Tool/Resource News

MRtrix version 0.2.10 released

jdtournier@www.nitrc.org (J-Donald Tournier) — Fri, 10 Feb 2012 5:10:13 GMT

MRtrix version 0.2.10 is now available for download. This is a minor release with the following enhancements:

- easier install via './build install'
- support for MacOS X
- new filter_tracks command to edit tractography output after tracking
- new tracks2vtk command for output to VTK applications
- new MatLab scripts to read/write MRtrix image and track files
- new features in MRView:
- images can be loaded into viewer using drag & drop;
- position of focus can be dropped onto command-line by dragging from statusbar
- faster rendering of FOD overlay
- other minor bug fixes

Other more minor changes:

- new length-scaled TDI option in tracks2prob
- '-stop' option in streamtrack now stops once all include ROIs have been reached
- for NIfTI: both qform and sform entries are now written with equivalent transform information
- other minor bug fixes (see full changelog for details).

Function biomedical informatics research network recommendations for prospective multicenter functional MRI studies.

nitrcadmin@www.nitrc.org (NITRC ADMIN) — Thu, 09 Feb 2012 13:30:10 GMT

Function biomedical informatics research network recommendations for prospective multicenter functional MRI studies.

J Magn Reson Imaging. 2012 Feb 7;

Authors: Glover GH, Mueller BA, Turner JA, van Erp TG, Liu TT, Greve DN, Voyvodic JT, Rasmussen J, Brown GG, Keator DB, Calhoun VD, Lee HJ, Ford JM, Mathalon DH, Diaz M, O'Leary DS, Gadde S, Preda A, Lim KO, Wible CG, Stern HS, Belger A, McCarthy G, Ozyurt B, Potkin SG

Abstract

This report provides practical recommendations for the design and execution of multicenter functional MRI (MC-fMRI) studies based on the collective experience of the Function Biomedical Informatics Research Network (FBIRN). The study was inspired by many requests from the fMRI community to FBIRN group members for advice on how to conduct MC-fMRI studies. The introduction briefly discusses the advantages and complexities of MC-fMRI studies. Prerequisites for MC-fMRI studies are addressed before delving into the practical aspects of carefully and efficiently setting up a MC-fMRI study. Practical multisite aspects include: (i) establishing and verifying scan parameters including scanner types and magnetic fields, (ii) establishing and monitoring of a scanner quality program, (iii) developing task paradigms and scan session documentation, (iv) establishing clinical and scanner training to ensure consistency over time, (v) developing means for uploading, storing, and monitoring of imaging and other data, (vi) the use of a traveling fMRI expert, and (vii) collectively analyzing imaging data and disseminating results. We conclude that when MC-fMRI studies are organized well with careful attention to unification of hardware, software and procedural aspects, the process can be a highly effective means for accessing a desired participant demographics while accelerating scientific discovery. J. Magn. Reson. Imaging 2012;. © 2012 Wiley Periodicals, Inc.

PMID: 22314879 [PubMed - as supplied by publisher]

Role of New Functional MRI Techniques in the Diagnosis, Staging, and Followup of Gynecological Cancer: Comparison with PET-CT.

nitrcadmin@www.nitrc.org (NITRC ADMIN) — Thu, 09 Feb 2012 13:30:10 GMT

Role of New Functional MRI Techniques in the Diagnosis, Staging, and Followup of Gynecological Cancer: Comparison with PET-CT.

Radiol Res Pract. 2012;2012:219546

Authors: Alvarez Moreno E, Jimenez de la Peña M, Cano Alonso R

Abstract

Recent developments in diagnostic imaging techniques have magnified the role and potential of both MRI and PET-CT in female pelvic imaging. This article reviews the techniques and clinical applications of new functional MRI (fMRI) including diffusion-weighted MRI (DWI), dynamic contrast-enhanced (DCE)-MRI, comparing with PET-CT. These new emerging provide not only anatomic but also functional imaging, allowing detection of small volumes of active tumor at diagnosis and early disease relapse, which may not result in detectable morphological changes at conventional imaging. This information is useful in distinguishing between recurrent/residual tumor and post-treatment changes and assessing treatment response, with a clear impact on patient management. Both PET-CT and now fMRI have proved to be very valuable tools for evaluation of gynecologic tumors. Most papers try to compare these techniques, but in our experience both are complementary in management of these patients. Meanwhile PET-CT is superior in diagnosis of ganglionar disease; fMRI presents higher accuracy in local preoperative staging. Both techniques can be used as biomarkers of tumor response and present high accuracy in diagnosis of local recurrence and peritoneal dissemination, with complementary roles depending on histological type, anatomic location and tumoral volume.

PMID: 22315683 [PubMed - in process]

Memantine, an NMDA receptor antagonist, differentially influences Go/No-Go performance and fMRI activity in individuals with and without a family history of alcoholism.

nitrcadmin@www.nitrc.org (NITRC ADMIN) — Thu, 09 Feb 2012 13:30:10 GMT

Memantine, an NMDA receptor antagonist, differentially influences Go/No-Go performance and fMRI activity in individuals with and without a family history of alcoholism.

Psychopharmacology (Berl). 2012 Feb 4;

Authors: Jamadar S, Devito EE, Jiantonio RE, Meda SA, Stevens MC, Potenza MN, Krystal JH, Pearlson GD

Abstract

RATIONALE: Individuals with a family history of alcoholism (family history positive [FHP]) show higher alcoholism rates and are more impulsive than those without such a family history (family history negative [FHN]), possibly due to altered N-methyl-D: -aspartate (NMDA) receptor function. OBJECTIVES: We investigated whether memantine, an NMDA receptor antagonist, differentially influences impulsivity measures and Go/No-Go behavior and fMRI activity in matched FHP and FHN individuals. METHODS: On separate days, participants received a single dose of 40 mg memantine or identical-appearing placebo. RESULTS: No group performance differences were observed on placebo for Go correct hit or No-Go false alarm reaction time on the Go/No-Go task. During fMRI, right cingulate activation differed for FHP vs. FHN subjects during No-Go correct rejects. Memantine had attenuated effects in FHP vs. FHN subjects: For No-Go false alarms, memantine was associated with limited reduction in subcortical, cingulate, and temporal regions in FHP subjects and reduced activity in fronto-striatal-parietal networks in FHN subjects. For No-Go correct rejects, memantine (relative to placebo) reduced activity in left cingulate and caudate in FHP but not FHN subjects. CONCLUSIONS: Lower sensitivity to the effects of memantine in FHP subjects is consistent with greater NMDA receptor function in this group.

PMID: 22311382 [PubMed - as supplied by publisher]

SRI24 Atlas now in NeuroDebian

torstenrohlfing@www.nitrc.org (Torsten Rohlfing) — Wed, 08 Feb 2012 14:40:08 GMT

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

apt-get install sri24-atlas

Enactive Cog Sci

dnkennedy@www.nitrc.org (David Kennedy) — Tue, 07 Feb 2012 20:33:28 GMT

Dear colleagues,

We are excited to announce the organisation of the conference "Foundations of Enactive Cognitive Science", held February 27-28th, 2012. The conference is sponsored by the Centre for Integrative Neuroscience and Neurodynamics, with the support of the UK Engineering and Physical Sciences Research Council. If you intend to participate (even if you do not plan to submit a poster or a talk), we kindly ask that you send us an email, as we need to make some arrangements with the venue.

More information at: http://reading.ac.uk/cinn/enactivism

Dr. Etienne Roesch (Goldsmiths Univ. London; Univ. of Reading)
Dr. Slawomir Nasuto (Univ. of Reading)
Prof. John Mark Bishop (Goldsmiths Univ. London)

The pursuit of cognitive science is concerned with the scientific study of the mind. Interdisciplinary in nature, the discipline spans philosophy, cognitive psychology, neuroscience, artificial intelligence, linguistics, anthropology, social sciences, biology and physics - as well as any other discipline with a perspective on the workings of the mind. From the natural evolution of the concepts that formed the building blocks of cognitive science, arose the need for an integrative account of the interaction of the organism with the world, and recent years witnessed the emergence of what is believed to be a paradigm shift in the discipline: enactive cognitive science.

Enactive cognitive science emerges from diverse research interests, and has yet to mature into a discipline on its own. It now faces the challenge of gathering these views and frameworks, which were merely critics of the classical paradigm, into cohesive research agendas: Enactive cognitive science distances itself from classical cognitivist and computational perspectives, by broadening the current focus on the brain and including the body and its relationship to the outside world.

The objective of the conference is to gather as many researchers as possible, from all disciplines, with an interest in the development and the future of enactive cognitive science.

Venue and accommodation – The conference will be hosted in the unique setting of the Cumberland Lodge (http://cumberlandlodge.ac.uk), in the Great Park of Windsor. Participants will have the choice to stay for the night at the Lodge, or to stay in one of the nearby accommodations. The Cumberland Lodge is genuinely conducive for these types of meetings, and we hope this will maximize interactions between participants. The Lodge is conveniently located 25 minutes away from Heathrow airport. We reserved a number of rooms at the Lodge for Monday night, and we are told there will be rooms available for Tuesday night as well. The Lodge is fully licensed, and we encourage attendees to bring along their favourite music instrument.. :)

Call for posters and talks – Posters will be on display throughout the whole conference, and submitted talks will complement invited keynote addresses. If needed, attendance certificates will be provided. If you are willing to participate, please send a title and an abstract (max. 300 words) to Dr. Etienne Roesch (etienne.roesch@gmail.com) by January 30th (of course you can send it before that date!), stating whether you would like to present a poster or give a talk, and if you will be staying at the Lodge or make your own arrangements.

We hope to see you there!

Best regards,

Dr. Etienne Roesch
Dr. Slawomir Nasuto
Prof. John Mark Bishop

Convergence in Computational Neuroscience 2012

dnkennedy@www.nitrc.org (David Kennedy) — Tue, 07 Feb 2012 20:33:28 GMT

Announcing the Convergence in Computational Neuroscience 2012 workshop
which will be held in Edinburgh from 12-16th March. The NeuroML
Development Workshop and the BrainScaleS (previously FACETS) CodeJam
have been two important workshops for developers of software tools for
computational neuroscience for the past number of years, and this year
they are being held over the same week.

The first 2 days will focus on the specifications & tool support for
NeuroML, which has traditionally been focused on multicompartmental,
conductance based neuronal models, but with version 2.0 is being
extended to support more abstract point neuron models and interaction
with systems biology languages like SBML.

More details for these days are here: http://www.neuroml.org/workshop2012

The remaining 3 days will have a similar format to previous CodeJams:
presentations in the mornings with discussions & code sprints in the
afternoon. The goal will be to catalyze open-source, collaborative
software development in computational and systems neuroscience and
neuroinformatics, by bringing together researchers, students and
engineers to share ideas, present their work, and write code together.
Wednesday afternoon includes a mini workshop with the theme
"Convergence, Interoperability and Reuse in Neuroscience Modelling
Software", and seeks to develop a perspective on where the field is at
and where we are going to.

More details are here: http://neuralensemble.org/meetings/CodeJam5

This should be a very informative and useful week for anyone interested
in learning about/sharing/integrating software tools for computational
neuroscience.

There will be a limited number of bursaries available for travel to the
meeting for UK based attendees through the UK Node of the INCF
(http://www.neuroinformatics.org.uk/special-interest-groups-sigs/18-sig4).
Contact p.gleeson@ucl.ac.uk for more details.

German INCF Node Short Course

dnkennedy@www.nitrc.org (David Kennedy) — Tue, 07 Feb 2012 20:33:28 GMT

The German Neuroinformatics Node (G-Node) organizes its fourth international training course to promote state-of-the-art methods of neural data analysis among PhD students and postdocs. During 4 days the course offers hands-on experience with model-driven analysis of data from intra- and extracellular electrophysiology. We encourage applications from students/postdocs with an experimental background that want to widen their repertoire of analysis methods, as well as from students with a theoretical background that have an interest in analyzing physiological data.

For more information visit http://www.g-node.org/dataanalysis-course-2012

2nd UK NI Node Congress

dnkennedy@www.nitrc.org (David Kennedy) — Tue, 07 Feb 2012 20:33:28 GMT

The UK Node of the International Neuroinformatics Coordinating Facility (INCF) is holding its biennial conference at the Informatics Forum, University of Edinburgh, from 26th to 28th March 2012.
The aim of the conference is to bring together people who are already working in the field and showcase opportunities in neuroinformatics to people working in related disciplines.

The conference will have:

    An array of international speakers
    Posters and Demonstrations including Poster Spotlights
    Stimulating contributed sessions from UK people working in neuroinformatics
    Update from our Special Interest Groups (SIGs)
    Conference Dinner in the Playfair Building at Surgeons Hall including private tour of the Museum
    Discussions on the future of the Node

Confirmed speakers so far are:

Gaute Einevoll, Norwegian University of Life Sciences, Norway

Simon Laughlin, Cambridge University, UK

Read Montague, Virginia Tech Carilion, USA

Further information, including a call for contributed sessions, and registration details will follow.

Who should attend?

The conference will bring together leading researchers from around the world and provide an excellent opportunity for researchers at all stages of their career – from Ph.D. students through early career researchers, to established scientists – to network and form new collaborations.

Winter Course in Neural Data Analysis

dnkennedy@www.nitrc.org (David Kennedy) — Tue, 07 Feb 2012 20:33:28 GMT

For more information visit http://www.g-node.org/dataanalysis-course-2012