Papers related to Mindboggle

	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)
	ROYGBIV brain visualization paper: A Keshavan, A Klein, B Cipollini. 2017. Interactive online brain shape visualization. Research Ideas and Outcomes 3: e12358. doi: https://doi.org/10.3897/rio.3.e12358 (bioRxiv 2016 preprint)
	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: https://dx.doi.org/10.1101/079145
	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. DOI: dx.doi.org/10.1016/j.jalz.2016.02.006 Alzheimer's Disease Challenge website
	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. dx.doi.org/10.3389/fnins.2012.00171 Supplementary website and Open Science Framework repository
	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
	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
Conferences
	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.
	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).
	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. doi:10.3389/conf.fninf.2014.08.00086
	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).
	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).
	J Tourville, A Klein. 2012. 101 labeled brains and a new human cortical labeling protocol. Neuroinformatics 2012 (Munich, Germany).
	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
	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.
	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).
	N Lee, A Klein. 2011. A graph-based database of hierarchical brain features. Frontiers in Neuroinformatics (Neuroinformatics 2011). dx.doi.org/10.3389/conf.fninf.2011.08.00139
	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
	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. Website: https://binarybottle.github.io/braincolor/colormaps/
	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.
	A Klein. 2004. Activity patterns in the brain: breaking up the problem into pieces. International Conference on Complex Systems (ICCS2004 talk).
	A Klein, J Hirsch. 2003. Mindboggle: new developments in automated brain labeling. 9th Annual Meeting for the Organization of Human Brain Mapping.
	A Klein, J Hirsch. 2002. Fully-automated nonlinear labeling of human brain activity. 8th Annual Meeting for the Organization of Human Brain Mapping.
	A Klein, J Hirsch. 2001. Automatic labeling of brain anatomy and fMRI brain activity. 7th Annual Meeting for the Organization of Human Brain Mapping.