NITRC Community News

Update of iBEAT 1.1 package

daiyakang@www.nitrc.org (Yakang Dai) — Tue, 15 May 2012 11:35:33 GMT

A bug on tissue segmentation of single-time-point image is reported and fixed.

The Neuro-Bureau Brain-Art Competition 2012

milham01@www.nitrc.org (Michael Milham) — Thu, 10 May 2012 17:19:50 GMT

NEURO-BUREAU BRAIN-ART COMPETITION 2012
http://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We are inviting researchers to submit their favorite unpublished works for entry.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/)

CMTK 2.2 release adds new features

torstenrohlfing@www.nitrc.org (Torsten Rohlfing) — Tue, 08 May 2012 11:28:19 GMT

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]

Matlab Files Added

mtakemiya@www.nitrc.org (Makoto Takemiya) — Fri, 04 May 2012 12:32:02 GMT

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.

Announcing the INDI Summer of Sharing 2012

milham01@www.nitrc.org (Michael Milham) — Wed, 02 May 2012 19:13:24 GMT

THE INTERNATIONAL NEUROIMAGING DATA-SHARING INITIATIVE (INDI) SUMMER OF SHARING 2012
http://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

dnkennedy@www.nitrc.org (David Kennedy) — Mon, 30 Apr 2012 20:11:30 GMT

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

NIH Pediatric MRI Data Repository - 5th Release

ndar@www.nitrc.org (NDAR Administrator) — Thu, 26 Apr 2012 12:06:04 GMT

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

nitrcadmin@www.nitrc.org (NITRC ADMIN) — Tue, 24 Apr 2012 14:28:53 GMT

BIRN announces a new capability that allows you to view a "topic map" of NIH grants that can be queried in several ways.

2012 Brainhack, Sept 1-4, Leipzig Germany

ccraddock@www.nitrc.org (Cameron Craddock) — Fri, 20 Apr 2012 15:36:55 GMT

The Neuro Bureau is proud to announce the 2012 Brainhack to be held from September 1-4 at the Max Plank Institute for Human Cognitive and Brain Sciences in Leipzig, Germany.

Brainhack is a unique event with the goals of fostering interdisciplinary collaboration and open neuroscience. The structure for the conference builds from the concepts of an unconference and hackathon. The term “unconference” refers to a conference structure in which most of the content is dynamically chosen by the participants – and a hackathon is an event where participants collaborate intensively on science-related projects. Brainhack will be a blend of both elements. On the last day, collaborative groups will give a brief presentation detailing their project, and the progress that was made over the course of the Brainhack.

We encourage participants across all disciplines related to neuroimaging to come prepared to present and discuss their research interests. Additionally, there will be the opportunity to present a poster during the first evening of the workshop.

Please visit: (http://www.cbs.mpg.de/events/workshops/brainhack) for more information and to register and prepare for the conference.

Registration Deadline: 30 July 2012 (However, we encourage early registration, as space will be limited).

3D Slicer version 4.1 released!

pieper@www.nitrc.org (Steve Pieper) — Wed, 18 Apr 2012 21:00:42 GMT

The 3D Slicer community is pleased to announce the release of version 4.1:

http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Announcements

Binary installers for Mac, Linux 64 bit, and Windows 32 and 64 bit
versions are available now for download at:

http://download.slicer.org/

Interested parties can sign up for a 20 minute live webinar to introduce the new features of Slicer 4.1. The webinar will be held Thursday, April 26, 2012 1:00 PM EDT. Experts will be available for text based Q&A during the webinar. Please register here (space limited to 100 participants):

https://www3.gotomeeting.com/register/250936886

The webinar will be recorded and made available for those who can't attend the live event.

Video of a previous 1.5 hour webinar describing various features of 3D Slicer 4.0 is available at:

http://vimeo.com/37671358

And, everything else you need to know about slicer is available at:

http://www.slicer.org