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Mindboggling morphometry of human brains

Arno Klein, Satrajit S. Ghosh, Forrest S. Bao, Joachim Giard, Yrjö Häme, Eliezer Stavsky, Noah Lee, Brian Rossa, Martin Reuter, Elias Chaibub Neto, Anisha Keshavan, Dina Schneidman
2017 PLoS Computational Biology  
The number of different shape measures and the size of the populations make this the largest and most detailed shape analysis of human brains ever conducted.  ...  Mindboggle (http://mindboggle.info) is an open source brain morphometry platform that takes in preprocessed T1-weighted MRI data and outputs volume, surface, and tabular data containing label, feature,  ...  Acknowledgments We sincerely thank everyone who has contributed to the Mindboggle open science project over the years, including Nolan Nichols, Oliver Hinds, Arthur Mikhno, Hal Canary, and Ben Cipollini  ... 
doi:10.1371/journal.pcbi.1005350 pmid:28231282 pmcid:PMC5322885 fatcat:lsqa2kigtzfivlkqzrnmkri37u

Mindboggling morphometry of human brains [article]

Arno Klein, Satrajit S. Ghosh, Forrest S. Bao, Joachim Giard, Yrjo Hame, Eliezer Stavsky, Noah Lee, Brian Rossa, Martin Reuter, Elias Chaibub Neto, Anisha Keshavan
2016 bioRxiv   pre-print
The number of different shape measures and the size of the populations make this the largest and most detailed shape analysis of human brains every conducted.  ...  Mindboggle (http://mindboggle.info) is an open source brain morphometry platform that takes in preprocessed T1-weighted MRI data and outputs volume, surface, and tabular data containing label, feature,  ...  open source brain morphometry platform and 968 demonstrated its use in studies of shape variation in healthy and diseased humans.  ... 
doi:10.1101/091322 fatcat:kfgcikresvcntlem6eyrjh2lmu

Interactive online brain shape visualization [article]

Anisha Keshavan, Arno Klein, Benjamin Cipollini
2016 bioRxiv   pre-print
The Mindboggle project was initiated to improve the labeling as well as morphometry of brain imaging data, and to promote open science by making all data, software, and documentation freely and openly  ...  We completed an initial version of our browser-based interactive visualization tool; a left hemisphere of a human brain is available at http://roygbiv.mindboggle.info.  ...  Acknowledgements The authors would like to thank the organizers and attendees of the 2015 OHBM Hackathon. This project is supported in part by a grant from the NSF (award 1429999).  ... 
doi:10.1101/067678 fatcat:sjxxfy2hvben5e6yivcofmj2su

Interactive online brain shape visualization

Anisha Keshavan, Arno Klein, Ben Cipollini
2017 Research Ideas and Outcomes  
The open-source Mindboggle package improves the labeling and morphometry estimates of brain imaging data.  ...  At the 2015 Brainhack event, we developed a web-based, interactive, brain shape visualization of Mindboggle outputs.  ...  The Mindboggle project was initiated to improve the labeling as well as morphometry of brain imaging data, and to promote open science by making all data, software, and documentation freely and openly  ... 
doi:10.3897/rio.3.e12358 fatcat:leorlscgbrbyhhfr53bw4q36tu

Brain Morphometry and Diminished Physical Growth in Bangladeshi Children Growing up in Extreme Poverty: a Longitudinal Study [article]

Ted K Turesky, Talat Shama, Shahria Hafiz Kakon, Rashidul Haque, Amala Someshwar, Nazrul Islam, William Petri, Charles A Nelson, Nadine Gaab
2021 bioRxiv   pre-print
Diminished growth predicted brain morphometry and mediated the link between poverty and brain morphometry most consistently for white matter and subcortical volumes.  ...  Structural brain images were submitted to Mindboggle software, a Docker-compliant and highly reproducible tool for tissue segmentation and regional estimations of volume, surface area, cortical thickness  ...  on human development.  ... 
doi:10.1101/2021.02.24.432797 fatcat:4p5peqvq3jeuvirfww622wnktm

CerebrA: Accurate registration and manual label correction of Mindboggle-101 atlas for MNI-ICBM152 template [article]

Ana L. Manera, Mahsa Dadar, Vladimir Fonov, D. Louis Collins
2019 bioRxiv   pre-print
in neurodegenerative diseases where different brain morphometry analyses are being broadly used in an effort to improve diagnostic biomarkers.  ...  MNI-ICBM2009c is the most recent version of the MNI-ICBM152 brain average, providing a higher level of anatomical details.  ...  Mindboggle-101 is the largest, publicly available set of manually labelled human brain images created from 101 human scans, labelled according to a surface-based cortical labelling protocol (DKT-Desikan-Killiany-Tourville  ... 
doi:10.1101/2019.12.19.883330 fatcat:ozlxtrgixzbkdixedlytyejxae

Shape-based multifeature brain parcellation

Saad Nadeem, Arie Kaufman, Martin A. Styner, Elsa D. Angelini
2016 Medical Imaging 2016: Image Processing  
We evaluate our approach using Mindboggle manually labeled brain datasets and achieve the following accuracies: 72.4% for gyri, 78.5% for major sulci, and 98.4% for folds.  ...  Our method does not require any non-linear registration of a given brain dataset to a generic atlas and hence, does away with the structure similarity assumption critical to the atlas-based approaches.  ...  ACKNOWLEDGEMENTS We are much grateful to Dr Arno Klein, Director of Neuroimaging, Sage Bionetworks and the lead for Mindboggle, for his help and guidance in this project.  ... 
doi:10.1117/12.2216979 dblp:conf/miip/NadeemK16 fatcat:irh7f2t5szbxhkfxagyyio7ymu

CerebrA, registration and manual label correction of Mindboggle-101 atlas for MNI-ICBM152 template

Ana L. Manera, Mahsa Dadar, Vladimir Fonov, D. Louis Collins
2020 Scientific Data  
in neurodegenerative diseases where different brain morphometry analyses are being broadly used in an effort to improve diagnostic biomarkers.  ...  MNI-ICBM2009c is the most recent version of the MNI-ICBM152 brain average, providing a higher level of anatomical details.  ...  Manera: Study concept and design, manual correction of the labels, analysis and interpretation of the data, drafting and revision of the manuscript.  ... 
doi:10.1038/s41597-020-0557-9 pmid:32669554 fatcat:o2zjzofgdrandprs5qd2i7gfqi

Brain Graph Interface

Arno Klein
2016 Research Ideas and Outcomes  
Executive summary We will analyze variations in brain anatomy and create the first integrated software environment to extract patterns from brains and target differences related to inter-individual variability  ...  We will evaluate how well these differences can help diagnose and predict treatment outcome for major depressive disorder, which affects millions of Americans, but our work is intended to be applied to  ...  Mindboggle features Our neuromarkers will be derived from an analysis of features extracted with the Mindboggle software (www.mindboggle.info), which automates anatomical labeling of human brain MR data  ... 
doi:10.3897/rio.2.e8817 fatcat:iopsorwl4jeibnxqrvmud6upca

Brain Morphometry and Chronic Inflammation in Bangladeshi Children Growing up in Extreme Poverty [article]

Ted K Turesky, Laura Pirazzoli, Talat Shama, Shahria Hafiz Kakon, Rashidul Haque, Nazrul Islam, Amala Someshwar, Borjan Gagoski, William Petri, Charles A Nelson, Nadine Gaab
2021 bioRxiv   pre-print
Structural brain images were submitted to Mindboggle software, a Docker-compliant and high-reproducibility tool for tissue segmentation and regional estimations of volume, surface area, cortical thickness  ...  These findings suggest that chronic inflammation is associated with brain morphometry globally and in the putamen, and further suggests that inflammation may be a potential mechanism linking SES to brain  ...  Consequently, we examined indirect effects only where frequency of CRP elevations correlated with a measure of SES and a measure of brain morphometry (after FDR correction).  ... 
doi:10.1101/2021.12.26.474220 fatcat:3ctxmzbfirhw7gum756nhm4rwm

101 Labeled Brain Images and a Consistent Human Cortical Labeling Protocol

Arno Klein, Jason Tourville
2012 Frontiers in Neuroscience  
We introduce the Mindboggle-101 dataset, the largest and most complete set of free, publicly accessible, manually labeled human brain images.  ...  Given how difficult it is to label brains, the Mindboggle-101 dataset is intended to serve as brain atlases for use in labeling other brains, as a normative dataset to establish morphometric variation  ...  Labeled regions are important in and of themselves for use in characterizing the morphometry of the brain.  ... 
doi:10.3389/fnins.2012.00171 pmid:23227001 pmcid:PMC3514540 fatcat:5vegnunlvba5fiwp2lcmdpld4q

Is it Time to Switch Your T1W Sequence? Assessing the Impact of Prospective Motion Correction on the Reliability and Quality of Structural Imaging

Lei Ai, R. Cameron Craddock, Nim Tottenham, Jonathan P Dyke, Ryan Lim, Stanley Colcombe, Michael Milham, Alexandre R. Franco
2020 NeuroImage  
New large neuroimaging studies, such as the Adolescent Brain Cognitive Development study (ABCD) and Human Connectome Project (HCP) Development studies are adopting a new T1-weighted imaging sequence with  ...  Here, we used a developmental dataset (ages 5-21, N=348) from the Healthy Brain Network (HBN) Initiative to directly compare two widely used MRI structural sequences: one based on the Human Connectome  ...  We would also like to thank the many individuals who have provided financial support to the CMI Healthy Brain Network to make the creation and sharing of this resource possible and the partial support  ... 
doi:10.1016/j.neuroimage.2020.117585 pmid:33248256 pmcid:PMC7898192 fatcat:ixy7u6cok5cvpexbjjwyebrrmy

Reliability and Reproducibility of T1-weighted images: comparing MPRAGE and Prospective Motion Correction with Volumetric Navigators [article]

Lei Ai, R. Cameron Craddock, Nim Tottenham, Stanley Colcombe, Michael Milham, Alexandre R. Franco
2019 bioRxiv   pre-print
ICC scores were also higher for the MPRAGE-vNav pair then the MPRAGE-MPRAGE pair, possibly due to the higher motion in one of the MPRAGE runs.  ...  Reliability and reproducibility were assessed with a subset of subjects (N=61) that performed two MPRAGE and two vNav sequences within the same imaging session.  ...  MPRAGE can be considered as the basic acquisition protocol for brain morphometry studies 2 . As such, large neuroimaging studies such as the WU-Minn Human Connectome Project (HCP) (David C.  ... 
doi:10.1101/666289 fatcat:qd2o2x7j2bgp3p2mwlnjjflzui

Amygdala size varies with stress perception

Inês Caetano, Liliana Amorim, José Miguel Soares, Sónia Ferreira, Ana Coelho, Joana Reis, Nadine Correia Santos, Pedro Silva Moreira, Paulo Marques, Ricardo Magalhães, Madalena Esteves, Maria Picó-Pérez (+1 others)
2021 Neurobiology of Stress  
Indeed, moved by the increasing number of stress-triggered pathologies, several groups drew on advanced neuroimaging techniques to explore stress effects on the brain.  ...  Notably, perception of stressful stimuli is an important factor when mounting stress responses and measuring its impact.  ...  Herein, this external brain mask is also refined using the internal mask of the FreeSurfer's aseg.mgz segmentation, reconciling ANTs-derived, and FreeSurfer-derived segmentation of the cortical GM of Mindboggle  ... 
doi:10.1016/j.ynstr.2021.100334 pmid:34013000 pmcid:PMC8114169 fatcat:xd3nzbfv7jer5fwc5vivncwtda

Multimodal neuroimaging computing: the workflows, methods, and platforms

Sidong Liu, Weidong Cai, Siqi Liu, Fan Zhang, Michael Fulham, Dagan Feng, Sonia Pujol, Ron Kikinis
2015 Brain Informatics  
The last two decades have witnessed the explosive growth in the development and use of noninvasive neuroimaging technologies that advance the research on human brain under normal and pathological conditions  ...  Multimodal neuroimaging has become a major driver of current neuroimaging research due to the recognition of the clinical benefits of multimodal data, and the better access to hybrid devices.  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://crea tivecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution  ... 
doi:10.1007/s40708-015-0020-4 pmid:27747508 pmcid:PMC4737665 fatcat:hr5otfj36ngm7pyvbmvzwlyv4q
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