Processing ==

=== [[Algorithm:GATech:Finsler_Active_Contour_DWI|Finsler Active Contour DWI Tractography]] ===

In this work, we provide an energy minimization framework which allows one to find optimal curves in direction-dependent data (i.e. where the cost associated with the curve depends both upon its position and orientation)

'''New: ''' E. Pichon, J. Melonakos, S. Angenet, A. Tannenbaum. Publication currently under review.

== Shape Analysis ==

=== [[Algorithm:GATech:Multiscale_Shape_Analysis|Multiscale Shape Analysis]] ===

We present a novel method of statistical surface-based morphometry based on the use of non-parametric permutation tests and a spherical wavelet (SWC) shape representation.

'''New: ''' D. Nain, M. Styner, M. Niethammer, J. J. Levitt, M E Shenton, G Gerig, A. Bobick, A. Tannenbaum. Statistical Shape Analysis of Brain Structures using Spherical Wavelets. Submitted to ISBI 2007.

=== [[Algorithm:GATech:Centerline_Generation_for_Vessels|Centerline Generation for Vessels]] ===

The goal of this work is to generate centerlines from segmented 3D surfaces of blood vessels using a harmonic skeletonization technique. The generated centerlines are used as a guide to visualize and evaluate stenoses in human coronary arteries.

=== [[Algorithm:GATech:KPCA_LLE_KLLE_Shape_Analysis|KPCA, LLE, KLLE Shape Analysis]] ===

The goal of this work is to study and compare shape learning techniques. The techniques considered are Linear Principal Components Analysis (PCA), Kernel PCA, Locally Linear Embedding (LLE) and Kernel LLE.

 

= Completed Projects =

== Segmentation ==

=== [[Algorithm:GATech:Fast_Marching_Slicer_2|Fast Marching Slicer 2 Module]] ===

The Fast Marching Algorithm was added as a module to Slicer 2.

=== [[Algorithm:GATech:Statistical_Segmentation_Slicer_2|Statistical/PDE Methods for Segmentation]] ===

This flow was added to Slicer 2.

=== [[Algorithm:GATech:Image_Smooth_Slicer_2|Image Smooth Slicer 2 Module]] ===

2D and 3D smoothing of images.

=== [[Algorithm:Affine_Segment_Slicer_2|Affine Segment Slicer 2 Module]] ===

This module can be used to perform edge based segmentation.