Jetstream may be used for prototyping, for creating tailored workflows to either use at smaller scale with a handful of CPUs or to port to larger environments after doing your proof of concept work at a smaller level.
Function
865 Matching Annotations
- Dec 2017
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iujetstream.atlassian.net iujetstream.atlassian.net
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Jetstream is meant primarily for interactive research, small scale processing on demand, or as the backend to science gateways to send research jobs to other HPC or HTC resources.
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Jetstream is an NSF-funded (NSF-1445604), user-friendly cloud environment designed to give researchers access to interactive computing and data analysis resources on demand, whenever and wherever they want to analyze their data.
Function
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It provides a library of virtual machines designed to do discipline specific scientific analysis.
Function
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- Nov 2017
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ibg.colorado.edu ibg.colorado.edu
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- Oct 2017
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www.pnas.org www.pnas.org
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day-long audio recordings
Duration = "day long"
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elifesciences.org elifesciences.org
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faseb.org faseb.org
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stolkarjen.github.io stolkarjen.github.io
- Sep 2017
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collaboration.humanbrainproject.eu collaboration.humanbrainproject.eu
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www.reproducibleimaging.org www.reproducibleimaging.org
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elifesciences.org elifesciences.org
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www.mcleanhospital.org www.mcleanhospital.org
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mriqc.readthedocs.io mriqc.readthedocs.io
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Run
I get some warnings, that I presume is OK to ignore: 2017-09-08 17:21:57,916 interface:WARNING AFNI is outdated, detected version Debian-16.2.07~dfsg.1-5~nd16.04+1 and AFNI_17.2.12 is available. 2017-09-08 17:21:58,400 interface:WARNING AFNI is outdated, detected version Debian-16.2.07~dfsg.1-5~nd16.04+1 and AFNI_17.2.12 is available.
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blogs.lse.ac.uk blogs.lse.ac.uk
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neurohackweek.github.io neurohackweek.github.io
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not some cooler and newer tool
Such as???
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- Aug 2017
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fairsharing.org fairsharing.org
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osf.io osf.io
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github.com github.com
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www.neurosciencenetwork.org www.neurosciencenetwork.org
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neuroscience.uchicago.edu neuroscience.uchicago.edu
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October 24-27
Date of event
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journals.plos.org journals.plos.org
- Jun 2017
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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The Experiment Factory: Standardizing Behavioral Experiments
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www.sjscience.org www.sjscience.org
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The Self-Journals of Science
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www.nature.com www.nature.com
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Finding useful data across multiple biomedical data repositories using DataMed
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ucsdnews.ucsd.edu ucsdnews.ucsd.edu
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NSF Awards $15 Million to Create Science Gateways Community Institute
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nsf.gov nsf.gov
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NSF commits $35 million to improve scientific software
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www.nature.com www.nature.com
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Extending transparency to code
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jea.acm.org jea.acm.orgACM JEA1
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RCR: Replicated Computational Results Initiaitve
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URL
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toms.acm.org toms.acm.orgACM TOMS1
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Replicated Computational Results (RCR)
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www.ieee.org www.ieee.org
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The Future of Research Curation and Research Reproducibility
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www.software.ac.uk www.software.ac.uk
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The Software Sustainability Institute
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science.sciencemag.org science.sciencemag.org
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Enhancing reproducibility for computational methods
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- May 2017
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www.nature.com www.nature.com
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Containerization technology takes the hassle out of setting up software and can boost the reproducibility of data-driven research.
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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automatic quality control on the measurements computed by FreeSurfer by identifying outliers; if >25% of the used morphometric variables exhibited values that were more than two SDs away from the population mean, we deemed that subject an outlier and discarded it.
Automatic outlier detection
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3,800 unique individuals spanning nine large-scale studies: the Harvard/Massachusetts General Hospital Brain Genomic Superstruct Project (GSP) (26), the Human Connectome Project (HCP) (27), the Alzheimer’s Disease Neuroimaging Initiative (ADNI) (28), the Attention-Deficit Hyperactivity Disorder (ADHD 200) sample (29), the Open Access Series of Imaging Studies (OASIS) cross-sectional sample (30), the Center for Biomedical Research Excellence (COBRE) schizophrenia sample (31), the MIND Clinical Imaging Consortium (MCIC) schizophrenia sample (32), the Autism Brain Imaging Data Exchange (ABIDE) (33), and the Parkinson Progression Marker Initiative (PPMI) (34).
Datasets
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FreeSurfer (20), a freely available, widely used, and extensively validated brain MRI analysis software package, to automatically process structural MRI scans and obtain a vector of volumetric measurements across subcortical structures and cortical thickness measurements across the entire cortical mantle, which constitute a comprehensive description of the structural neuroanatomy.
Method: RRID:SCR_001847
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- Apr 2017
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openmediascholarship.org openmediascholarship.org
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URL
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- Mar 2017
- Feb 2017
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github.com github.com
- Jan 2017
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www.nature.com www.nature.com
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www.datacarpentry.org www.datacarpentry.org
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callingbullshit.org callingbullshit.org
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URL
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dev.openanatomy.org dev.openanatomy.org
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URL
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ohif.org ohif.org
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clowder.ncsa.illinois.edu clowder.ncsa.illinois.eduClowder1
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URL
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browndog.ncsa.illinois.edu browndog.ncsa.illinois.edu
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www.thelancet.com www.thelancet.com
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concern for the purpose and ambitions of science, and their role in strengthening the health and resilience of the societies they so depend upon
Refocus of publishers
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The defi ning quality of publishing is judgment
Whose judgement?
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The purpose of publishing should be to make sense of the world in which we live
Purpose statement.
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atabases are not designed to improve either communication or understanding
Well, we better make better databases then!
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www.thelancet.com www.thelancet.com
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If it’s compulsory, it’s not data sharing, many agreed
Interesting.
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- Dec 2016
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github.com github.com
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URL
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boutiques.github.io boutiques.github.io
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URL
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www.frontiersin.org www.frontiersin.org
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www.secretgeek.net www.secretgeek.net
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URL
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benchling.com benchling.com
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journal.frontiersin.org journal.frontiersin.org
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joss.theoj.org joss.theoj.org
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URL
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www.force11.org www.force11.org
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depend on the specific version used
And operating system. See, for example, Glatard T, Lewis LB, Ferreira da Silva R, Adalat R, Beck N, Lepage C, Rioux P, Rousseau ME, Sherif T, Deelman E, Khalili-Mahani N, Evans AC. Reproducibility of neuroimaging analyses across operating systems. Front Neuroinform. 2015 Apr 24;9:12. doi: 10.3389/fninf.2015.00012. PubMed PMID: 25964757; PubMed Central PMCID: PMC4408913. and others.
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- Nov 2016
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guides.github.com guides.github.com
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What is GitHub?
Some pretty useful training material here.
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www.frontiersin.org www.frontiersin.org
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$25,000 (for entire degree-granting institutions)
This is the statement that is corrected in the Corrigendum. It should read: "The University of California EZID service offers annual DOI creation at $835 (for non-degree granting departments) to $2500 (for entire degree-granting institutions) per 1 million DOIs minted."
See http://ezid.cdlib.org/learn/ for the ezid details.
See http://journal.frontiersin.org/article/10.3389/fninf.2016.00043/full for the Corrigendum
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http://doi.org/10.5281/zenodo.61456
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URL
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www.scientificpaperofthefuture.org www.scientificpaperofthefuture.org
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github.com github.com
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URL
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repod.pon.edu.pl repod.pon.edu.pl
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URL
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- Sep 2016
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camh-scwg.github.io camh-scwg.github.io
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camh-scwg.github.io camh-scwg.github.io
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Cool R tricks, Thanks, Erin!
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royalsocietypublishing.org royalsocietypublishing.org
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Natural Selection argument...
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neurohackweek.github.io neurohackweek.github.io
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www.nhlbi.nih.gov www.nhlbi.nih.gov
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events.brainhack.org events.brainhack.org
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2016 Brainhack LA
ReproNim co-sponsored event.
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URL
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neurohackweek.github.io neurohackweek.github.io
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Summer school
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URL
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www.bigdatau.org www.bigdatau.org
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The BD2K Guide to the Fundamentals of Data Science Series
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URL
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f1000research.com f1000research.com
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ReproNim
Neuroinformatics 2016 poster
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- Aug 2016
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projectreporter.nih.gov projectreporter.nih.gov
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Related to ReproNim TR&D2
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grants.nih.gov grants.nih.gov
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Metrics to Assess Value of Biomedical Digital Repositories
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bd2kccc.org bd2kccc.org
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BD2KCCC Webinars
BD2K Events that may be of general interest.
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Annotators
URL
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www.frontiersin.org www.frontiersin.org
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Data Citation in Neuroimaging: Proposed Best Practices for Data Identification and Attribution
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journals.plos.org journals.plos.org
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The Virtuous Cycle of a Data Ecosystem
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www.nitrc.org www.nitrc.org
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Find neuroimaging tools here
NITRC is a really useful resource
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wibih.unomaha.edu wibih.unomaha.edu
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October 13-16, 2016
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October 13-16, 2016
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2016 International Conference on Brain Informatics & Health
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events.brainhack.org events.brainhack.org
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Dates: September 18-20, 2016 Location: Vienna Austria Title: BrainHack Vienna
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URL
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- Jul 2016
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journals.plos.org journals.plos.org
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Ten Simple Rules for Reproducible Computational Research
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force11.github.io force11.github.io
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Data Citations: A Primer
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wibih.unomaha.edu wibih.unomaha.edu
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2016 International Conference on Brain Informatics & Health October 13-16, 2016 in Omaha, Nebraska, USA
Date: October 13-16, 2016 Location: Omaha, Nebraska, USA
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URL
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identifiers.org identifiers.org
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Identifiers.org Identifiers.org is a system providing resolvable persistent URIs used to identify data for the scientific community, with a current focus on the Life Sciences domain. The provision of a resolvable identifiers (URLs) fits well with the Semantic Web vision, and the Linked Data initiative.
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URL
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biosharing.org biosharing.org
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A curated, searchable portal of inter-related data standards, databases, and policies in the life, environmental and biomedical sciences
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URL
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www.w3.org www.w3.org
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Dataset Descriptions: HCLS Community Profile
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URL
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www.nationaldataservice.org www.nationaldataservice.org
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The NationalDATA SERVICE
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URL
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psycnet.apa.org psycnet.apa.org
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europepmc.org europepmc.org
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Sizing the Problem of Improving Discovery and Access to NIH-Funded Data: A Preliminary Study
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opendatabutton.org opendatabutton.org
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URL
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opennessinitiative.org opennessinitiative.org
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URL
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brainx.io brainx.io
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ieeexplore.ieee.org ieeexplore.ieee.org
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datamed.org datamed.org
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URL
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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right insula (peak: 43,−13,−1)
ID: 008 Variable: gray matter density Groups: SMD, BD, HV Model: VBM AnatomicLocation: right insula PeakLocation: 43,−13,−1
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right globus pallidus (peak: 16,−2,−7)
ID: 007 Variable: gray matter density Groups: SMD, BD, HV Model: VBM AnatomicLocation: right globus pallidus PeakLocation: 16,−2,−7
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globus pallidus differences were driven by increased GM volume in BD compared to both HV and SMD.
ID: 007 Interpretation: increased GM volume in BD compared to both HV and SMD
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Post-hoc analyses indicated that between-group differences in the cortical clusters were driven mainly by increased GM volume in HV compared to both BD and SMD,
ID: 006 Interpretation: increased GM volume in HV compared to both BD and SMD ID: 008 Interpretation: increased GM volume in HV compared to both BD and SMD ID: 009 Interpretation: increased GM volume in HV compared to both BD and SMD
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right dorsolateral prefrontal cortex (DLPFC, BA 9/46, peak: 41,52,16)
ID: 009 Variable: gray matter density Groups: SMD, BD, HV Model: VBM AnatomicLocation: right dorsolateral prefrontal cortex PeakLocation: 41,52,16
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bilateral pre-supplementary motor area (pre-SMA, BA 6/8, peak: 4,26,53)
ID: 006 Variable: gray matter density Groups: SMD, BD, HV Model: VBM AnatomicLocation: bilateral pre-supplementary motor PeakLocation: 4,26,53
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voxel-based morphometry
Scope: VBM
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trend difference in TBV (p=0.09), driven by a trend for larger TBV in HV than BD (p=0.08)
ID:004 Variable: TBV Groups: SMD, BD, HV P: 0.09 Model: ANOVA Interpretation: TBV trend different between groups ID: 005 Variable: TBV Groups: HV, BD P: 0.08 Model: T-test Interpretation: TBV trend larger in HV compared to BD
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Age at scan differed between groups (p=0.001); the SMD group was younger than the BD (p<0.01) and HV (p=0.02) groups.
ID: 001 Variable: Age Groups: SMD, BD, HV P: 0.001 Model: ANOVA Interpretation: Age Differed between groups ID: 002 Variable: Age Groups: SMD, BD P: <0.01 Model: T-test Interpretation: SMD younger than BD ID: 003 Variable: Age Groups: SMD, HV P: 0.02 Model: T-test Interpretation: SMD younger than HV
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Cross-sectional and longitudinal abnormalities in brain structure in children with severe mood dysregulation or bipolar disorder
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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functional connectivity
Scope = Functional Connectivity
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Aberrant amygdala intrinsic functional connectivity distinguishes youths with bipolar disorder from those with severe mood dysregulation
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Annotators
URL
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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Image analysis was done on Sun Microsystems, Inc. (Mountainview, CA) workstations using Cardviews software (Caviness et al. 1996).
ID: VolumeAnalysis Method: MethodURL: Software: Cardviews
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docs.google.com docs.google.com
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Spreadsheet of potential data resources for the Open Science Prize
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www.openscienceprize.org www.openscienceprize.org
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Open Science Prize
Initiative to promote and award open science
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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Cluster failure: Why fMRI inferences for spatial extent have inflated false-positive rates
Title
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Neuroimaging Informatics Tools and Resources Clearinghouse
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- Jun 2016
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aws.amazon.com aws.amazon.com
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URL
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github.com github.com
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Annotators
URL
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cos.io cos.io
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www.biorxiv.org www.biorxiv.org
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URL
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www.humanbrainmapping.org www.humanbrainmapping.org
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Open Science Special Interest Group
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github.com github.com
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URL
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open-brain-consent.readthedocs.org open-brain-consent.readthedocs.org
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www.openwebfoundation.org www.openwebfoundation.org
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Annotators
URL
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contentmine.org contentmine.org
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Annotators
URL
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www.scienceintheclassroom.org www.scienceintheclassroom.org
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dumontierlab.stanford.edu dumontierlab.stanford.edu
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URL
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biocaddie.org biocaddie.org
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URL
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www.codata.org www.codata.org
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DATA CITATION WORKSHOP: DEVELOPING POLICY AND PRACTICE
Title: DATA CITATION WORKSHOP: DEVELOPING POLICY AND PRACTICE Date: Tuesday, 12 July 2016 from 8:00 AM to 5:00 PM (EDT) Location: National Academies of Sciences, Engineering & Medicine - Keck Center, 500 Fifth St., NW, Room 100, Washington, DC, United States
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ckan.incf.org ckan.incf.org
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About
INCF DataSpace Powered by CKAN
Tags
Annotators
URL
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incf.github.io incf.github.io
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MINDS Schema
Minimal Information for Neuroscience Data Standard INCF - Dataspace effort
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Annotators
URL
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datascience.nih.gov datascience.nih.gov
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The Commons supports biomedical discovery by enabling sharing of digital objects
Tags
Annotators
URL
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The open source data portal software
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www.humanconnectome.org www.humanconnectome.org
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Exploring the Human Connectome
Title: Exploring the Human Connectome Date: Aug 28-Sep1, 2016 Location: HMS, Boston, MA
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www.incf.org www.incf.org
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INCF Short course 2016
TItle: INCF Short course 2016 Dates: 31 August – 1 September, 2016 Location: Penta Hotel, Oxford Road, Reading RG1 7RH, United Kingdom
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python.g-node.org python.g-node.org
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Advanced Scientific Programming in Python
Title: Advanced Scientific Programming in Python Dates: September 5—11, 2016. Location: Reading, UK
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Annotators
URL
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www.eventbrite.com www.eventbrite.com
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THOR Workshop
Date: July 7, 2016 Location: Amsterdam, Netherlands Type: Workshop
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datascience.nih.gov datascience.nih.gov
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Title: Wold-Scale Personalized Learning through Crowdsourcing and Algorithms
Date: June 1, 2016 Time: 3:30pm - 4:30pm EST
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arxiv.org arxiv.org
- May 2016
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americanbiomedicalinformatics.org americanbiomedicalinformatics.org
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Graph Based Analysis of Biomedical BigData
Title: Graph Based Analysis of Biomedical BigData Date: Thursday July 7 - Friday July 8, 2016 Location: University of District of Columbia CC, Washington DC Type: 2 Day Hands-on Training
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- Mar 2016
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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A series of Analyses of Variance (ANOVA) were performed on CC1 through CC7 and total CC as dependent variables with sex, age, and TCV as covariates to compare CC volumes and CC midsagittal areas between youths with BPD and HC to determine if there were group differences.
ID: ANOVAvol Variable: CC1vol Variable: CC2vol Variable: CC3vol Variable: CC4vol Variable: CC5vol Variable: CC6vol Variable: CC7vol Variable: CCvol Variable: age Variable:sex Variable:TCV
ID: ANOVAarea Variable: CC1area Variable: CC2area Variable: CC3area Variable: CC4area Variable: CC5area Variable: CC6area Variable: CC7area Variable: CCarea Variable: age Variable:sex Variable:TCV
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Equality of groups on demographic and clinical variables was evaluated by t-tests for continuous variables and chi-square tests for categorical variables
ID: Ttest Variable:
ID: chi-square Variable:
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Total cerebral volume (TCV) was defined as all gray and white matter in the cerebrum and did not include CSF, cerebellum or brainstem.
ID: StructuralVolumes Measure: TCV AnalysisWorkflow: VolumeAnalysis Data:
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volumetric measures of the CC, we utilized a comprehensive white matter parcellation method to subdivide the cerebral WM into peripheral and deep divisions based upon a set of topographic relationships and geometric constraints related to cortical and subcortical structures as guided by known generalized white matter organizational principles (Makris et al. 1999; Meyer et al. 1999)
ID: CCvolumes Measure: CCvol, CC1vol, CC2vol, CC3vol, CC4vol, CC5vol, CC6vol, CC7vol AnalysisWorkflow: VolumeAnalysis Data:
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cross-sectional area measurements were obtained for total CC and the seven subregions based on the subdivisions described by Witelson
ID: CCareas Measure: CCarea, CC1area, CC2area, CC3area, CC4area, CC5area, CC6area, CC7area AnalysisWorkflow: VolumeAnalysis Data:
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SPSS 15.0 for Windows (SPSS, Inc., Chicago, IL) was used for statistical analysis.
ID: VolumeAnalysis URL: Software: SPSS 15.0 for Windows (SPSS, Inc., Chicago, IL) Observation: CCVolumes Model: ANOVA
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The acquisitions included a 3-D inversion recovery-prepped spoiled gradient recalled echo coronal series, which was used for structural analysis (124 slices, prep=300 msec, TE=1 min, flip angle=25°, FOV= 24 cm2, slice thickness 1.5 mm, acquisition matrix 256×192, number of excitations=2).
ID: SPGR AcquisitionInstrument: MRIScanner Type: SPGR
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Structural imaging was performed at the McLean Hospital Brain Imaging Center on a 1.5 Tesla Scanner (Signa; GE Medical Systems, Milwaukee, WI).
ID: MRIScanner Type: MRI Location: McLean Hospital Brain Imaging Center Field: 1.5 Tesla Manufacturer: General Electric Model: Signa
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Significant effects for TCV (F=18.1, p<0.01) and for age group-by-diagnosis interaction term (F=6.97, p<0.01) for the CC4 volumetric measurements were found
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Significant effects of TCV (F=19.4, p<0.01) and for age group-by-diagnosis interaction term (F=4.60, p=0.01) for the volumetric measurements of total CC were found
ObsID: 002 MeasureID: CC vol GroupID: HC_young, HC_old, BPD_young, BPD_old CovariateID: TCV StatID: ANOVA F: 19.4 P: <0.01 ObsID:003 MeasureID: CC vol GroupID: HC, BPD CovariateID: age group-by-diagnosis interaction term StatID: ANOVA F: 4.60 P: 0.01
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For the area measurement of the total CC, significant effects were also found for TCV (F=5.15, p=0.03) and age group-by-diagnosis interaction term (F=3.08, p=0.05).
ObsID: 004 MeasureID: CC area GroupID: HC, BPD CovariateID: TCV StatID: ANOVA F: 5.15 P: 0.03 ObsID:005 MeasureID: CC area GroupID: HC, BPD CovariateID: age group-by-diagnosis interaction term StatID: ANOVA F: 3.08 P: 0.05
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For CC2, significant effects were found for TCV in CC2 volume (F=12.64, p<0.01) and area (F=5.18, p=0.03) measurements, respectively
ObsID: 014 MeasureID: CC2 vol GroupID: HC, BPD CovariateID: TCV StatID: ANOVA F: 12.64 P: <0.01 ObsID: 015 MeasureID: CC2 area GroupID: HC, BPD CovariateID: TCV StatID: ANOVA F: 5.18 P: 0.03
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For CC1, area measurement found age (F=5.28, p=0.03) to be a significant covariate.
ObsID: 013 MeasureID: CC1 area GroupID: HC, BPD CovariateID: age StatID: ANOVA F: 5.28 P: 0.03
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There was no significant difference between the younger BPD the younger HC.
ObsID: 012 ObsType: GroupComparison GroupID: BPD_young, HC_young MeasureID: CC Vol StatID: TTEST P: not significant
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Volumetric and area measurements found that the older HC (15.5 cc) had significantly larger total CC than the younger HC group (13.1 cc), whereas there was not a significant difference among the BPD age groups (13.6 and 13.7 cc).
ObsID: 006 MeasureID: CC vol GroupID: HC_old, HC_young CovariateID: Group StatID: TTEST P: significant ObsID: 007 MeasureID: CC vol GroupID: HC_old MeanValue: 15.5 Units: cc ObsID: 008 MeasureID: CC vol GroupID: HC_young MeanValue: 13.1 Units: cc ObsID: 009 MeasureID: CC Vol GroupID: BPD_old, BPD_young CovariateID: Group StatID: TTEST P: not significant ObsID: 010 MeasureID: CC area GroupID: BPD_old MeanValue: 13.6 Units: cc ObsID: 011 MeasureID: CC vol GroupID: BPD_young MeanValue: 13.7 Units: cc
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The youths with BPD had a mean MRS score of 20.8±9.5 (range 0–38)
ObsID: 001 GroupID: BPD MeasureID: MRS StatID: Descriptive Mean: 20.8 Std: 9.5 RangeMin: 0 RangeMax: 38
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the CC is divided into seven subregions which include: rostrum (CC1), genu (CC2), anterior body (CC3), midbody (CC4), posterior body (CC5), isthmus (CC6) and splenium (CC7) using anterior and posterior definitions as described in Witelson
AnalysisMethodID: CC area Inputs: MRI Software: proc_cc OutputVariables: CC area, CC1 area, CC2 area, CC3 area, CC4 area, CC5 area, CC6 area, CC7 area MeasurementType: Regional area MeasurementUnits: cm2 (square centimeters)
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Volu-metric assessment of the CC is provided as a distinct subset of regions within this WM parcellation system.
AnalysisMethodID: CC Volume Inputs: MRI Software: WM_Parc OutputVariables: CC Vol, CC1 Vol, CC2 Vol, CC3 Vol, CC4 Vol, CC5 Vol, CC6 Vol, CC7 Vol MeasurementType: Regional Volume MeasurementUnits: cc (cubic centimeters)
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Data from 66 participants (44 children with DSM-IV BPD, age 10.6±3.0 years (mean ± SD) and 22 HC, age 10.5±3.1 years (mean ± SD) are included in this report
GroupID: BPD N: 44 AgeMean: 10.6 AgeStd: 3.0 GroupID: HC N: 22 AgeMean: 10.5 AgeStd: 3.1
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Measures of current psychopathology were obtained using the Mania Rating Scale (MRS) (Young et al. 1978) and Global Assessment of Functioning scale (GAF
MeasureID: MRS MeasureDescription: Mania Rating Scale (MRS) MeasureDomain: current psychopathology MeasureReference: Young et al. 1978
MeasureID: GAF MeasureDescription: Global Assessment of Functioning scale (GAF) MeasureDomain: current psychopathology MeasureReference: American Psychiatric Association 1994)
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Individuals with BPD were diagnosed using DSM-IV criteria in semi-structured and clinical interviews; HC participants had no DSM-IV Axis I diagnoses or a family history of mood or psychotic disorders in first-degree relatives, based on parental interview.
GroupID: BPD Dx: Bipolar Disorder DxStandard: DSM-IV DxMethod: semi-structured and clinical interviews GroupID: HC GroupCharacteristic: no DSM-IV Axis I diagnoses or a family history of mood or psychotic disorders in first-degree relatives, based on parental interview
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youths with BPD were hypothesized to have reduced callosal growth in posterior regions.
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We hypothesized that (1) posterior callosal volumes would be reduced in youths with BPD given that these structures are rapidly maturing during childhood and adolescence and as a result may be more vulnerable during this time of significant brain myelination and pruning, particularly around the time of illness onset; (2) consistent with the hypothesized role of the prefrontal cortex in mood dysregulation and cognitive abnormalities in BPD (Soares and Mann 1997; Wilder-Willis et al. 2001), genual volume was expected to be abnormal (i.e., smaller) in youths with BPD; and (3) consistent with Brambilla and colleagues’ findings, there would be an absence of typical age-related changes in specific callosal volumes in youths with BPD (Brambilla et al. 2003).
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The present study represents the first application of a comprehensive set of measures that permit the comparison of total CC and callosal subregion areas and volumes in youths with BPD and HC.
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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Significant diagnostic differences were seen in the left and right cerebral volumes in interaction with sex (right: F3,93 = 2.9, P = .04; left: F3,93 = 3.1, P = .04).
ObservationID: 001 ObservationDepVar: Diagnostic Groups ObervationIndVar: Left Cerebral volume ObservationStat: what test was run? Pointer to StatisticMethod ObservationStatP: 0.04 ObservationStatF: 3.1 ObservationStatFDOF: 3 ObservationStatFN: 93 LinktoSourcedata: ??? LinktoStatExec: ??? ObservationID: 002 ObservationDepVar: Diagnostic Groups ObervationIndVar: Right Cerebral volume ObservationStat: what test was run? Pointer to StatisticMethod ObservationStatP: 0.04 ObservationStatF: 2.9 ObservationStatFDOF: 3 ObservationStatFN: 93
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McLean Hospital Brain Imaging Center on a 1.5 Tesla General Electric Signa Scanner
AcquisitionType: MRI Location: McLean Hospital Brain Imaging Center MRField: 1.5 Tesla Manufacturer: General Electric Model: Signa
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- Feb 2016
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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ouths with BPD without psychosis had a significant inverse correlation between the MRS score and amygdala volumes (right: r = –0.411, P = .02; left: r = –0.379, P = .004). No significant correlations were found in the BPD with psychosis group.
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In the youths with SZ, there was a significant inverse correlation between GAS score and left amygdala volume (r = –0.634, P = .011). Also, there was a significant correlation between MRS scores and the right NA (r = 0.634, P = .03).
result
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HCs had increasing volumes with age in the thalamus (right: r = 0.38, P = .04; left: r = 0.36, P = .06). In addition, the right amygdala volume correlated with GAS scores in the HCs (r = 0.470, P = .01).
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significant sex differences were observed in bilateral cerebrum and pallidum volumes across groups, with females having significantly smaller volumes than males.
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The asymmetry indices for all structures also did not differ significantly between groups.
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There were no between-group differences in the amygdala; however, there was significant diagnostic-by-sex interaction in the left amygdala (F3,93 = 3.0, P = .04). SZ males had the smallest left amygdala volume (effect size relative to other males = 0.65–1.23); this structure was actually enlarged relative to HC in the BPD groups
ObservationID: ObservationDepVar: ObervationIndVar: ObservationType: ObservationQualitative: LinktoSourcedata:
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For the subcortical structures, the omnibus statistics showed no diagnostic differences in the hippocampus but did show a trend for diagnostic-by-sex differences in the left hippocampus (F3,93 = 2.3, P = .08); post hoc analyses showed that the diagnostic reduction was particularly marked in the female patient groups
ObservationID: ObservationDepVar: ObervationIndVar: ObservationType:<br> ObservationQualitative:<br> LinktoSourcedata:
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Post hoc comparisons showed that both bipolar groups (with and without psychosis) had significantly smaller left and right cerebral volumes than HCs; this difference was even more marked in the female BPD groups. The SZ group did not differ significantly from the other groups.
ObservationID: 003 ObservationDepVar: BPDwoPSY vs. HC ObervationIndVar: Right Cerebral volume ObservationType: Post hoc ObservationQualitative: smaller volume LinktoSourcedata:
ObservationID: 004 ObservationDepVar: BPDwPSY vs. HC ObervationIndVar: Right Cerebral volume ObservationType: Post hoc ObservationQualitative: smaller volume LinktoSourcedata:
ObservationID: 005 ObservationDepVar: BPDwoPSY vs. HC ObervationIndVar: Left Cerebral volume ObservationType: Post hoc ObservationQualitative: smaller volume LinktoSourcedata:
ObservationID: 006 ObservationDepVar: BPDwPSY vs. HC ObervationIndVar: Left Cerebral volume ObservationType: Post hoc ObservationQualitative: smaller volume LinktoSourcedata:
ObservationID: 007 ObservationDepVar: Female BPDwoPSY vs. Female HC ObervationIndVar: Left Cerebral volume ObservationType: Post hoc ObservationQualitative: smaller volume LinktoSourcedata:
ObservationID: 008 ObservationDepVar: Female BPDwPSY vs. Female HC ObervationIndVar: Left Cerebral volume ObservationType: Post hoc ObservationQualitative: smaller volume LinktoSourcedata:
ObservationID: 009 ObservationDepVar: SZ vs. HC ObervationIndVar: Left Cerebral volume ObservationType: Post hoc ObservationQualitative: same LinktoSourcedata:
ObservationID: 010 ObservationDepVar: SZ vs. BPDwoPSY ObervationIndVar: Left Cerebral volume ObservationType: Post hoc ObservationQualitative: same LinktoSourcedata:
ObservationID: 011 ObservationDepVar: SZ vs. BPDwPSY ObervationIndVar: Left Cerebral volume ObservationType: Post hoc ObservationQualitative: same LinktoSourcedata:
ObservationID: 012 ObservationDepVar: SZ vs. HC ObervationIndVar: Right Cerebral volume ObservationType: Post hoc ObservationQualitative: same LinktoSourcedata:
ObservationID: 013 ObservationDepVar: SZ vs. BPDwoPSY ObervationIndVar: Right Cerebral volume ObservationType: Post hoc ObservationQualitative: same LinktoSourcedata:
ObservationID: 014 ObservationDepVar: SZ vs. BPDwPSY ObervationIndVar: Right Cerebral volume ObservationType: Post hoc ObservationQualitative: same LinktoSourcedata:
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35 youths with BPD I without psychosis (mean age = 10.4 ± 3.0 years), 19 with BPD I with psychosis (mean age = 11.6 ± 2.6 years), 20 with SZ or schizoaffective disorder (mean age = 13.5 ± 2.9 years), and 29 HCs (mean age = 10.5 ± 2.9 years). The proportion of males in each group ranged from 47.4% to 58.8%
SubjectGroup: BPDwoPSY N: 35 Diag: BPD I without psychosis MeanAge: 10.4 AgeSTD: 3.0
SubjectGroup: BPDwPSY Diag: BPD I with psychosis N: 19 MeanAge: 11.6 AgeSTD: 2.6
SubjectGroup: SZ Diag: SZ or schizoaffective disorder N: 20 MeanAge: 13.5 AgeSTD: 2.9
SubjectGroup: HC Diag: Healthy Control N: 29 MeanAge: 10.5 AgeSTD: 2.9
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Differences in right and left subcortical brain volumes were evaluated using 2-way (diagnosis, sex) univariate analyses covarying for TCV and age. Similar models were also evaluated on the asymmetry index for each structure, which was calculated as (right volume−left volume)/(right volume + left volume)÷ 2. Post hoc between-group tests were corrected for multiple comparisons using the Tukey-Cramer honestly significant difference method. Differences in demographic and clinical variables between groups were assessed using analyses of variance for continuous variables and chi-square tests for categorical variables. In addition, within-group Pearson and Spearman correlations were performed on clinical variables and those structures which were found to be significantly different between diagnostic groups. These clinical variables included MRS and GAF scores, age at onset of illness, duration of illness, and chlorpromazine equivalents. In an effort to be conservative, we report only clinical correlations that reached significance on both Spearman and Pearson tests; the r and P value for the Pearson correlations are reported. Effect sizes were calculated and interpreted using Cohen d statistic. All statistical tests were 2 sided with alpha = .05. JMP 7 for Mac (SAS Institute, Cary, NC) was used for statistical analysis.
Statistical Method - Steve to add formalisms... But, I guess it might include:_
StatSoftare: JMP StatSoftwareOS: Mac StatSoftwareVersion: 7 StatSoftwareManufacturer: SAS Institute StatSoftwareManufacturerLocation: Cary, NC
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The caudate was measured in its entirety (head, body, tail superior to ventricular trigone, and ventral striatum), defined superomedially by the interface with the lateral ventricles, inferiorly by the interface with the adjacent rostral peduncle of the thalamus (when present), and otherwise by the interface with adjacent white matter; putamen was defined medially by the external medullary lamina of the globus pallidus, laterally by the external capsule, and otherwise by adjacent white matter; globus pallidus was defined superomedially by the interface with the internal capsule, inferiorly by the anterior commissure, ansa lenticularis, or nucleus basalis, when present, and laterally by the external medullary lamina.43 The NA was separated from putamen and caudate superiorly by a segmentation line that connects the inferiormost tip of the lateral ventricle to the most ventral point of the internal capsule at the level of the ventral putamen. From this last point, a vertical line is drawn to define the lateral border with the putamen.45
Anatomic analysis method details - caudate
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The amygdala and hippocampus were defined as a continuous gray matter structure in the primary segmentation. The hippocampus was then separated from the amygdala at the rostral-coronal plane, where the hippocampus first appears. The segmentation of the amygdala was performed manually in its entirety. The cross-referencing capability of Cardviews was used to outline the amygdala in axial and sagittal views, allowing a reliable preliminary separation of the amygdala from surrounding gray structures. The anterior portion of the amygdala was segmented because it appears beneath the medial temporal cortex. The choroidal fissure was used as the superior border of the amygdala along with the gray-white matter contrast between the amygdala and the surrounding white matter. The lateral border was defined using the gray-white matter contrast between the amygdala and the surrounding temporal white matter and the gray-CSF contrast between the amygdala and temporal horn of the lateral ventricle. The medial borders consisted of the parahippocampal cortex, the brain exterior at the inferior lip of the choroidal fissure, and partially the hippocampus. Finally, the inferior border consisted of the gray-white matter contrast between the amygdala and the surrounding temporal white matter and the alveus of the hippocampus and temporal horn of the lateral ventricle.
Anatomic analysis method details - amygdala and hippocampus
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Segmentation of the thalamus traced the trajectory of the hypothalamic fissure in the sagittal plane to separate the thalamus proper from the ventral diencephalon. The structure was bounded medially by the third ventricle and laterally by the internal capsule. The superior border was the body of the lateral ventricle, and the inferior border was the hypothalamic fissure.
Anatomic analysis method details - thalamus
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using Cardviews software.
OutcomeType: Volume AnalysisSoftware: Cardviews AnalysisSoftwareLink: http:...
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