See my Open Science Framework page for all papers, posters, proposals, and presentations or Google Scholar for some of my publications.

LM Alexander, J Escalera, L Ai, C Andreotti, K Febre, A Mangone, NV Potler, N Langer, A Alexander, M Kovacs, S Litke, B O'Hagan, B Bronstein, A Bui, M Bushey, V Castagna, N Camacho, E Chan, D Citera, J Clucas, S Cohen, M Eaves, B Fradera, N Grant-Villegas, G Green, C Gregory, E Hart, S Harris, C Lord, D Kahn, K Kabotyanski, K Kleinman, B Koo, E Kramer, A Margolis, KR Merikangas, J Milham, G Minniti, R Neuhaus, A Nussbaum, Y Osman, LC Parra, KR Pugh, A Racanello, A Restrepo, T Saltzman, B Septimus, R Tobe, R Waltz, A Williams, A Yeo, FX Castellanos, A Klein, T Paus, BL Leventhal, RC Craddock, HS Koplewicz, MP Milham. 2017.
The Healthy Brain Network Biobank: An open resource for transdiagnostic research in pediatric mental health and learning disorders
bioRxiv. doi:

A Klein, SS Ghosh, FS Bao, J Giard, Y Hame, E Stavsky, N Lee, B Rossa, M Reuter, EC Neto, A Keshavan. 2017.
Mindboggling morphometry of human brains.
PLoS Computational Biology 13(3): e1005350.
(bioRxiv 2016 preprint)

MP Milham, RC Craddock, A Klein. 2017.
Clinically useful brain imaging for neuropsychiatry: How can we get there?
Depression and Anxiety 2017:1-10. doi:

A Keshavan, A Klein, B Cipollini. 2017.
Interactive online brain shape visualization.
Research Ideas and Outcomes 3: e12358.
(bioRxiv 2016 preprint)
papers/BIDS-Apps_bioRxiv2016.png KJ Gorgolewski, F Alfaro-Almagro, T Auer, P Bellec, M Capota, M Mallar Chakravarty, NW Churchill, RC Craddock, GA Devenyi, A Eklund, O Esteban, G Flandin, SS Ghosh, JS Guntupalli, M Jenkinson, A Keshavan, G Kiar, PR Raamana, D Raffelt, CJ Steele, P-O Quirion, RE Smith, SC Strother, G Varoquaux, T Yarkoni, Y Wang, RA Poldrack. 2016.
BIDS Apps: Improving ease of use, accessibility and reproducibility of neuroimaging data analysis methods.
bioRxiv. doi:
papers/doctor-as-data-scientist_Medium2016_300px.png A Klein, SS Ghosh. 2016.
Doctor as data scientist: a high-dimensional view of health.
mPower2 SS Ghosh, G Ciccarelli, TF Quatieri, A Klein. 2016.
Speaking one's mind: Vocal biomarkers of depression and Parkinson disease.
Journal of the Acoustical Society of America. 139:2193.
mPower2 E Chaibub Neto, BM Bot, T Perumal, L Omberg, J Guinney, M Kellen, A Klein, SH Friend, AD Trister. 2016.
Personalized hypothesis tests for detecting medication response in Parkinson disease patients using iPhone sensor data.
Pacific Symposium on Biocomputing. 21:273-284. PMID:26776193.
mPower B Bot, C Suver, EC Neto, M Kellen, A Klein, C Bare, M Doerr, A Pratap, J Wilbanks, ER Dorsey, SH Friend, AD Trister. 2016.
The mPower Study, Parkinson Disease Mobile Data Collected Using ResearchKit.
Scientific Data 3, Article number: 160011.
papers/SageChallenge_AlzheimersAndDementia2016_small_crop.jpg GI Allen, N Amoroso, C Anghel, V Balagurusamy, CJ Bare, D Beaton, R Bellotti, DA Bennett, K Boehme, PC Boutros, L Caberlotto, C Caloian, F Campbell, E Chaibub Neto, Y-C Chang, B Chen, C-Y Chen, T-Y Chien, T Clark, S Das, C Davatzikos, J Deng, D Dillenberger, RJB Dobson, Q Dong, J Doshi, D Duma, R Errico, G Erus, E Everett, DW Fardo, SH Friend, H Fröhlich, J Gan, P St George-Hyslop, SS Ghosh, E Glaab, RC Green, Y Guan, M-Y Hong, C Huang, J Hwang, J Ibrahim, P Inglese, Q Jiang, Y Katsumata, JSK Kauwe, A Klein, D Kong, R Krause, E Lalonde, M Lauria, E Lee X Lin, Z Liu, J Livingstone, BA Logsdon, S Lovestone, T-W Ma, A Malhotra, LM Mangravite, TJ Maxwell, E Merrill, J Nagorksi, A Namasivayam, M Narayan, M Naz, SJ Newhouse, TC Norman, RN Nurtdinov, Y-J Oyang, Y Pawitan, S Peng, MA Peters, SR Piccolo, P Praveen, C Priami, VY Sabelnykova, P Senger, X Shen, A Simmons, A Sotiras, G Stolovitzky, S Tangaro, A Tateo, Y-A Tung, NJ Tustison, S Varol, G Vradenburg, MW Weiner, G Xiao, L Xie, Y Xie, J Xu, H Yang, X Zhan, Y Zhou, F Zhu, H Zhu, S Zhu, Alzheimer's Disease Neuroimaging Initiative. 2016.
Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.
Alzheimer's & Dementia 12(6): 645-653. PMID: 27079753.
Alzheimer's Disease Challenge website
CloudWorkshop H Muller, J Kalpathy-Cramer, A Hanbury, K Farahani, R Sergeev, JH Paik, A Klein, A Criminisi, A Trister, T Norman, D Kennedy, G Srinivasa, A Mamonov, N Preuss. 2016.
Report on the Cloud-Based Evaluation Approaches Workshop 2015.
ACM SIGIR Forum. 50(1):35-41. Workshop Website
pic_pres16 A Klein. 2016.
A game for crowdsourcing the segmentation of BigBrain data (NIH proposal).
Research Ideas and Outcomes. 2: e8816. doi:
pic_pres16 A Klein. 2016.
Crowdsourcing voice editing and quality assessment of data collected from the largest mobile phone-based research study of Parkinson disease (NIH proposal).
Research Ideas and Outcomes. 2: e8848. doi:
pic_pres16 A Klein. 2016.
Visual Parkinson's Disease Rating Scale: A Universal Iconic Questionnaire for Epidemiological Studies in India (NIH proposal).
Research Ideas and Outcomes. 2: e8834. doi:
pic_pres16 A Klein, S Ghosh. 2016.
Graph-based clinical diagnosis and prediction using multi-modal neuroimaging data (NIH proposal).
Research Ideas and Outcomes. 2: e8835. doi:
pic_pres16 A Klein. 2016.
Brain Graph Interface (NIH proposal).
Research Ideas and Outcomes. 2: e8817. doi:
pic_pres16 A Klein. 2016.
Data-Visual Relationships to Subject Performance and Eye Movements (NSF proposal).
Research Ideas and Outcomes. 2: e8814. doi:
mPower2 A Klein. 2016.
A composition-based taxonomy of information graphics.
Journal of Design and Science (also published on Medium).
pic_pres16 A Klein, SP Ellis. 2016.
Concurrence Topology: Finding High-Order Dependence in Neuropsychiatric Data (NIH proposal).
Research Ideas and Outcomes. 2: e8815. doi:

SP Ellis, A Klein. 2015.
"Concurrence Topology:" A New Method for Describing High-Order Statistical Dependence in Data.
31st International Symposium on Computational Geometry (Eindhover, the Netherlands).
posters/HBM2015_MindboggleADshapes.png A Klein, EC Neto, S Ghosh, ADNI. 2015.
Detailed shape analysis of healthy brains and brains with Alzheimer's disease.
Human Brain Mapping 2015 (Honolulu, Hawaii). Abstract
posters/NIH_BigData_GranteeMeeting2015_NCANDA_ROYGBIV_200px.png BN Nichols, JB Poline, RA Poldrack, A Klein, D Kwon, W Chu, KM Pohl. 2015.
Implementing Semantics-Driven Data Exchange in Brain Science: The NCANDA Case Study.
Big Data to Knowledge All Hands Grantee Meeting.
National Institutes of Health, Bethesda, MD.
pic_pres16 DB Keator, J Poline, BN Nichols, SS Ghosh, C Maumet, KJ Gorgolewski, T Auer, C Craddock, G Chen, G Flandin, YO Halchenko, M Hanke, C Haselgrove, K Helmer, M Jenkinson, A Klein, L Lanyon, D Marcus, D Margulies, F Michel, TE Nichols, RA Poldrack, R Reynolds, Z Saad, T Schmah, J Steffener, JA Turner, JD Van Horn, S Das, DN Kennedy. 2015.
Standardizing Metadata in Brain Imaging.
Front. Neurosci. Conference Abstract: Neuroinformatics 2015.
Online presentation by David Keator.
pic_pres16 DB Keator, SS Ghosh, C Maumet, G Flandin, BN Nichols, TE Nichols, GA Burns, R Bruehl, C Craddock, B Federick, K Gorgolewski, YO Halchenko, M Hanke, C Haselgrove, K Helmer, A Klein, D Marcus, M Milham, F Michel, R Poldrack, J Steffener, Y Schwartz, RM Stoner, JA Turner, DN Kennedy, J Poline. 2014.
Developing and using the data models for neuroimaging: the NIDASH Working Group.
Front. Neuroinform. Conference Abstract: Neuroinformatics 2014.
pic_pres16 S Ghosh, A Keshavan, J Salvatore, A Klein. 2014.
BIPS: A Framework for Curating and Executing Brain Imaging Pipelines.
Front. Neuroinform. Conference Abstract: 5th INCF Congress of Neuroinformatics.
pic_bees5 BA Klein, M Stiegler, A Klein, Tautz J. 2014.
Mapping sleeping bees within their nest: spatial and temporal analysis of worker honey bee sleep.
PLoS ONE. 9(7): e102316. doi:
Harvard Dataverse
pic_math1 SP Ellis, A Klein. 2014.
Describing high-order statistical dependence using “Concurrence Topology,” with application to functional MRI brain data.
Homology, Homotopy and Applications. 16(1): 245-264.
Earlier version on arXiv and poster
Concurrence Topology website
posters/Neuroinformatics2012_Mindboggle.png A Klein, N Nichols, D Haehn. 2014.
Mindboggle 2 interface: online visualization of extracted brain features with XTK.
Front. Neuroinform. Conference Abstract: 5th INCF Congress of Neuroinformatics.
  posters/HBM2014_Mindboggle101shapes.png A Klein, EN Neto, J Giard, F Bao, Y Hame, M Reuter, N Tustison, B Avants, J Tourville, H Dai, N Nichols, S Ghosh. 2014.
Shape analysis of 101 healthy human brains.
Human Brain Mapping 2014 (Hamburg, Germany).
pic_paper8 TJ Tustison, PA Cook, A Klein, G Song, SR Das, JT Duda, BM Kandel, N van Strien, JR Stone, JC Gee, BB Avants. 2014.
Large-scale evaluation of ANTs and FreeSurfer cortical thickness measurements.
NeuroImage. 99:166-179. doi:
pic_opensci2 NJ Tustison, HJ Johnson, T Rohlfing, A Klein, SS Ghosh, L Ibanez, B Avants. 2013.
Instrumentation bias in the use and evaluation of scientific software: Recommendations for reproducible practices in the computational sciences.
Frontiers in Brain Imaging Methods. 7:162. doi:
5-Semper_Book-color-128-958.pdf Ellora Cave Temple photographs on page 958, architecture textbook:
AJ Ignacio (translator and editor) 2013.
Semper: El estilo. Buenos Aires: Azpiazu Ediciones.
pic_bees4 BA Klein, L Rath, A Klein, SS Ghosh, G Galizia, C Kleineidam. 2013.
Imaging brain activity of honey bees sensing odors during sleep.
Sleep Research Society (Baltimore, MD, USA).
pic_bees3 A Klein, SS Ghosh, BA Klein, L Rath, G Galizia, C Kleineidam. 2012.
Applying human brain image processing methods to honeybee calcium image data.
Neuroinformatics 2012 (Munich, Germany).
pic_opensci1 SS Ghosh, A Klein, B Avants, J Millman. 2012.
Learning from open source software projects to improve scientific review.
Frontiers in Computational Neuroscience. 6:18.
doi: A Klein, FS Bao, Y Hame, E Stavsky, J Giard, D Haehn, N Nichols, SS Ghosh. 2012.
Mindboggle: Automated human brain MRI feature extraction, labeling, morphometry, and online visualization.
Neuroinformatics 2012 (Munich, Germany).
papers/Mindboggle101_FIBIM2012.png A Klein, J Tourville. 2012.
101 labeled brain images and a consistent human cortical labeling protocol.
Frontiers in Brain Imaging Methods. 6:171. doi:
Supplementary website and Open Science Framework repository
posters/Neuroinformatics2012_Mindboggle101.png J Tourville, A Klein. 2012.
101 labeled brains and a new human cortical labeling protocol.
Neuroinformatics 2012 (Munich, Germany).
posters/ISBI2011_deeplearning3.png N Lee, AF Laine, A Klein. 2011.
Towards a deep learning approach to brain parcellation.
IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2011:321-324.
posters/SFN2011_MDDremission.png FS Bao, SS Ghosh, J Giard, RV Parsey, A Klein. 2011.
Brain shape analysis for predicting treatment remission in major depressive disorder.
41st Annual Meeting for the Society for Neuroscience.
posters/JaneliaFarm2011_small.png A Klein. 2011.
Mindboggle: an informatics framework for open research in quantifying the shape of the human brain.
BioImage Informatics II (talk at Janelia Farm).
posters/Neuroinformatics2011_small.png N Lee, A Klein. 2011.
A graph-based database of hierarchical brain features.
Frontiers in Neuroinformatics (Neuroinformatics 2011).
posters/HBM2011_small.png F Bao, N Lee, Y Hame, K Im, D Riviere, G Li, A Klein. 2011.
Automated extraction of nested sulcal features from human brain MRI data.
17th Annual Meeting for the Organization of Human Brain Mapping.
GitHub repository
pic_paper6 BB Avants, NJ Tustison, G Song, PA Cook, A Klein, JC Gee. 2011.
A reproducible evaluation of ANTs similarity metric performance in brain image registration.
NeuroImage. 54(3): 2033-2044. PMCID: PMC3065962.
pic_pres10 D Peruzzo, A Bertoldo, R Parsey, A Klein. 2011.
Automatic detection of corrupted volumes in DTI data.
28th Annual Meeting for the European Society for Magnetic Resonance in Medicine and Biology.
pic_bees2 BA Klein, A Klein, MK Wray, UG Mueller, TD Seeley. 2010.
Sleep Deprivation impairs precision of waggle dance signaling in honey bees.
Proceedings of the National Academy of Sciences. 107(52): 22705-22709.
Nature News, New Scientist, Wired,...
posters/SFN2010_OptimalColormaps.png A Klein, A Worth, J Tourville, B Landman, T Dal Canton, SS Ghosh, D Shattuck. 2010.
An interactive tool for constructing optimal brain colormaps.
40th Annual Meeting for the Society for Neuroscience.
posters/HBM2010_OpenLabels.png A Klein, T Dal Canton, SS Ghosh, B Landman, J Lee, A Worth. 2010.
Open labels: online feedback for a public resource of manually labeled brain images.
16th Annual Meeting for the Organization of Human Brain Mapping.
posters/Atropos_HBM2010.png B Avants, A Klein, N Tustison, J Woo, JC Gee. 2010.
Evaluation of open-access, automated brain extraction methods on multi-site multi-disorder data.
16th Annual Meeting for the Organization of Human Brain Mapping.
Synapse website
papers/SurfaceVolumeEval_NeuroImage_2009.jpg A Klein, SS Ghosh, B Avants, BTT Yeo, B Fischl, B Ardekani, JC Gee, JJ Mann, RV Parsey. 2010.
Evaluation of volume-based and surface-based brain image registration methods.
NeuroImage. 51: 214-220. PMCID: PMC2862732.
Synapse website
HBM2009_eval_poster A Klein, SS Ghosh, B Avants, B Fischl, T Yeo, JJ Mann, RV Parsey. 2009.
An evaluation of volume- and surface-based nonlinear registration of human brain MRI data.
15th Annual Meeting for the Organization of Human Brain Mapping.*
papers/EvaluationData_NeuroImage2009_half.png A Klein, J Andersson, BA Ardekani, J Ashburner, B Avants, M-C Chiang, GE Christensen, DL Collins, J Gee, P Hellier, JH Song, M Jenkinson, C Lepage, D Rueckert, P Thompson, T Vercauteren, RP Woods, JJ Mann, RV Parsey. 2009.
Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration.
NeuroImage. 46(3): 786-802. PMCID: PMC2747506
Synapse website
pic_paper3 C DeLorenzo, A Klein, A Mikhno, N Gray, F Zanderigo, JJ Mann, RV Parsey. 2009.
A new method for assessing PET-MRI coregistration.
Proc. SPIE - Medical Imaging. 7259, 72592W.
pic_bees1 BA Klein, KM Olzsowy, A Klein, KM Saunders, TD Seeley. 2008.
Caste-dependent sleep of worker honey bees.
Journal of Experimental Biology. 211: 3028-3040.
pic_optics2 A Klein. 2008.
Relating vector ray-tracing equations for holograms of arbitrary shape and thickness.
Journal of the Optical Society of America A. 25(4): 979-983.
pic_infovis1 A Klein, W Bevington. 2008.
“Information visualization” entry in: Erlhoff Michael, Marshall Tim, eds.
Design Dictionary: Perspectives on Design Terminology. Basel, Boston, Berlin: Birkhauser Verlag.
papers/Mindboggle_BMCMedicalImaging_2005.png A Klein, B Mensh, S Ghosh, J Tourville, J Hirsch. 2005.
Mindboggle: Automated brain labeling with multiple atlases.
BMC Medical Imaging. 5:7. PMCID: PMC1283974
papers/Mindboggle_NeuroImage_2005.png A Klein, J Hirsch. 2005.
Mindboggle: A scatterbrained approach to automate brain labeling.
NeuroImage. 24(2): 261-280. PMID: 15627570
Thesis: Automated brain labeling with Mindboggle
posters/HBM2003_2.png A Klein. 2004.
Activity patterns in the brain: breaking up the problem into pieces.
International Conference on Complex Systems (ICCS2004 talk).
posters/HBM2003_1.png A Klein, J Hirsch. 2003.
Mindboggle: new developments in automated brain labeling.
9th Annual Meeting for the Organization of Human Brain Mapping.
posters/HBM2002.png A Klein, J Hirsch. 2002.
Fully-automated nonlinear labeling of human brain activity.
8th Annual Meeting for the Organization of Human Brain Mapping.
posters/HBM2001.png A Klein, J Hirsch. 2001.
Automatic labeling of brain anatomy and fMRI brain activity.
7th Annual Meeting for the Organization of Human Brain Mapping.
pic_optics1 MA Klug, A Klein, W Plesniak, A Kropp, B Chen. 1997.
Optics for full-parallax holographic stereograms.
Proc. SPIE. 3011 (78) “Practical Holography XI”
Thesis: Dispersion Compensation for Reflection Holography