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FastSurfer-HypVINN: Automated sub-segmentation of the hypothalamus and adjacent structures on high-resolutional brain MRI [article]

Santiago Estrada, David Kügler, Emad Bahrami, Peng Xu, Dilshad Mousa, Monique M.B. Breteler, N. Ahmad Aziz, Martin Reuter
2023 arXiv   pre-print

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2023 accepted doi:10.1162/imag_a_00034 arXiv:2308.12736v2 fatcat:v2i3ydaq4nhybgyirx5ch4rlxy
While the only previous attempt to automatically sub-segment the hypothalamus with a neural network showed promise for 1.0 mm isotropic T1-weighted (T1w) MRI, there is a need for an automated tool to sub-segment  ...  We, therefore, introduce a novel, fast, and fully automated deep learning method named HypVINN for sub-segmentation of the hypothalamus and adjacent structures on 0.8 mm isotropic T1w and T2w brain MR  ...  These multi-modal protocols recommend segmenting the hypothalamus using simultaneous visualization of registered T1-weighted (T1w) and T2-weighted (T2w) MR images.  ... 
arXiv:2308.12736v1 fatcat:llxmpqyowzcmbd7ly42pku4cny
Open Access Multiple Versions
Citation

Santiago Estrada, David Kügler, Emad Bahrami, Peng Xu, Dilshad Mousa, Monique M.B. Breteler, N. Ahmad Aziz, Martin Reuter. "FastSurfer-HypVINN: Automated sub-segmentation of the hypothalamus and adjacent structures on high-resolutional brain MRI." arXiv (2023)

Development and Evaluation of an Algorithm for the Computer-Assisted Segmentation of the Human Hypothalamus on 7-Tesla Magnetic Resonance Images

Stephanie Schindler, Peter Schönknecht, Laura Schmidt, Alfred Anwander, Maria Strauß, Robert Trampel, Pierre-Louis Bazin, Harald E. Möller, Ulrich Hegerl, Robert Turner, Stefan Geyer, Wang Zhan
2013 PLoS ONE  

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We present a computer-assisted algorithm for the manual segmentation of the human hypothalamus using T1-weighted 7T magnetic resonance imaging.  ...  A detailed segmentation algorithm (unilateral hypothalamus) was developed for colour-coded, histogram-matched images, and evaluated in a sample of 10 subjects.  ...  [23] , we have developed a detailed segmentation algorithm for the hypothalamus on 7T MR images.  ... 
doi:10.1371/journal.pone.0066394 pmid:23935821 pmcid:PMC3720799 fatcat:pkg5dv57dvew3l4yxmejwtupju
DOAJ
Citation

Stephanie Schindler, Peter Schönknecht, Laura Schmidt, Alfred Anwander, Maria Strauß, Robert Trampel, Pierre-Louis Bazin, Harald E. Möller, Ulrich Hegerl, Robert Turner, Stefan Geyer, Wang Zhan. "Development and Evaluation of an Algorithm for the Computer-Assisted Segmentation of the Human Hypothalamus on 7-Tesla Magnetic Resonance Images." PLoS ONE 8.7 (2013) e66394

Hypothalamus enlargement in mood disorders

S. Schindler, L. Schmidt, M. Stroske, M. Storch, A. Anwander, R. Trampel, M. Strauß, U. Hegerl, S. Geyer, P. Schönknecht
2018 Acta Psychiatrica Scandinavica  

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Focus When the setting sun can't shine, The broken moon won't glow, And in a lone ant's shadow Myriads more long gone Vie for glory on and on Step out, Son of Man, breathe in.  ...  In vivo Strukturveränderungen des Hypothalamus bei uni-und bipolaren affektiven Störungen Als Kopf der Hypothalamus-Hypophysen-Nebennierenrinden-Achse spielt der Hypothalamus eine Schlüsselrolle für die  ...  Acknowledgements We are most grateful to Professor Ulrich Hegerl for stimulating discussions and for his longstanding support.  ... 
doi:10.1111/acps.12958 pmid:30229855 fatcat:tttmtyclcrazxho2gklyabnhgq
Citation

S. Schindler, L. Schmidt, M. Stroske, M. Storch, A. Anwander, R. Trampel, M. Strauß, U. Hegerl, S. Geyer, P. Schönknecht. "Hypothalamus enlargement in mood disorders." Acta Psychiatrica Scandinavica 139.1 (2018)

Multi-Coil MRI Reconstruction Challenge – Assessing Brain MRI Reconstruction Models and their Generalizability to Varying Coil Configurations [article]

Youssef Beauferris, Jonas Teuwen, Dimitrios Karkalousos, Nikita Moriakov, Mattha Caan, George Yiasemis, Lívia Rodrigues, Alexandre Lopes, Hélio Pedrini, Letícia Rittner, Maik Dannecker, Viktor Studenyak (+11 others)
2021 arXiv   pre-print

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2020 pre-print
arXiv:2011.07952v1 fatcat:nhocfkmpvvggzpluf5kectzhei
The Multi-Coil Magnetic Resonance Image (MC-MRI) Reconstruction Challenge provides a benchmark that aims at addressing these issues, using a large dataset of high-resolution, three-dimensional, T1-weighted  ...  The challenge has two primary goals: 1) to compare different MRI reconstruction models on this dataset and 2) to assess the generalizability of these models to data acquired with a different number of  ...  The organizers of the challenge also acknowledge Nvidia for providing a Titan V graphics processing unit and Amazon Web Services for providing computational infra-structure that was used by some of the  ... 
arXiv:2011.07952v2 fatcat:t55wnasrpveuzio2kfne756fhq
Multiple Versions
Citation

Youssef Beauferris, Jonas Teuwen, Dimitrios Karkalousos, Nikita Moriakov, Mattha Caan, George Yiasemis, Lívia Rodrigues, Alexandre Lopes, Hélio Pedrini, Letícia Rittner, Maik Dannecker, Viktor Studenyak, Fabian Gröger, Devendra Vyas, Shahrooz Faghih-Roohi, Amrit Kumar Jethi, Jaya Chandra Raju, Mohanasankar Sivaprakasam, Mike Lasby, Nikita Nogovitsyn, Wallace Loos, Richard Frayne, Roberto Souza. "Multi-Coil MRI Reconstruction Challenge – Assessing Brain MRI Reconstruction Models and their Generalizability to Varying Coil Configurations." arXiv (2021)

A practical Alzheimer's disease classifier via brain imaging-based deep learning on 85,721 samples

Bin Lu, Hui-Xian Li, Zhi-Kai Chang, Le Li, Ning-Xuan Chen, Zhi-Chen Zhu, Hui-Xia Zhou, Xue-Ying Li, Yu-Wei Wang, Shi-Xian Cui, Zhao-Yu Deng, Zhen Fan (+5 others)
2022 Journal of Big Data  

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The sex classifier achieved 94.9% accuracy and served as a base model in transfer learning for the objective diagnosis of AD.  ...  Therefore, we built a practical brain MRI-based AD diagnostic classifier using deep learning/transfer learning on a dataset of unprecedented size and diversity.  ...  All 50,876 participants (contributing 85,721 samples) had at least one session with a T1-weighted structural brain image and information on their sex and age.  ... 
doi:10.1186/s40537-022-00650-y fatcat:t3jkxmdrwjhtzk2zknamqe2mre
DOAJ Szczepanski
Citation

Bin Lu, Hui-Xian Li, Zhi-Kai Chang, Le Li, Ning-Xuan Chen, Zhi-Chen Zhu, Hui-Xia Zhou, Xue-Ying Li, Yu-Wei Wang, Shi-Xian Cui, Zhao-Yu Deng, Zhen Fan, Hong Yang, Xiao Chen, Paul M. Thompson, Francisco Xavier Castellanos, Chao-Gan Yan. "A practical Alzheimer's disease classifier via brain imaging-based deep learning on 85,721 samples." Journal of Big Data 9.1 (2022)

Manually segmented template library for 8-year-old pediatric brain MRI data with 16 subcortical structures

Amanmeet Garg, Darren Wong, Karteek Popuri, Kenneth J. Poskitt, Kevin Fitzpatrick, Bruce Bjornson, Ruth E. Grunau, Mirza Faisal Beg
2014 Journal of Medical Imaging  

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A manually delineated pediatric template library such as the one described here could provide a useful benchmark for testing segmentation algorithms.  ...  labels onto the unlabeled MRI images.  ...  R01 HD039783 to R.E.G., We would like to thank Ivan Cepeda and Gisela Gosse for recruitment and data collection, staff of the B.C.  ... 
doi:10.1117/1.jmi.1.3.034502 pmid:26158067 pmcid:PMC4478774 fatcat:zfn6ycecufazbfcak5ce462bbq
Citation

Amanmeet Garg, Darren Wong, Karteek Popuri, Kenneth J. Poskitt, Kevin Fitzpatrick, Bruce Bjornson, Ruth E. Grunau, Mirza Faisal Beg. "Manually segmented template library for 8-year-old pediatric brain MRI data with 16 subcortical structures." Journal of Medical Imaging 1.3 (2014) 034502

Imaging dopamine receptors in humans with [11C]-(+)-PHNO: Dissection of D3 signal and anatomy

Andri C. Tziortzi, Graham E. Searle, Sofia Tzimopoulou, Cristian Salinas, John D. Beaver, Mark Jenkinson, Marc Laruelle, Eugenii A. Rabiner, Roger N. Gunn
2011 NeuroImage  

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We present a set of anatomical guidelines for the delineation of D3 relevant ROIs including substantia nigra, hypothalamus, ventral pallidum/substantia innominata, ventral striatum, globus pallidus and  ...  Keywords: dopamine D3 receptors PET PHNO region of interest ROI ventral striatum VST ventral pallidum hypothalamus extended amygdala [ 11 C]-(+)-PHNO is a D3 preferring PET radioligand which has recently  ...  Acknowledgments The authors would like to acknowledge Charalampos Tsoumpas, Paul Shotbolt, Christopher Long, Qi Guo, and Vincent Cunningham for useful discussions and Robert Comley for his role in acquisition  ... 
doi:10.1016/j.neuroimage.2010.06.044 pmid:20600980 fatcat:pc7wpu4r2vhlrc3mo5dc6a2rd4
DOAJ
Citation

Andri C. Tziortzi, Graham E. Searle, Sofia Tzimopoulou, Cristian Salinas, John D. Beaver, Mark Jenkinson, Marc Laruelle, Eugenii A. Rabiner, Roger N. Gunn. "Imaging dopamine receptors in humans with [11C]-(+)-PHNO: Dissection of D3 signal and anatomy." NeuroImage 54.1 (2011) 264-277

Consistent cortical reconstruction and multi-atlas brain segmentation

Yuankai Huo, Andrew J. Plassard, Aaron Carass, Susan M. Resnick, Dzung L. Pham, Jerry L. Prince, Bennett A. Landman
2016 NeuroImage  

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Finally, 200 MR volumetric images from an older adult sample are used to assess the robustness of MaCRUISE and FreeSurfer.  ...  Whole brain segmentation and cortical surface reconstruction are two essential techniques for investigating the human brain.  ...  This study was also supported by NIH 5R01NS056307, 5R21NS082891 and in part using the resources of the Advanced Computing Center for Research and Education  ... 
doi:10.1016/j.neuroimage.2016.05.030 pmid:27184203 pmcid:PMC4927397 fatcat:aagizrwmujaktlmfkp7atpou2i
DOAJ
Citation

Yuankai Huo, Andrew J. Plassard, Aaron Carass, Susan M. Resnick, Dzung L. Pham, Jerry L. Prince, Bennett A. Landman. "Consistent cortical reconstruction and multi-atlas brain segmentation." NeuroImage (2016) 197-210

Imaging characteristics of H3 K27M histone-mutant diffuse midline glioma in teenagers and adults

Stefanie Thust, Caroline Micallef, Sachi Okuchi, Sebastian Brandner, Atul Kumar, Kshitij Mankad, Stephen Wastling, Laura Mancini, Hans Rolf Jäger, Ananth Shankar
2021 Quantitative Imaging in Medicine and Surgery  

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To assess anatomical and quantitative diffusion-weighted MR imaging features in a recently classified lethal neoplasm, H3 K27M histone-mutant diffuse midline glioma [World Health Organization (WHO) IV]  ...  The structural MR imaging findings varied between individuals and within tumours, often featuring signal heterogeneity on all MR sequences.  ...  and ATRX, and Ki67 on a Roche Ventana benchmark platform (21) (22) (23) .  ... 
doi:10.21037/qims-19-954 pmid:33392010 pmcid:PMC7719951 fatcat:6w4mgavvz5hova7pt52qxdnhh4
Open Access
Citation

Stefanie Thust, Caroline Micallef, Sachi Okuchi, Sebastian Brandner, Atul Kumar, Kshitij Mankad, Stephen Wastling, Laura Mancini, Hans Rolf Jäger, Ananth Shankar. "Imaging characteristics of H3 K27M histone-mutant diffuse midline glioma in teenagers and adults." Quantitative Imaging in Medicine and Surgery 11.1 (2021) 43-56

A Novel Receive-Only Liquid Nitrogen ($\hbox{LN}_{2}$ )-Cooled RF Coil for High-Resolution In Vivo Imaging on a 3-Tesla Whole-Body Scanner

Bobo Hu, Gopal Varma, Chris Randell, Stephen F. Keevil, Tobias Schaeffter, Paul Glover
2012 IEEE Transactions on Instrumentation and Measurement  

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Abstract: The design and operation of a receive-only liquid nitrogen (LN 2 ) cooled coil and cryostat suitable for medical image on 3T whole body MR scanner is presented.  ...  Paul (2012) A novel receive-only liquid nitrogen (LN2)cooled RF coil for high-resolution in vivo imaging on a 3-Tesla whole-body scanner.  ...  For the MR image experiments, micron scale high resolution MR images of small animal were obtained on a clinical whole body scanner by using this engineering solution.  ... 
doi:10.1109/tim.2011.2157575 fatcat:xivpidaalrdxlfh6xk7nw6usca
Citation

Bobo Hu, Gopal Varma, Chris Randell, Stephen F. Keevil, Tobias Schaeffter, Paul Glover. "A Novel Receive-Only Liquid Nitrogen ($\hbox{LN}_{2}$ )-Cooled RF Coil for High-Resolution In Vivo Imaging on a 3-Tesla Whole-Body Scanner." IEEE Transactions on Instrumentation and Measurement 61.1 (2012) 129-139

What is new in computer vision and artificial intelligence in medical image analysis applications

Jimena Olveres, Germán González, Fabian Torres, José Carlos Moreno-Tagle, Erik Carbajal-Degante, Alejandro Valencia-Rodríguez, Nahum Méndez-Sánchez, Boris Escalante-Ramírez
2021 Quantitative Imaging in Medicine and Surgery  

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We show how both areas have resulted in a large variety of methods that range from enhancement, detection, segmentation and characterizations of anatomical structures and lesions to complete systems that  ...  However, these imaging modalities also impose important limitations to the design of automatic image analysis systems for diagnosis aid due to their inherent characteristics such as signal to noise ratio  ...  (90) which provides a set of algorithms to segment the whole brain from T1-weighted images.  ... 
doi:10.21037/qims-20-1151 fatcat:mgzndm34bfcofdngnrzdvw5kyq
Open Access
Citation

Jimena Olveres, Germán González, Fabian Torres, José Carlos Moreno-Tagle, Erik Carbajal-Degante, Alejandro Valencia-Rodríguez, Nahum Méndez-Sánchez, Boris Escalante-Ramírez. "What is new in computer vision and artificial intelligence in medical image analysis applications." Quantitative Imaging in Medicine and Surgery 11.8 (2021) 3830-3853

A - Postgraduate Educational Programme

2010 Insights into Imaging  

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A S39 C B D E F G The majority of metastases are bright on T2-weighted and iso-or hypo-intense in liver on T1-weighted MR images. Desmoplastic reaction may render a metastasis dark at MRI.  ...  resulting in a homogeneous high-signal intensity on heavily T1-weighted 3D gradient echo images.  ...  Diffusion-weighted MR sequences can also help for that purpose.  ... 
doi:10.1007/s13244-010-0010-2 pmid:23099630 pmcid:PMC3534349 fatcat:5fiszmj5unftrhizcn3encksgy
DOAJ
Citation

"A - Postgraduate Educational Programme." Insights into Imaging 1.S1 (2010) 1-126

Postgraduate Educational Programme

2008 European Radiology Supplements  

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A S39 C B D E F G The majority of metastases are bright on T2-weighted and iso-or hypo-intense in liver on T1-weighted MR images. Desmoplastic reaction may render a metastasis dark at MRI.  ...  resulting in a homogeneous high-signal intensity on heavily T1-weighted 3D gradient echo images.  ...  Diffusion-weighted MR sequences can also help for that purpose.  ... 
doi:10.1007/s10406-008-0001-2 fatcat:gzbh2ky3enhabmfr7tz42qqqwi
Citation

"Postgraduate Educational Programme." European Radiology Supplements 18.S1 (2008) 1-136

Postgraduate Educational Programme

2009 European Radiology  

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A S39 C B D E F G The majority of metastases are bright on T2-weighted and iso-or hypo-intense in liver on T1-weighted MR images. Desmoplastic reaction may render a metastasis dark at MRI.  ...  resulting in a homogeneous high-signal intensity on heavily T1-weighted 3D gradient echo images.  ...  Diffusion-weighted MR sequences can also help for that purpose.  ... 
doi:10.1007/s00330-009-1374-x pmid:19288110 fatcat:blzt6eohybeqjngnpyzlw7un6a
Citation

"Postgraduate Educational Programme." European Radiology 19.S1 (2009) 1-136

A postgraduate educational programme

2002 European Radiology  

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A S39 C B D E F G The majority of metastases are bright on T2-weighted and iso-or hypo-intense in liver on T1-weighted MR images. Desmoplastic reaction may render a metastasis dark at MRI.  ...  resulting in a homogeneous high-signal intensity on heavily T1-weighted 3D gradient echo images.  ...  Diffusion-weighted MR sequences can also help for that purpose.  ... 
doi:10.1007/s00330-002-0001-x fatcat:swpi4r6hzrgozpfxwqgz55bmvi
Citation

"A postgraduate educational programme." European Radiology 12.S1 (2002) 3-104

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