Tool/Resource News

International Congress on Default Mode Network

dmn@www.nitrc.org (viajes iberia) — Tue, 09 Mar 2010 20:55:20 GMT

We are pleased to announce a forthcoming conference: Default Mode Network and other intrinsic networks in health and disease.

The last decade has seen important advances in functional brain imaging. As part of these, since 2001 there has been growing interest in default mode network, a series of interconnected brain regions which are highly active at rest but de-activate during performance of many cognitive tasks. This network appears to have important functions related to self-directed thought and is being increasingly implicated in disorders such as dementia, schizophrenia and affective disorder.

This meeting will take place in Barcelona on the 4th and 5th of June. It will bring together leading researchers on the default mode network, and will provide a forum for sharing the latest information on the rapid evolving knowledge in the field. There will be keynote speeches from Marcus Raichle and Michael Greicius, and sessions will be devoted to recent advances in understanding of the default mode network, changes across the lifespan (including aging and age-related neurodegenerative disorders), and the default mode network in a range of psychiatric disorders. Connectivity and other brain networks will be also part of the programme.

This meeting will take place in Barcelona on the 4th and 5th of June. It will bring together leading researchers on the default mode network, and will provide a forum for sharing the latest information on the rapid evolving knowledge in the field. There will be keynote speeches from Marcus Raichle and Michael Greicius, and sessions will be devoted to recent advances in understanding of the default mode network, changes across the lifespan (including aging and age-related neurodegenerative disorders), and the default mode network in a range of psychiatric disorders. Connectivity and other brain networks will be also part of the programme.

The conference takes place immediately before the Human Brain Mapping Conference in Barcelona and will be an official satellite of this meeting.

For more information, please visit: www.defaultmodenetwork.com

Bassett brain dissections

binarybottle@www.nitrc.org (Arno Klein) — Tue, 09 Mar 2010 13:21:20 GMT

Stanford University is making available a very valuable collection of stereophotographs taken by William Gruber, the inventor of the View-Master, of brains painstakingly dissected over the course of 17 years by David Bassett -- 225 photographs of brains are now viewable online.

http://lane.stanford.edu/bassett/bassettView.html?bn=70-7#bassett=/bassettsView.html%3Fr%3DHead--Brain

NYTimes article: http://www.nytimes.com/2008/04/22/science/22bass.html?_r=1

Cheers,
@rno

NIBIB Director Elected to National Academy of Engineering

dnkennedy@www.nitrc.org (David Kennedy) — Mon, 08 Mar 2010 18:02:46 GMT

Roderic I. Pettigrew, Ph.D., M.D., Director of the National Institute of Biomedical Imaging and Bioengineering, has been elected to the National Academy of Engineering. Dr. Pettigrew was recognized for "the use of MRI in human blood-flow studies and leading advancements in bioengineering research and education as the initial director of NIBIB."

The National Academy of Engineering (NAE), a member of the National Academies, has peer-elected members who are among the world's most accomplished engineers and physical scientists. The NAE was founded to provide engineering leadership in service to the nation, and election to the NAE is one of the highest professional distinctions accorded to an engineer. The Academy honors those who have made outstanding contributions to this scientific and educational discipline. Dr. Pettigrew is one of 68 new members elected nationwide in 2010.

With his election to the National Academy of Engineering, Dr. Pettigrew becomes the first member of the NIH community to be elected to both the NAE and the Institute of Medicine (IOM), an honor he received in 2007. The IOM is renowned for its research program and serves as an honorific organization whose members are elected for their excellence and professional achievements. Election to the IOM is considered one of the highest honors in the fields of medicine and health.

1000 Functional Connectomes Project Script Distribution

milham01@www.nitrc.org (Michael Milham) — Thu, 04 Mar 2010 14:51:05 GMT

We are pleased to announce the beta-release of the scripts that supported the initial feasibility analyses recently reported in PNAS (Biswal et al., 2010). The release is comprised of a series of Unix-/Linux-based scripts that can readily batch process the 1000 Functional Connectomes Project dataset (in its entirety or any subset of sites), carrying out both image-preprocessing and individual level functional connectivity analyses.

It is our hope that the release of this set of scripts will facilitate the introduction of resting state fMRI approaches to the larger scientific community. The scripts have been modified from their original form to increase the ease of distribution and user-friendliness. Processing steps included in the scripts are the same as reported in the PNAS paper. The scripts can easily be modified by users to address individual needs.

The current release is a beta-release. Additional functionality (e.g., ALFF/fALFF) will be added in the official first release, anticipated for March 10, 2010. Any comments suggestions regarding the scripts are welcomed – an email forum is easily accessible on the 1000 Functional Connectomes Project website located on NITRC (www.nitrc.org/projects/fcon_1000).

We would like to thank Maarten Mennes and Clare Kelly for their many efforts in making this release possible.

Disclaimer: Usage of the scripts provided by 1000 Functional Connectomes Project (www.nitrc.org/projects/fcon_1000) is unrestricted. It is the user’s responsibility to ensure the accuracy of any results obtained with the 1000 Functional Connectomes Project scripts. The 1000 Functional Connectomes Project and its contributors are not responsible for the accuracy of any data obtained using the scripts provided.

Dallas Data Temporarily Unavailable

maartenmennes@www.nitrc.org (Maarten Mennes) — Thu, 04 Mar 2010 14:50:34 GMT

We temporally disabled the download of the Dallas dataset. As brought to our attention on the forums, there appears to be a disparity in the left-right orientation between the anatomical and resting-state scan.

We are working with the original contributors to resolve this issue as quickly as possible. We will provide you with a new dataset and correct information as soon as possible!

In addition, we disabled the download of the Cambridge-Withfield-Gabrieli dataset due to IRB issues. We hope these will get resolved soon, upon which the dataset will be available again.

We apologize for any inconvenience this is causing. And as always: please feel free to give any feedback you have on the project through the forums!

Wiki page added on how to use the scripts

maartenmennes@www.nitrc.org (Maarten Mennes) — Wed, 03 Mar 2010 22:48:18 GMT

Instructions on how to setup and use the 1000 Functional Connectomes Scripts are now also available on the MediaWiki page.

NIFSTD 1.7 Released

dnkennedy@www.nitrc.org (David Kennedy) — Wed, 03 Mar 2010 21:02:04 GMT

Our friends at NIF are very excited and pleased to announce the new release of NIFSTD 1.7. Please visit http://purl.org/nif/ontology/nif.owl to access the owl file.

Major changes include:

* Retirement of OBO-UBO layer: Eliminated the need of BIRNLex-OBO-UBO module (a common bridge between all NIF modules and BFO) to be imported

* Content Enhancement and Improvements:
o Inclusion of Protein Ontology (PRO) under NIF-Molecule module.
+ A bridge file has been generated to assign equivalencies between NIF-Molecule and PRO mapping terms (based on exact or synonymous lexical matches). It also places the PRO terms under NIF’s macromolecule. Bridge file location: http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule-PRO-Bridge.owl
o Molecules hierarchy has been modified to reflect close alignment between NIF’s Chemical and CHEBI’s upper level hierarchies
o More neuron labels are altered in NIF-Cell module to conform with standardized naming convention by NIF cell working group
o Additional partonomy relations for NIF-Anatomy
o New classes and annotations from NeuroLex wiki contributions in different modules

* Neuron by Brain Region classification: Another bridge file (between NIF-Cell, NIF-Subcellular, and NIF-Anatomy) has been constructed based on NeuroLex contributions by NIF-Cell working group.

Detailed release notes can be found available at https://confluence.crbs.ucsd.edu/display/NIF/NIFSTD+Release+Notes.

Sincerely,
Jade Kwan
NIF Communications Student Assistant
Neuroscience Information Framework
Center for Research in Biological Systems
University of California, San Diego
http://www.neuinfo.org
(858) 822 0755

Research and Clinical Fellowships in the Imaging Sciences Tr

dnkennedy@www.nitrc.org (David Kennedy) — Wed, 03 Mar 2010 20:58:32 GMT

The Imaging Sciences Training Program (ISTP), jointly sponsored by Radiology and Imaging Sciences (RAD) in the NIH Clinical Center and the NIBIB Intramural Research Program, is accepting applications for one to two-year fellowship positions beginning in July 2010 and July 2011. This program provides an excellent opportunity for individuals who plan a research career in imaging and biomedical sciences.

The ISTP provides opportunities in clinical, translational, and basic imaging research available in Radiology and Imaging Sciences, Nuclear Medicine, Positron Emission Tomography, Interventional Radiology Laboratory, and Molecular and Cellular Imaging. The program spans research in all aspects of clinical and basic imaging sciences.

Applicants can choose to work in research areas including: neuroimaging; interventional, oncological, vascular, and metabolic imaging; and computer-aided diagnosis using various imaging techniques. There are bench-to-bedside research opportunities in MRI/MRS, MR microscopy, PET radiochemistry, contrast agent development, cellular and molecular imaging, high intensity focused ultrasound, targeted drug delivery, and innovative image processing and visualization algorithms. Qualified applicants also will be able to have clinical exposure to a unique research patient population found at the NIH. Fellows in the ISTP will have access to state-of-the-art imaging and computer facilities dedicated to research found in the Clinical Center, In Vivo NMR Research Center, and various basic science laboratories. Collaboration with imaging scientists on the NIH campus will be encouraged.

For more information about this program, visit http://www.nibib.nih.gov/About/JobVacancies.

New JIST modules: T1 Mapping

bennett@www.nitrc.org (Bennett Landman) — Wed, 03 Mar 2010 16:10:51 GMT

Hi all!

I'd like to introduce two new JIST modules, and a supporting algorithm:
-plugins.quantitative.UnshuffleT1MappingVolumes
-plugins.quantitative.T1Mapping_SliceShift
-algorithms.quantitative.T1Fitting

Although this slice-shift technique is rather specialized, the T1 fitting might
appeal to a wider audience, so I thought to share it with all.

This set of modules allows for post-processing of a quantitative T1 sequence using
the slice-shift technique. By 'sharing' a global inversion pulse a volume of ~50
slices are acquired at different times. Next repetition, the order in which these
slices are acquired is shifted, and in ~25 repetitions all slices are measured at 25
different time points.
The result is a relatively quick method to acquire 20-30 time points to fit a T1
value to, which allows for high quality T1 fitting. The disadvantage of this
slice-shifting is that the slices need to be re-ordered before fitting can be done.

These modules allow for automatic reordering of slices, based on our current
implementation of the slice-shift technique (over the dynamics), and the
slice-ordering of the sequence (interleaved/ascending/descending) (over one volume).

The second module, responsible for the actual T1 fitting, is an implementation of
the Levenberg-Marquardt optimizer. The optimization was -drastically- sped up by
using the analytical solutions for the 1st and 2nd derivatives of the function to be
optimized (with thanks to Mathematica). Of course this wont work for all functions
and applications, but it increased the processing speed from 455 to roughly 7500
voxels per minute. I am in no way a real programmer however, and I am sure there are
many more steps that can be taken to optimize this code.

While I think I did a reasonable job at annotating the code and explaining the
modules in the description fields, I will have a stab at writing a small manual for
the Wiki. Not sure when that will be finished though.

I look forward to getting some feedback, or even -gasp- user questions!

kind regards,
Daniel

-- the NITRC team

International Computer Vision Summer School

dnkennedy@www.nitrc.org (David Kennedy) — Thu, 25 Feb 2010 17:21:05 GMT

International Computer Vision Summer School
REGISTRATION AND VIDEO ANALYSIS
Sicily 12-17 July 2010

WEB: http://www.dmi.unict.it/icvss
Email: icvss@dmi.unict.it

APPLICATION DEADLINE: 21 March 2010
http://svg.dmi.unict.it/icvss2010/application.htm

The fourth edition of the International Computer Vision Summer School aims to provide an objective and clear overview of the state-of-the-art in the areas of recognition and reconstruction and focuses on registration and video analysis. The courses will be delivered by world renowned experts in the field, from both academia and industry, and will cover both theoretical and practical aspects of real Computer Vision problems.

LIST OF SPEAKERS (OTHER SPEAKERS ARE COMING SOON…)
Title, Syllabus, Abstract: http://svg.dmi.unict.it/icvss2010/speakers&Syllabus.htm

Alberto Broggi (Computer Vision for Autonomous Vehicles)
University of Parma, IT

Tim Cootes (Registration, Active Shape Model)
University of Manchester, UK

Mark Everingham (Recognition)
University of Leeds, UK

Brendan J. Frey (Video Segmentation and Analysis)
University of Toronto, CA

Pascal Fua (Deformation Models, Non-Rigid Registration)
Ecole Polytechnique Fédérale de Lausanne, CH

Kristen Grauman (Recognition, Registration)
University of Texas at Austin, USA

Michal Irani (Video Analysis)
The Weizmann Institute of Science, Israel

Patrick Pérez (Video Analysis)
Technicolor Corporate Research, FR

Tomaso Poggio (Biological Vision, Learning Theories, Recognition)
Massachusetts Institute of Technology, USA

Marc Polleyfeys (Real-time Reconstruction, Structure from Motion)
ETH, Zurich

Stefano Soatto (Reading Group)
UCLA, USA

Rick Szeliski (Reconstruction)
Microsoft Research Ltd, Redmond, USA

DIRECTORS

Roberto Cipolla
University of Cambridge, UK

Sebastiano Battiato
University of Catania, IT

Giovanni Maria Farinella
University of Catania, IT

APPLICATION
The school will be open to about 100 qualified, motivated and pre-selected candidates. Ph. D. students, post-docs, young researchers (both academic and industrial), senior researchers (both academic and industrial) or academic/industrial professionals are encouraged to apply: http://svg.dmi.unict.it/icvss2010/application.htm
The expected school fee will be in the order of 600,00 € for Master and Phd students, 750 € for others academic position and 900 € for all the others. The fee will include, all courses, handling material, coffee breaks, welcome cocktail, bus service from Catania Airport to School Location and viceversa, WiFi Internet Connession, a guided tour and social dinner to Ragusa Ibla, a folcloristic exhibition of the Herbessus Sicilian Group Dancers, and bus service from School Location to Catania, Siracusa and Taormina at the end of the school.
The application at ICVSS 2010 should be done before 21 March 2010.
Applicants will receive notification of acceptance by 31 March 2010.

POSTER SUBMISSION
The International Computer Vision Summer School is especially aimed to provide a stimulating space for young researchers and Ph.D. Students. They will have the possibility to present the results of their research on the topic of the school, and to interact with their scientific peers, in a friendly and constructive environment. Accepted students may submit a poster to present their research activity. The poster should be submitted before 10 May 2010. Suitable space will be reserved to students for showing their posters. The electronic version of the posters will also be available from the ICVSS web site.

BEST PRESENTATION PRIZE
A selected subset from the submitted posters will be selected by the school committee for short oral presentation. A best presentation prize of 700 euros (supported by Toshiba Research Europe) will be given to the best presentation selected by the school committee.

SCHOLARSHIP
A scholarship of 600 Euros (grant offered by the GIRPR) will be awarded to the best PhD student attending the school. The decision will be made by the school committee at the time of the school, taking into account candidates'cv, poster and oral presentation. All PhD students attending the school will be considered for the GIRPR grant.

LOCATION OF ICVSS 2010
ICVSS 2010 will be hosted by Hotel Village Baia Samuele in Punta Sampieri - Scicli (Ragusa), Sicily from 12-17 July 2010. Sicily is one of the most beautiful islands of the Mediterranean. The island is very rich in archeological sites from various Ancient Civilizations. The sea, weather, food and the wine are excellent. In particular Punta Sampieri - Scicli (RG) is located in the south east of Sicily in a late Baroque area called Val di Noto. The Val di Noto area is included in the Unesco World Heritage List and includes eight nearby towns: Caltagirone, Militello Val di Catania, Catania, Modica, Noto, Palazzolo, Ragusa and Scicli. The location of the school rises in the middle of an ample bay delimited on the west from Sampieri and on the east from a cliff, on which is founded an ancient furnace, rare example of industrial archaeology. The Hotel Village "Baia Samuele" stretches in a gentle slant to the beach: 120 thousand square meters delimited from rows of secular cypresses. An ultramodern village with an original architecture, pleasant design and all comforts you can imagine. The frame of plants and flowers, typical of this angle of Sicily, in front of the island of Malta, completes this gilded dream of the Mediterranean.

ACCOMMODATION RESERVATION AT HOTEL VILLAGE BAIA SAMUELE
ICVSS participants must make reservations for accommodation at Hotel Village Baia Samuele (http://www.baiasamuele.it/) at very special rates. More info are available on the website of the school http://svg.dmi.unict.it/icvss2010/SchoolLocation.htm

MORE INFORMATION
www.dmi.unict.it/icvss
icvss@dmi.unict.it