Bayesian estimation of templates in computational anatomy: Difference between revisions

Revision as of 03:34, 16 November 2019

Revision as of 19:28, 25 January 2020

Line 68:

== Surface templates for computational neuroanatomy and subcortical structures ==

The study of sub-cortical neuroanatomy has been the focus of many studies. Since the original publications by Csernansky and colleagues of hippocampal change in Schizophrenia,<ref>{{Cite journal|last=Csernansky|first=John G.|last2=Joshi|first2=Sarang|last3=Wang|first3=Lei|last4=Haller|first4=John W.|last5=Gado|first5=Mokhtar|last6=Miller|first6=J. Philip|last7=Grenander|first7=Ulf|last8=Miller|first8=Michael I.|date=1998-09-15|title=Hippocampal morphometry in schizophrenia by high dimensional brain mapping|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=95|issue=19|pages=11406–11411|issn=0027-8424|pmc=21655|pmid=9736749|doi=10.1073/pnas.95.19.11406|bibcode=1998PNAS...9511406C}}</ref><ref>{{Cite journal|last=Csernansky|first=John G.|last2=Wang|first2=Lei|last3=Jones|first3=Donald|last4=Rastogi-Cruz|first4=Devna|last5=Posener|first5=Joel A.|last6=Heydebrand|first6=Gitry|last7=Miller|first7=J. Philip|last8=Miller|first8=Michael I.|date=2002-12-01|title=Hippocampal deformities in schizophrenia characterized by high dimensional brain mapping|journal=The American Journal of Psychiatry|volume=159|issue=12|pages=2000–2006|doi=10.1176/appi.ajp.159.12.2000|issn=0002-953X|pmid=12450948|url=https://semanticscholar.org/paper/30c54ba2eba1be26e44f38a24b4cb0ee61c1e2d0}}</ref><ref>{{Cite journal|last=Wang|first=L.|last2=Joshi|first2=S. C.|last3=Miller|first3=M. I.|last4=Csernansky|first4=J. G.|date=2001-09-01|title=Statistical analysis of hippocampal asymmetry in schizophrenia|journal=NeuroImage|volume=14|issue=3|pages=531–545|doi=10.1006/nimg.2001.0830|issn=1053-8119|pmid=11506528|url=https://semanticscholar.org/paper/714b1cf37708e377294c05f68187123d355393e1}}</ref><ref>{{Cite journal|last=Csernansky|first=John G.|last2=Schindler|first2=Mathew K.|last3=Splinter|first3=N. Reagan|last4=Wang|first4=Lei|last5=Gado|first5=Mohktar|last6=Selemon|first6=Lynn D.|last7=Rastogi-Cruz|first7=Devna|last8=Posener|first8=Joel A.|last9=Thompson|first9=Paul A.|date=2004-05-01|title=Abnormalities of thalamic volume and shape in schizophrenia|journal=The American Journal of Psychiatry|volume=161|issue=5|pages=896–902|doi=10.1176/appi.ajp.161.5.896|issn=0002-953X|pmid=15121656}}</ref> Alzheimer's disease,<ref>{{Cite journal|last=Csernansky|first=J. G.|last2=Wang|first2=L.|last3=Swank|first3=J.|last4=Miller|first4=J. P.|last5=Gado|first5=M.|last6=McKeel|first6=D.|last7=Miller|first7=M. I.|last8=Morris|first8=J. C.|date=2005-04-15|title=Preclinical detection of Alzheimer's disease: hippocampal shape and volume predict dementia onset in the elderly|journal=NeuroImage|volume=25|issue=3|pages=783–792|doi=10.1016/j.neuroimage.2004.12.036|issn=1053-8119|pmid=15808979}}</ref><ref>{{Cite journal|last=Wang|first=Lei|last2=Miller|first2=J. Philp|last3=Gado|first3=Mokhtar H.|last4=McKeel|first4=Daniel W.|last5=Rothermich|first5=Marcus|last6=Miller|first6=Michael I.|last7=Morris|first7=John C.|last8=Csernansky|first8=John G.|date=2006-03-01|title=Abnormalities of hippocampal surface structure in very mild dementia of the Alzheimer type|journal=NeuroImage|volume=30|issue=1|pages=52–60|doi=10.1016/j.neuroimage.2005.09.017|issn=1053-8119|pmc=2853193|pmid=16243546}}</ref><ref>{{Cite journal|last=Wang|first=Lei|last2=Swank|first2=Jeffrey S.|last3=Glick|first3=Irena E.|last4=Gado|first4=Mokhtar H.|last5=Miller|first5=Michael I.|last6=Morris|first6=John C.|last7=Csernansky|first7=John G.|date=2003-10-01|title=Changes in hippocampal volume and shape across time distinguish dementia of the Alzheimer type from healthy aging|journal=NeuroImage|volume=20|issue=2|pages=667–682|doi=10.1016/S1053-8119(03)00361-6|issn=1053-8119|pmid=14568443}}</ref> and Depression,<ref>{{Cite journal|last=Posener|first=Joel A.|last2=Wang|first2=Lei|last3=Price|first3=Joseph L.|last4=Gado|first4=Mokhtar H.|last5=Province|first5=Michael A.|last6=Miller|first6=Michael I.|last7=Babb|first7=Casey M.|last8=Csernansky|first8=John G.|date=2003-01-01|title=High-dimensional mapping of the hippocampus in depression|journal=The American Journal of Psychiatry|volume=160|issue=1|pages=83–89|doi=10.1176/appi.ajp.160.1.83|issn=0002-953X|pmid=12505805|url=https://semanticscholar.org/paper/c41b54f30f1fa0662fce739b8828826f0b02e979}}</ref><ref>{{Cite journal|last=Munn|first=Melissa A.|last2=Alexopoulos|first2=Jim|last3=Nishino|first3=Tomoyuki|last4=Babb|first4=Casey M.|last5=Flake|first5=Lisa A.|last6=Singer|first6=Tisha|last7=Ratnanather|first7=J. Tilak|last8=Huang|first8=Hongyan|last9=Todd|first9=Richard D.|date=2007-09-01|title=Amygdala Volume Analysis in Female Twins with Major Depression|journal=Biological Psychiatry|volume=62|issue=5|pages=415–422|doi=10.1016/j.biopsych.2006.11.031|issn=0006-3223|pmc=2904677|pmid=17511971}}</ref> many neuroanatomical shape statistical studies have now been completed using templates built from all of the subcortical structures for depression,<ref>{{Cite web|url=https://www.researchgate.net/publication/271515359|title=Amygdala and Hippocampal in ADHD: Volumetric and Morphometric Analysis and Relation to Mood Symptoms.|website=ResearchGate|access-date=2016-03-22}}</ref> Alzheimer's,<ref name="Tang 599–611"/><ref name="Tang 2093–2117"/><ref>{{Cite journal|last=Qiu|first=Anqi|last2=Fennema-Notestine|first2=Christine|last3=Dale|first3=Anders M.|last4=Miller|first4=Michael I.|date=2009-04-15|title=Regional shape abnormalities in mild cognitive impairment and Alzheimer's disease|journal=NeuroImage|volume=45|issue=3|pages=656–661|issn=1053-8119|pmc=2847795|pmid=19280688|doi=10.1016/j.neuroimage.2009.01.013}}</ref><ref>{{Cite journal|last=Qiu|first=Anqi|last2=Younes|first2=Laurent|last3=Miller|first3=Michael I.|last4=Csernansky|first4=John G.|date=2008-03-01|title=Parallel Transport in Diffeomorphisms Distinguishes the Time-Dependent Pattern of Hippocampal Surface Deformation due to Healthy Aging and the Dementia of the Alzheimer's Type|journal=NeuroImage|volume=40|issue=1|pages=68–76|doi=10.1016/j.neuroimage.2007.11.041|issn=1053-8119|pmc=3517912|pmid=18249009}}</ref><ref>{{Cite journal|last=Miller|first=Michael I.|last2=Younes|first2=Laurent|last3=Ratnanather|first3=J. Tilak|last4=Brown|first4=Timothy|last5=Reigel|first5=Tommy|last6=Trinh|first6=Huong|last7=Tang|first7=Xiaoying|last8=Barker|first8=Peter|last9=Mori|first9=Susumu|date=2012-10-01|title=Amygdala Atrophy in MCI/Alzheimer's Disease in the BIOCARD cohort based on Diffeomorphic Morphometry|journal=Medical Image Computing and Computer-assisted Intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention|volume=2012|pages=155–166|pmc=4063307|pmid=24955432}}</ref><ref>{{Cite journal|last=Miller|first=Michael I.|last2=Ratnanather|first2=J. Tilak|last3=Tward|first3=Daniel J.|last4=Brown|first4=Timothy|last5=Lee|first5=David S.|last6=Ketcha|first6=Michael|last7=Mori|first7=Kanami|last8=Wang|first8=Mei-Cheng|author8-link= Mei-Cheng Wang |last9=Mori|first9=Susumu|date=2015-01-01|title=Network neurodegeneration in Alzheimer's disease via MRI based shape diffeomorphometry and high-field atlasing|journal= Frontiers in Bioengineering and Biotechnology|pages=54|doi=10.3389/fbioe.2015.00054|pmc=4515983|pmid=26284236|volume=3}}</ref> Bipolar disorder, ADHD,<ref>{{Cite journal|last=Qiu|first=Anqi|last2=Crocetti|first2=Deana|last3=Adler|first3=Marcy|last4=Mahone|first4=E. Mark|last5=Denckla|first5=Martha B.|last6=Miller|first6=Michael I.|last7=Mostofsky|first7=Stewart H.|date=2009-01-01|title=Basal Ganglia Volume and Shape in Children With Attention Deficit Hyperactivity Disorder|journal=The American Journal of Psychiatry|volume=166|issue=1|pages=74–82|doi=10.1176/appi.ajp.2008.08030426|issn=0002-953X|pmc=2890266|pmid=19015232}}</ref> autism,<ref>{{Cite journal|url=http://www.jaacap.com/article/S0890-8567(10)00248-0/abstract|title=Basal Ganglia Shapes Predict Social, Communication, and Motor Dysfunctions in Boys With Autism Spectrum Disorder - Journal of the American Academy of Child & Adolescent Psychiatry|volume=49|issue=6|pages=539–51, 551.e1–4|journal=Journal of the American Academy of Child and Adolescent Psychiatry|access-date=2016-03-22|pmid=20494264|year=2010|last1=Qiu|first1=A.|last2=Adler|first2=M.|last3=Crocetti|first3=D.|last4=Miller|first4=M. I.|last5=Mostofsky|first5=S. H.|doi=10.1016/j.jaac.2010.02.012}}</ref> and Huntington's Disease.<ref>{{Cite journal|last=Younes|first=Laurent|last2=Ratnanather|first2=J. Tilak|last3=Brown|first3=Timothy|last4=Aylward|first4=Elizabeth|last5=Nopoulos|first5=Peg|last6=Johnson|first6=Hans|last7=Magnotta|first7=Vincent A.|last8=Paulsen|first8=Jane S.|last9=Margolis|first9=Russell L.|date=2014-03-01|title=Regionally selective atrophy of subcortical structures in prodromal HD as revealed by statistical shape analysis|journal=Human Brain Mapping|volume=35|issue=3|pages=792–809|doi=10.1002/hbm.22214|issn=1097-0193|pmc=3715588|pmid=23281100}}</ref><ref>{{Cite journal|url=http://f1000research.com/posters/1096125|title=f1000research.com/posters/1096125|journal=F1000Research|volume=5|doi=10.7490/f1000research.1096125.1|access-date=2016-03-22|date=2014-07-18|last1=Miller|first1=Michael|last2=Younes|first2=Laurent|last3=Mori|first3=Susumu|last4=Ross|first4=Christopher|last5=Ratnanather|first5=Tilak|last6=Faria|first6=Andreia|last7=Noort|first7=Frieda van den|last8=Van Den Noort|first8=Frieda|last9=Faria|first9=Andreia|last10=Ratnanather|first10=Tilak|last11=Ross|first11=Christopher|last12=Mori|first12=Susumu|last13=Younes|first13=Laurent|last14=Miller|first14=Michael|doi-broken-date=20192020-1101-1125}}</ref> Templates were generated using Bayesian template estimation data back to Ma, Younes and Miller.<ref>{{Cite journal|last=Ma|first=Jun|last2=Miller|first2=Michael I.|last3=Younes|first3=Laurent|date=2010-01-01|title=A Bayesian Generative Model for Surface Template Estimation|journal=International Journal of Biomedical Imaging|volume=2010|doi=10.1155/2010/974957|issn=1687-4188|pmc=2946602|pmid=20885934|pages=1–14}}</ref>

Shown in the accompanying Figure is an example of subcortical structure templates generated from T1-weighted [[Magnetic resonance imaging|magnetic resonance imagery]] by Tang et al.<ref name="Tang 599–611"/><ref name="Tang 2093–2117"/><ref name="Tang 645–660"/> for the study of Alzheimer's disease in the ADNI population of subjects.

Line 74:

== Surface estimation in cardiac computational anatomy ==

[[File:Siamak atlas.tif|alt=Showing population heart atlases with superimposed hypertrophy.|thumb|Showing population atlases identifying regional differences in radial thickness at end-systolic cardiac phase between patients with hypertrophic cardiomyopathy (left) and hypertensive heart disease (right). Gray mesh shows the common surface template to the population, with the color map representing basilar septal and anterior epicardial wall with larger radial thickness in patients with hypertrophic cardiomyopathy vs. hypertensive heart disease.<ref name="Semantic Scholar">{{Cite web|url=https://www.semanticscholar.org/paper/Shape-analysis-of-hypertrophic-and-hypertensive-Ardekani-Jain/4073fc2af6ef7fb978d5203be3e84c999e1a0dbd|title=Semantic Scholar|website=www.semanticscholar.org|language=en-US|access-date=2016-04-05}}{{Dead link|date=October 2019 |bot=InternetArchiveBot |fix-attempted=yes }}</ref>]]

Numerous studies have now been done on cardiac hypertrophy and the role of the structural integraties in the functional mechanics of the heart. Siamak Ardekani has been working on populations of Cardiac anatomies reconstructing atlas coordinate systems from populations.<ref>{{Cite journal|last=Ardekani|first=Siamak|last2=Weiss|first2=Robert G.|last3=Lardo|first3=Albert C.|last4=George|first4=Richard T.|last5=Lima|first5=Joao A. C.|last6=Wu|first6=Katherine C.|last7=Miller|first7=Michael I.|last8=Winslow|first8=Raimond L.|last9=Younes|first9=Laurent|date=2009-06-01|title=Computational method for identifying and quantifying shape features of human left ventricular remodeling|journal=Annals of Biomedical Engineering|volume=37|issue=6|pages=1043–1054|doi=10.1007/s10439-009-9677-2|issn=1573-9686|pmc=2819012|pmid=19322659}}</ref><ref>{{Cite journal|last=Steinert-Threlkeld|first=Shane|last2=Ardekani|first2=Siamak|last3=Mejino|first3=Jose L. V.|last4=Detwiler|first4=Landon Todd|last5=Brinkley|first5=James F.|last6=Halle|first6=Michael|last7=Kikinis|first7=Ron|last8=Winslow|first8=Raimond L.|last9=Miller|first9=Michael I.|date=2012-06-01|title=Ontological labels for automated ___location of anatomical shape differences|journal=Journal of Biomedical Informatics|volume=45|issue=3|pages=522–527|doi=10.1016/j.jbi.2012.02.013|issn=1532-0480|pmc=3371096|pmid=22490168}}</ref><ref>{{Cite book |doi=10.1109/EMBC.2014.6944772|issn=1557-170X|pmc=4474039|pmid=25571140|isbn=978-1-4244-7929-0|chapter=Estimating dense cardiac 3D motion using sparse 2D tagged MRI cross-sections|title=2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society e|journal=Engineering in Medicine and Biology Society, 2008. Embs 2008. 30Th Annual International Conference of the IEEE|volume=2014|pages=5101–5104|year=2014|last1=Ardekani|first1=Siamak|last2=Gunter|first2=Geoffrey|last3=Jain|first3=Saurabh|last4=Weiss|first4=Robert G.|last5=Miller|first5=Michael I.|last6=Younes|first6=Laurent}}</ref> The figure on the right shows the computational cardiac anatomy method being used to identify regional differences in radial thickness at end-systolic cardiac phase between patients with hypertrophic cardiomyopathy (left) and hypertensive heart disease (right). Color map that is placed on a common surface template (gray mesh) represents region ( basilar septal and the anterior epicardial wall) that has on average significantly larger radial thickness in patients with hypertrophic cardiomyopathy vs. hypertensive heart disease (reference below).<ref name="Semantic Scholar"/>

== MAP Estimation of volume templates from populations and the EM algorithm ==