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Papers related to Mindboggle

papers/Mindboggle_bioRxiv2016.png Mindboggle primary reference article:

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. doi:10.1371/journal.pcbi.1005350
bioRxiv 2016 preprint paper
papers/HBM2015_ROYGBIV.png ROYGBIV brain visualization paper:

A Keshavan, A Klein, B Cipollini. 2017.
Interactive online brain shape visualization.
Research Ideas and Outcomes 3: e12358. doi:
bioRxiv 2016 preprint paper.
papers/BIDS-Apps_bioRxiv2016.png Docker app paper:

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/SageChallenge_AlzheimersAndDementia2016_small_crop.jpg First large-scale, public use of Mindboggle:

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
papers/Mindboggle101_FIBIM2012.png Mindboggle's DKT31 labeling protocol and the Mindboggle-101 dataset:

A Klein, J Tourville. 2012.
101 labeled brain images and a consistent human cortical labeling protocol.
Frontiers in Brain Imaging Methods. 6:171.
Supplementary website and Open Science Framework repository
papers/Mindboggle_BMCMedicalImaging_2005.png First multiple-atlas paper:

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 Early (deprecated) version of Mindboggle:

A Klein, J Hirsch. 2005.
Mindboggle: A scatterbrained approach to automate brain labeling.
NeuroImage. 24(2): 261-280. PMID: 15627570


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.
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).
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).
papers/Mindboggle101_FIBIM2012.png 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).
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. doi:10.1109/ISBI.2011.5872414
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
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/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.