News
Data sharing in neuroimaging research - Review Article
By David Kennedy from NITRC Community News. Published on May 22, 2012.
With apologies for the slightly shameless promotion, but an interesting review article by JB Poline, et al. has recently been published in Frontiers in Neuroinformatics (as part of a special issue on "Electronic Data Capture, Representation, and Applications in Neuroimaging" hosted by John Van Horn and Jessica A. Turner) entitled "Data sharing in neuroimaging research". See http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00009/abstract for the details.Abstract: Significant resources around the world have been invested in neuroimaging studies of brain function and disease. Easier access to this large body of work should have profound impact on research in cognitive neuroscience and psychiatry, leading to advances in the diagnosis and treatment of psychiatric and neurological disease. A trend toward increased sharing of neuroimaging data has emerged in recent years. Nevertheless, a number of barriers continue to impede momentum. Many researchers and institutions remain uncertain about how to share data or lack the tools and expertise to participate in data sharing. The use of electronic data capture (EDC) methods for neuroimaging greatly simplifies the task of data collection and has the potential to help standardize many aspects of data sharing. We review here the motivations for sharing neuroimaging data, the current data sharing landscape, and the sociological or technical barriers that still need to be addressed. The INCF Task Force on Neuroimaging Datasharing, in conjunction with several collaborative groups around the world, has started work on several tools to ease and eventually automate the practice of data sharing. It is hoped that such tools will allow researchers to easily share raw, processed, and derived neuroimaging data, with appropriate metadata and provenance records, and will improve the reproducibility of neuroimaging studies. By providing seamless integration of data sharing and analysis tools within a commodity research environment, the Task Force seeks to identify and minimize barriers to data sharing in the field of neuroimaging.
Entertaining read for fMRI practitioners!
By David Kennedy from NITRC Community News. Published on May 18, 2012.
Just spotted at online at http://www.sciencedirect.com/science/article/pii/S1053811912003990 is an upcoming 'Comments and Controversies' article in NeuroImage by Karl Friston entitled "Ten ironic rules for non-statistical reviewers". Looks like a 'must read' for your summer vacation!Abstract: As an expert reviewer, it is sometimes necessary to ensure a paper is rejected. This can sometimes be achieved by highlighting improper statistical practice. This technical note provides guidance on how to critique the statistical analysis of neuroimaging studies to maximise the chance that the paper will be declined. We will review a series of critiques that can be applied universally to any neuroimaging paper and consider responses to potential rebuttals that reviewers might encounter from authors or editors.
Update of iBEAT 1.1 package
By Yakang Dai from NITRC Community News. Published on May 15, 2012.
A bug on tissue segmentation of single-time-point image is reported and fixed.The Neuro-Bureau Brain-Art Competition 2012
By Michael Milham from NITRC Community News. Published on May 10, 2012.
NEURO-BUREAU BRAIN-ART COMPETITION 2012http://www.neurobureau.org/BrainArt/
Submission Deadline: 11:59PM CDT, Friday, June 1st, 2012
Award Notification: June 11th during the OHBM Annual Meeting, Beijing.
In order to recognize the beauty and creativity of artistic renderings emerging from the neuroimaging community, we are launching the second annual Brain-Art Competition.
Countless hours are devoted to the creation of informative visualizations for communicating neuroscientific findings. The Brain-Art Competition aims to recognize this often unappreciated aspect of the publication process, and highlight the artistic creativity of our community.
We are inviting researchers to submit their favorite unpublished works for entry. Both team and single-person entries are welcomed. The competition will have four award categories:
1) Best Representation of the Human Connectome
2) Best Educational Brain Illustration
3) Best Abstract Brain Illustration
4) Best Humorous Brain Illustration
5) Best Video Illustration of the Brain
Sponsored by: Child Mind Institute (http://www.childmind.org/)
NIF Webinar Recording Available – May 8, 2012
By Lee Hornbrook from NIF Blog. Published on May 08, 2012.
Miss today's Webinar? You're in luck. Check out the NIF Webinar archive for a recording of Cognitive Atlas, by Russell Poldrack.CMTK 2.2 release adds new features
By Torsten Rohlfing from NITRC Community News. Published on May 08, 2012.
We are pleased to announce the release of CMTK 2.2 with some exciting new features. Source code and pre-compiled packages are available from CMTK's "Downloads" section on NITRC.Most importantly, CMTK now has two tools to perform structural MRI unwarping using reference scans of the "ADNI Phantom." The workflow is described in a brief paper over at the InsightJournal:
http://hdl.handle.net/10380/3354
This article can also be downloaded from the CMTK/Docs section on NITRC.
Many other detail fixes and improvements have also gone into this release - check out the ChangeLog for details.
As always, all of CMTK is free as in beer and speech, and you don't even have to make us authors on any of your papers just for using it. Imagine that! (Please do mention CMTK in your Acknowledgments if you use it, though.)
[Note: the original 2.2.0 release had a packaging bug and was replaced with release 2.2.1]
Top 25 Accessed Databases at NIF for April 2012
By Lee Hornbrook from NIF Blog. Published on May 07, 2012.
Want to know the top 25 accessed databases at NIF? Find out here!Top 25 Search Terms at NIF for April
By Lee Hornbrook from NIF Blog. Published on May 07, 2012.
Want to know the top search terms at NIF? Find out here!Matlab Files Added
By Makoto Takemiya from NITRC Community News. Published on May 04, 2012.
In addition to being able to download Neuroshare (.nsn) files, we added the ability to download Matlab (v7.3) .mat files, which can be read natively by Matlab and by HDF5 libraries in languages like Python and R.This is a huge update to our project and we are happy to now offer automatic conversion of all uploaded .nsn files to Matlab.
NIF Webinar – May 8, 2012 at 11:00 am PDT
By Lee Hornbrook from NIF Blog. Published on May 03, 2012.
Join Dr. Russell Poldrack for a discussion of the Cognitive Atlas at the next NIF Webinar on May 8 at 11:00 am PDT.Announcing the INDI Summer of Sharing 2012
By Michael Milham from NITRC Community News. Published on May 02, 2012.
THE INTERNATIONAL NEUROIMAGING DATA-SHARING INITIATIVE (INDI) SUMMER OF SHARING 2012http://fcon_1000.projects.nitrc.org/
Open science initiatives are transforming the neuroimaging community. Researchers who once struggled to obtain 20-30 datasets now have unrestricted access to thousands of scans, including data obtained from developing, aging and clinical populations. Equally important, the sharing of data analysis scripts and code is becoming increasingly common, thereby enhancing the dissemination of knowledge and capabilities among laboratories – as well as facilitating replication efforts. Although exciting, we are only at the beginning. The success of open science initiatives remains dependent upon continued community participation.
Against this background, the International Neuroimaging Data-sharing Initiative (INDI) is pleased to announce the launch of its 2012 Summer of Sharing – an effort dedicated to the sustenance and acceleration of data and analytic resource sharing among imaging community members. In order to accomplish its goal the INDI Summer of Sharing initiative is requesting pledges for the contribution of:
1) DATA: Resting state fMRI and/or diffusion data employed in published studies, along with any available meta-data you’d like to share (See INDI Retro for previously shared datasets; examples include Kelly C. et al., 2011 Bio Psych, Keller C. et al., 2011 PNAS, and Power J. et al., 2012 Neuroimage).
2) ANALYTIC RESOURCES: Python, Matlab, BASH, C/C++ - we’re not choosy! INDI is actively promoting the sharing of analytic scripts and codes employed in published and/or ongoing studies through NITRC and GitHub – if you post them, we’ll help to make sure you’re recognized for it.
3) OPEN SCIENCE EVENTS: Just provide us the information and we’ll help to get the word out!
4) MISCELLANEOUS RESOURCES: Atlases, parcellation schemes, reference resources, etc. – everyone can benefit from them.
We are actively asking investigators around the world to get involved in the sharing process. Already, the following resources are scheduled for sharing this summer:
1) The Autism Brain Imaging Data Exchange (ABIDE): a global, multisite consortium of laboratories dedicated to the study of autism that will release an aggregate dataset that is expected to consist of nearly 500 individuals with autism, and their matched typically developing controls.
2) The Enhanced NKI Rockland Sample: a recently launched large-scale, R-fMRI and DTI cross-sectional, community ascertained sample of individuals between 6 and 85 years of age, accompanied by a deep phenotypic protocol that broadly samples psychiatrically relevant behavioral domains.
3) Brainhack: a Neuro-Bureau resource (http://brainhack.org/) that points to collaborative projects in the field; the resource will be complemented by the Brainhack 2012 Unconference – a workshop that will blend the “unconference” and “hackathon” concepts to create a unique collaborative experience for participants interested in advancing analytic techniques and resources for functional and structural imaging.
4) The Configurable Pipeline for the Analysis of Connectomes (C-PAC): Building on the success of the release of the 1000 Functional Connectomes Project analysis scripts, the INDI team will be releasing a plug-and-play Nipype-based pipeline package that is easily configurable to accomplish a broad array of resting-state fMRI analyses.
5) DPARSF and REST: With the new releases of MATLAB-based user-friendly pipelines of Data Processing Assistant for Resting-State fMRI (DPARSF 2.2) and Resting-State fMRI Data Analysis Toolkit (REST 1.8) (www.restfmri.net), users can acquire resting-state fMRI measures efficiently (by parallel computing) and conveniently (by GUI or command line).
6) Power et al. 2011 (Neuron): The authors are now sharing the summary community assignments from their work on fcMRI networks (http://sumsdb.wustl.edu/sums/directory.do?id=8293343&dir_name=power_Neuron11), and will release a suite of scripts through NITRC this summer, so that others can replicate these analyses and carry out related work. Additionally, later this summer, the dataset used for this work will be released through INDI.
7) The Child Mind Institute (CMI) Librarian Initiative: Comprehensive hand-vetted and sorted reference libraries for various literatures, including Resting State fMRI and Diffusion Tensor Imaging are now available via Mendeley, with monthly updates scheduled (http://www.mendeley.com/profiles/cmi-librarian/).
It is our hope that this list is just the beginning. We will follow with updates throughout the summer months. The success of open science depends on all of us – so get involved, and Share That Brain!
Contact us at INDI_SummerOfSharing@childmind.org to make a pledge or learn more about how to get involved.
The International Neuroimaging Data-sharing Initiative (INDI) is now sponsored by the Child Mind Institute (http://childmind.org).
NIF Webinar - Mind Research Network and BrainMap
By David Kennedy from NITRC Community News. Published on Apr 30, 2012.
The next NIF Webinar will be held on Tuesday, May 1, 2012 at 11:00 am PDT. Please join Drs. Angie Laird & Jessica Turner as they discuss the Mind Research Network and BrainMap projects.The following is a description of the webinar:
Drs. Turner and Laird will discuss a cooperative project between the Mind Research Network and BrainMap projects to consistently gather and annotate fMRI data. Both projects represent cognitive processes using the CogPO ontology, a community standard for representing cognitive paradigms. CogPO is used because while the experimental psychology and cognitive neuroscience literature may refer to certain behavioral paradigms by name (eg. the Stroop paradigm or the Sternberg paradigm) or by function (a working memory task, a visual attention task), these paradigms can vary tremendously in the stimuli that are presented to the subject, the response expected from the subject, and the instructions given to the subject. Disentangling the various paradigms into their components may help to disentangle the complex data from fMRI experiments.
Background on BrainMap:
The BrainMap Project is developed at the Research Imaging Institute of the University of Texas Health Science Center San Antonio. BrainMap was conceived in 1988 and originally developed as a web-based interface. After more than 20 years of development, BrainMap has evolved into a much broader project whose software and data have been utilized in numerous publications. BrainMap provides not only data for meta-analyses and data mining, but also distributes software and concepts for quantitative integration of neuroimaging data. The BrainMap Project is developed at the Research Imaging Institute of the University of Texas Health Science Center San Antonio. BrainMap was conceived in 1988 and originally developed as a web-based interface. After more than 20 years of development, BrainMap has evolved into a much broader project whose software and data have been utilized in numerous publications. BrainMap provides not only data for meta-analyses and data mining, but also distributes software and concepts for quantitative integration of neuroimaging data.
Date and Time: Tuesday, May 1, 2012 • 11:00-12:00 PDT
Topic: Mind Research Network and BrainMap projects
Presenters: Drs. Angie Laird & Jessica Turner
URL: http://connect.neuinfo.org/webinar
NIF Webinar – May 1, 2012 at 11:00 am PDT
By Joanne from NIF Blog. Published on Apr 27, 2012.
The next NIF webinar is Tuesday, May 1, 2012 by Angie Laird and Jessica Turner who will discuss "Mind Research Network and BrainMap."NIF April 24, 2012 Webinar Available in Archives
By Joanne from NIF Blog. Published on Apr 27, 2012.
The webinar from April 24, 2012 by Janna Hastings is available for viewing in the webinar archives.NIH Pediatric MRI Data Repository - 5th Release
By NDAR Administrator from NITRC Community News. Published on Apr 26, 2012.
The National Institutes of Health (NIH) are pleased to make available the 5th data release of the NIH MRI Study of Normal Brain Development to qualified researchers. New in this release are longitudinally-registered anatomic MRI data (images and derived volumetric measures), processed single-voxel MRS data which has been corrected for CSF voxel content, raw multi-voxel MRSI files, low resolution (3mm) diffusion tensor imaging (DTI) data, additional demographic measures, and revised biospecimen collection dates. Previous releases contained non-longitudinally registered anatomic MRI data (scans and derived volumes), cortical surface analysis data, age-specific brain atlases, raw and preliminary single-voxel MRS data uncorrected for CSF voxel content, and clinical/behavioral data for subjects aged 10 days to young adult. To learn about accessing this data, please visit http://pediatricmri.nih.gov.New BIRN Capability: nihmaps.org
By NITRC ADMIN from NITRC Community News. Published on Apr 24, 2012.
BIRN announces a new capability that allows you to view a "topic map" of NIH grants that can be queried in several ways.NIF Webinar – April 24, 2012 at 11:00 AM PDT
By Joanne from NIF Blog. Published on Apr 23, 2012.
The next NIF webinar is Tuesday, April 24, 2012 by Janna Hastings who will discuss "Mental Functioning Ontology."Top 25 Search terms at NIF for the week of April 8, 2012
By Lee Hornbrook from NIF Blog. Published on Apr 16, 2012.
Want to know the top 25 search terms at NIF for the week of April 8, 2012? Find out here!Top 25 Accessed Databases for the week of April 8, 2012
By Lee Hornbrook from NIF Blog. Published on Apr 16, 2012.
Want to know the top access databases at NIF for the week of April 8, 2012? Find out here!NIF Webinar – April 17, 2012 at 11:00 PDT
By Lee Hornbrook from NIF Blog. Published on Apr 16, 2012.
The next NIF webinar is Tuesday, April 17, 2012 by Dr. Gwen Frishkoff who will discuss "Harmonizing the Representation of Coginitive Processes."CRCNS.org 2012 summer course
By admin from News. Published on Mar 01, 2012.
Mining and modeling of neuroscience dataCaDRE (Collaborative Database for Reaching Experiments) added.
By admin from News. Published on Feb 15, 2012.
Resources for scientists interested in reaching experiments (arm and hand movements) to share data, models, and ideas. Organized by Konrad Kording and Ben Walker of Northwestern University. (klab.smpp.northwestern.edu).compneuronews.org live.
By admin from News. Published on Nov 10, 2011.
A collaborative site for posting computational neuroscience news, articles, voting and getting feedback is now available.fMRI 'mind reading' data set available.
By admin from News. Published on Nov 10, 2011.
Quantitative receptive-field models that characterize the relationship between visual stimuli and fMRI activity in early visual areas make it possible to identify, from a large set of completely novel natural images, which specific image was seen by an observer.Visual Cortex area V2 data available
By admin from News. Published on May 25, 2011.
Consists of about 400 extracellular recordings recordings from about 100 well isolated neurons in area V2 in awake behaving macaque monkeys. Contributed by lab of Jack Gallant, of UC Berkeley.Zebra finch recordings added
By admin from News. Published on Mar 15, 2011.
New data set contains about 500 single-unit recordings from different audio areas in zebra finches. Most were simultaneously recorded from two different brain regions. Contributed by the Frederic Theunissen lab at UC Berkeley.CRCNS.org 2011 summer course
By admin from News. Published on Mar 04, 2011.
Mining and modeling of neuroscience dataHippocampus data set updated
By admin from News. Published on Jan 16, 2011.
Contributed by the Gyorgy Buzsáki lab, at Rutgers University.New auditory cortex data set available
By admin from News. Published on Jan 16, 2011.
Contains whole cell recordings from rat primary auditory cortex along with recordings of nearby local field potentials (LFP).Site upgraded
By admin from News. Published on Nov 05, 2010.
Site was upgraded to a newer version of Plone (3.3.5) and also moved to a new server. Let us know (via the contact form) if you experience any difficulties.2009 Prediction challenge data sets added
By admin from News. Published on Jan 22, 2010.
Data are from rat cortical neurons and rhesus monkey lateral geniculate nucleus and retinal ganglion cells.New Hippocampus data set added.
By admin from News. Published on Nov 25, 2009.
Contributed by the Gyorgy Buzsáki lab, at Rutgers University.Matlab script for pvc-2 data set updated.
By admin from News. Published on Nov 10, 2009.
The script to generate tuning curves has been updated.Insect Auditory data set added
By admin from News. Published on Jul 10, 2009.
Recordings from grasshopper (Locusta Migratoria) auditory receptor cells.Site upgraded to latest Plone
By admin from News. Published on Feb 25, 2009.
Site was upgraded to Plone version 3.2.1. Let us know (via the contact form) if you experience any difficulties.
