NITRC Community News

SRI24 Atlas now in NeuroDebian

Torsten Rohlfing — Wed, 08 Feb 2012 2:40:08 GMT

Users of NeuroDebian can now install the SRI24 atlas (NIFTI file format) via

apt-get install sri24-atlas

Imaging the Alzheimer Brain - Special Issue in JAD

David Kennedy — Mon, 06 Feb 2012 12:37:07 GMT

Volume 26, Supplement 3, October 2011 - "Imaging the Alzheimer Brain" (Guest Editors: J.W. Ashford, A. Rosen, M. Adamson, P. Bayley, O. Sabri, A. Furst, S.E. Black and M. Weiner)

Lots of cool stuff here, check it out at: http://www.j-alz.com/issues/imaging.html

NIF says - Open Hardware in Science: Benefits and Challenges

David Kennedy — Fri, 03 Feb 2012 5:24:39 GMT

Forwarded from NIF: The next NIF Webinar will be held on Tuesday, February 7, 2012 at 11:00 am PST. Please join Carlo Quinonez as he discusses Open Hardware in Science: Benefits and Challenges.

The following is a description of the webinar:

The need for free and easy access to scientific data and other information essential to scientific experiments has been clearly recognized for decades. Developments such as open source software, open data, open access journals and open courseware rely on the easy and efficient transfer of information over the Internet. However, the dissemination and collaborative development of open hardware for the benefit of scientific progress poses unique challenges and opportunities. The widespread prevalence of scientist-developed tools has been driven by commercial instruments' lack of flexibility and detailed engineering data vital for user-improvements. While these technologies are put to good use by their developers, practical issues such as poor documentation, difficulty of fabrication, and idiosyncratic operation typically limit the utility to broader research community. In this webinar we will discuss the open hardware toolset, Aquinas, that addresses some of these issues and provides a shared hardware platform for biological experimentation. Currently, several micro-fluidics designs are available for fabrication. The facile reproduction of scientist-developed tools improves the reproducibility and transparency of science overall. Furthermore, a shared hardware platform for biological experimentation would also propel large-scale collaborative efforts to significantly accelerate the discovery of cures and scientific breakthroughs.

Date and Time: Tuesday, February 7, 2011 • 11:00-12:00 PST
Topic: OpenHardware in Science: Benefits and Challenges
Presenter: Carlo Quinonez, Ph.D., IRACDA Fellow in the Department of Pharmacology, University of California, San Diego.
URL: http://connect.neuinfo.org/webinar
Dial-In (toll-free): 866-740-1260
Access Code: 8220739

Mark your calendars! See you there.

Caret Version 5.65 Released

Jennifer Elam — Wed, 01 Feb 2012 2:59:52 GMT

Version 5.65 of Caret has been released. The new version includes:
* fixed a problem with PALS_B12 left case 03 and average fiducial surfaces
* error check added in case a file is truncated
* CCNMD FNIRT surfaces added to the fmri_mapping files subdirectory
* FNIRT stereotaxic space added
* myelin mapping function and documentation added

Caret can be downloaded at http://brainvis.wustl.edu/wiki/index.php/Caret:Download

Deep Brain Stimulation in the Wall Street Journal

David Kennedy — Mon, 30 Jan 2012 12:24:45 GMT

... Deep brain stimulation, sometimes called a pacemaker for the brain, has helped halt tremors in more than 100,000 patients with Parkinson's disease and other movement disorders since 1997. Now, researchers are reporting encouraging results using the procedure for psychiatric conditions as well. [...] in a study published this month in the Archives of General Psychiatry [...] after two years of DBS, 92% reported significant relief from their major depression or bipolar disorder and more than half were in remission, with no manic side effects.

Read the entire article at: http://online.wsj.com/article/SB10001424052970204555904577164813955136748.html#articleTabs=article

Measure Projection 1.41

Nima Bigdely-Shamlo — Thu, 26 Jan 2012 9:50:41 GMT

A new version of Measure Projection toolbox (MPT) is ready to download. New features includes:

(1) Cortex visualization: now you can show Domains and other brain regions directly on cortex (with some approximation of course, since we do not have subject-specific MRI).

(2) Topological Segmentation: Domain are now automatically separated so each forms a connected segment.

(3) Volume surface visualization is implemented and is the default visualization method in the GUI (no more Lego cubes, attached image).

(4) Automatic anatomical lookup, here is an example (percent dipole mass in each are is indicated in parenthesis) :

Domain 1
BA 10 (0.48)
BA 11 (0.22)
BA 32 (0.20)
------------------------------------------------
L Superior Frontal Gyrus (0.31)
R Superior Frontal Gyrus (0.27)
R Middle Orbitofrontal Gyrus (0.15)
R Middle Frontal Gyrus (0.12)
L Gyrus Rectus (0.05)
R Gyrus Rectus (0.05)

New generation of Symmetric HAMMER is released!

Qian Wang — Mon, 23 Jan 2012 5:30:32 GMT

Check our latest patch and upgrade your HAMMER Suite installation please. The new registration method provides more accurate registration results compared with our previous releases.

CMTK 2.1.1 released

Torsten Rohlfing — Wed, 18 Jan 2012 3:58:52 GMT

We are pleased to announce the release of CMTK 2.1.1.

Most significant addition in this release is a new tool, "epiunwarp", for correction of B0-field distortion in echo-planar MR images (e.g., diffusion-weighted images). The tool implements an algorithm by Holland et al. (NeuroImage 50(1):175-183, 2010; http://dx.doi.org/10.1016/j.neuroimage.2009.11.044) that requires two EPI acquisitions with opposing phase encoding directions, but no field map.

This release also adds a simple tool ("gmm") for tissue classification using a Gaussian mixture model and atlas-based tissue priors.

Allen Brain Atlas training offered at UCSD

David Kennedy — Thu, 12 Jan 2012 12:55:07 GMT

A training workshop is being offered at UCSD for the Allen Brain Atlas. "Using the Allen Brain Atlas Online Public Resources" will feature a training workshop on the Allen Brain Atlas online public resources for exploring gene expression in the nervous system. Basic data access, navigation and usability will be covered as well as more sophisticated search and visualization features.

Participation is free.
Advanced registration is required.

To register: Email info@alleninstitute.org and indicate "UCSD Training Workshop" in the subject line. Capacity is limited.

The workshop will be held:

Monday, January 23, 2012
1:30 pm - 4:30 pm
UCSD
CNCB Auditorium
La Jolla, CA

This workshop will touch on the full spectrum of resources available via the Allen Brain Atlas data portal (www.brain-map.org), but will focus primarily on navigation and search features of the following data sets:

> Adult human brain
> Adult mouse brain
> Non-human primate brain

For a hands-on experience, attendees are encourages to bring a laptop with Internet/Wi-Fi connectivity so that they can follow along.

Thank you!

Get ready for Brain Awareness Week

David Kennedy — Mon, 09 Jan 2012 4:21:14 GMT

Brain Awareness Week (BAW), March 12-18, 2012, is the global campaign to increase public awareness of the progress and benefits of brain research.

Every March, BAW unites the efforts of partner organizations worldwide in a celebration of the brain for people of all ages. Events are limited only by the organizers’ imaginations and include open days at neuroscience labs; exhibitions about the brain; lectures on brain-related topics; displays at libraries and community centers; classroom workshops; and more.

For information see: http://www.dana.org/brainweek/