ynic-users

ynic-users@ynic.york.ac.uk

2 participants
2788 discussions

Downtime for upgrade
by Mark Hymers 29 Sep '11

29 Sep '11

Hi, Just a final reminder that tomorrow morning starting at around 9am, the YNiC desktop, cluster and remote desktop systems will be undergoing upgrade work. We expect this to be complete by lunchtime, with the exception of the remote desktop service which may be out of action until next week. Thanks, Mark -- Mark Hymers York Neuroimaging Centre

1 1

Fwd: [megcommunity] MSc/PhD Positions at Dalhousie University
by Gary Green 29 Sep '11

29 Sep '11

FYI ------------------ We are recruiting MSc and PhD students for a funded MEG study looking at neuronal connectivity and stroke recovery. Students will have the opportunity to undergo research through the Depts of Kinesiology or Psychology/Neuroscience at Dalhousie University in Halifax, Nova Scotia, Canada. This research project will capitalize on the spatiotemporal resolution of MEG to examine changes in connectivity within the sensorimotor network of individuals post-stroke. Specifically, the goal of this research is to ‘pave the road to post-stroke rehabilitation’. Identifying the ‘normal’ sensorimotor network and establishing the relationship between network re-organization and functional recovery will permit the development and implementation of treatments to direct brain recovery. With regard to the proposed research project, and in groups of non-disabled controls and patients post-stroke, our objectives include: 1. To establish the connectivity pattern of the ‘normal’ sensorimotor network and demonstrate the ability to detect changes within the network using an established motor learning paradigm 2. Using clinical measures of upper limb function, we will establish the relationship between the pattern of sensorimotor network connectivity and functional recovery in well and poorly recovered patients You can find more information at: http://myweb.dal.ca/sh539856/ If interested, please e-mail Dr. Shaun Boe (s.boe(a)dal.ca <mailto:s.boe@dal.ca>) or Dr. Tim Bardouille (tim.bardouille(a)nrc.ca <mailto:tim.bardouille@nrc.ca>). Best, Tim Bardouille. --------------------------------------------------------- Timothy Bardouille, PhD, Research Officer Laboratory for Clinical MEG NRC Institute for Biodiagnostics (Atlantic) Office: Halifax Infirmary 3900 - 1796 Summer Street Halifax, Nova Scotia B3H 3A7 Phone: 902-473-1865 Lab: 902-470-3936 Fax: 902-473-1851 ---------------------------------------------------------

1 0

Fwd: [Eeglabnews] EEGLAB 10.2.5.5 now available - critical upgrade
by Gary Green 26 Sep '11

26 Sep '11

FYI These changes may be important if you are using EEGLAB for multiple subject analyses Gary -------- Original Message -------- Subject: [Eeglabnews] EEGLAB 10.2.5.5 now available - critical upgrade Date: Tue, 13 Sep 2011 09:43:48 +0200 From: Arnaud Delorme <arno(a)ucsd.edu> To: eeglabnews(a)sccn.ucsd.edu Dear EEGLAB users, New EEGLAB version 10.2.5.5 is now available. This is a critical update if you are using EEGLAB STUDY sets to process multiple subjects. This version fixes 3 important problems: - Plotting ERP and power spectral scalp topographies (a problem that appeared in EEGLAB 10.2.2.4 two months ago). You will not need to recompute anything. - Plotting ERSP data (for independent component clusters and channels) when a common baseline is being subtracted from the data (not the default option). You will not need to recompute anything. - Correctly computing component cluster ERSPs when independent components were selected using a residual variance threshold. Simply download the latest version of EEGLAB 10; upon opening a STUDY, a warning message will appear if you need to recompute ERSPs. EEGLAB 9.0.8.6 has also been updated. The list of all recent changes are available at: http://sccn.ucsd.edu/wiki/EEGLAB_revision_history We are constantly working on new test scripts to attempt to validate outputs for complex STUDY structures. Whenever you encounter a problem, please submit a bug report at http://sccn.ucsd.edu/eeglab/bugzilla. <http://sccn.ucsd.edu/eeglab/bugzilla> Thank you for using EEGLAB, A. Delorme

1 0

Help with mri analysis
by philip quinlan 19 Sep '11

19 Sep '11

I have two related but different tasks - task A and task B. I find that when you do task A regions x, y, z light up and when you do task B regions x, y, z, and w light up. As we all know all regions of the brain light up to varying degrees regardless what's going on but what I want to be able to demonstrate is that w really is a region unique to task B. I should add the data for tasks A and B were collected under different conditions so no simple 'contrast' is possible. Any help gratefully received. Philip. ******************************************************************** Philip Quinlan E-Mail: ptq1(a)york.ac.uk Department of Psychology FAX: (01904) 323181 The University of York Tel: (01904) 320000 Ext. 3135 Heslington Direct : (01904) 323135 York YO10 5DD U.K. ********************************************************************

1 0

YNiC Desktop and Cluster Upgrade
by Mark Hymers 09 Sep '11

09 Sep '11

Hi, On Friday 23rd September, we'll be upgrading the YNiC desktops and cluster machines to a new software release. The main changes are: * FSL 3.3 will no longer be available * FSL 4.1.4 will be upgraded to FSL 4.1.8 * The default Matlab version will move to 7.12 * python2.5 will move to python2.6 (2.5 will still be available but some modules may be missing) Unsupported software changes: * afni will be updated from 20101222 -> 20110610 * freesurfer 4.5 will no longer be available; 5.1 will be available instead (although possibly not immediately, we'll announce this at the time) This means that on the morning of Friday 23rd, there will be some disruption at YNiC and the remote desktop service will be unavailable. It is possible that the remote desktop service will remain unavailable for a couple of days after the migration in order to give us extra time to migrate it, although we are aiming to avoid this. Thanks, Mark -- Mark Hymers York Neuroimaging Centre

1 0

[Fwd: [megcommunity] MEG research position]
by Gary Green 06 Sep '11

06 Sep '11

FYI Research assistant, Pittsburgh, Pennsylvania, USA ________________________________________ Employment Type: Full-time 24-month appointment as a Research Assistant Institution: Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA Available: September 1, 2011 Job description: A research assistant position is available with the UPMC MEG Brain Mapping Center (http://www.meg-brain-mapping.pitt.edu/index.html) at the University of Pittsburgh Medical Center in Pittsburgh, PA. The research will consist of using MEG to study the temporal dynamics of how brain regions interact, both in spontaneously (when people are at rest) and in the service of visual processing. Candidates will be expected to: • Analyze MEG data using advanced mathematical and computational methods some of which have been developed in house primarily using MATLAB • Assist in data collection from healthy volunteers and clinical groups • Assist in the preparation of manuscripts • Work independently and liaise between collaborating laboratories Qualifications: • Undergraduate or Masters degree in Psychology, Neuroscience, Mathematics, Physics, Computer Science, Mathematics, Engineering or related field • Strong organizational skills • Previous experience in computer programming (MATLAB experience preferred) • Previous experience in image/signal processing would be highly advantageous • Prior experience in neuroimaging data analysis would be a plus • Prior experience in working with clinical groups would be a plus Salary: Commensurate with Experience How to Apply: If interested, please send a CV, cover letter, and names of references to Dr. Avniel Ghuman, Department of Neurological Surgery, University of Pittsburgh Medical Center at ghumana(a)cnbc.cmu.edu. Applications will be considered until the position is filled. -- Gary Green

1 0

YNiC Reception move
by Reception 30 Aug '11

30 Aug '11

Dear YNiC Users, preparations for the construction of the new Centre for Hyperpolarisation (CHyM) are scheduled to start with the next week, with the build anticipated to last for about 10 months. During the course of the building work the YNiC entrance doors will not be in use and all users and visitors are therefore requested to access YNiC via the main BioCentre reception doors. During the course of the works Claire and I will be in the temporary YNiC reception office which can be found to the left hand side of the BioCentre reception desk. Our contact details will remain the same. The participant forms will not be moved to the temporary office so anyone needing access to these is requested to see any member of YNiC staff for assistance. Please continue to drop off participant forms in the post box. Further updates about the progress of the building work will be issued in due course and a display including the building plans can be found in the BioCentre foyer area. With best wishes, Jo. -- ............................ Jo Saunders Centre Manager YNiC The BioCentre York Science Park YORK YO10 5DG Email: Joanna(a)ynic.york.ac.uk Tel: (01904) 435343 Fax: (01904) 435356 Tues, Wed & Thurs .............................

1 1

PhD research studentship
by gm654＠york.ac.uk 29 Aug '11

29 Aug '11

Dear All, please find below the announcement for a PhD studentship in the University of Milano-Bicocca. Regards, Giulia University of Milano-Bicocca, Department of Psychology Four-year Ph.D. Research Studentship Deadline: October 10th, 2011 A fully-funded Ph.D. studentship beginning in January 2012 for 4 years is available within the Doctoral School in Psychology and Cognitive Science, Department of Psychology at University of Milano-Bicocca, Milano, Italy, for applicants interested in the study of cognitive functions (language, verbal STM, executive functions) in neuropsychological patients and in unimpaired subjects by means of TMS, tDCS and fMRI. Also research on deaf and deafblind individuals is currently performed. These are topics available in the Doctoral Training Program in "Experimental Psychology, Linguistic and Cognitive Neuroscience", which has available a total of six 4-year full time studentships. Two summer schools will be also organized. The successful applicant will have access to all the facilities available within the TMS-EEG (and EMG) lab at the Department of Psychology, as well as Eye-Trackers, ERP, fMRI (the latter within a Hospital nearby the University), neurosurgery patients undergoing awake surgery for tumor removal and neuropsychological patients in several different hospitals in MIlano. We encourage application from candidates with a demonstrable interest in working with patients or with experience on the different methodologies. Applications are welcome from UK and EU as well as non-EU citizens. Candidates should have, or expect to get, an undergraduate degree in Psychology or a related discipline. A Master degree in psychological research methods or a cognate discipline would be an advantage. Funding will consist of a monthly salary of approximately 1,170 Euros plus support for travel and equipment. The deadline for application is October 10th, 2011. Selection will take place in the form of a written test and oral colloquium in October. Information about how to apply can be found at the following links: - italian version: http://www.unimib.it/open/news/Bando-XXVII-ciclo-corsi-di-Dottorato-condeco… - english version: courtesy english translation: http://www.unimib.it/open/news/Announcements-englishversion/824598639538508… "Announcement for courses that will begin on 1st January 2012" (page 15 of the .pdf file). Enquires about how to apply can be e-mailed to the following address: phdpsineco(a)unimib.it Please, feel free to contact prof. Costanza Papagno with questions. Dipartimento di Psicologia Università di Milano-Bicocca e-mail: costanza.papagno(a)unimib.it Skype: costanza1411 Please feel free to pass this information on to any interested undergraduate or master student you may know.

1 0

YNiC seminar today (external speaker)
by rem 24 Aug '11

24 Aug '11

Dear Users Today (4-5 pm in YNiC) there will be a talk by Dr. Peter van Zijl from Johns Hopkins University and the Kennedy Krieger Institute. http://www.kennedykrieger.org/kki_staff.jsp?pid=1064 The title of Dr van Zijl's talk is "Chemical Exchange Saturation Transfer (CEST) contrast agents". Please see below for the talk abstract. Everyone is welcome to attend and refreshments will be provided after the talk. Best wishes Rebecca Abstract: CEST agents1,2 exploit exchangeable protons to achieve contrast in MRI. This can be accomplished by using radiofrequency saturation at the NMR frequency of these protons and monitoring of the transfer of this saturation to the water protons imaged in MRI. When continuous saturation is applied, strong sensitivity enhancements (factors of hundred to hundreds of thousands depending on the protons) can be attained to image micromolar compounds. CEST agents have been broadly classified in terms of containing paramagnetic metals (paraCEST) or not (diaCEST). The main characteristic of diaCEST agents is that the chemical shift range of their exchangeable protons is limited to a range of approximately 6-7 ppm positive with respect to the water signal, which can be extended by another 6-7 ppm through hydrogen bonding of the exchangeable site. Currently, protons used for diaCEST include OH (hydroxyl, ~0-3ppm from water), NH2 (amine ~0-3 ppm from water), NH (amide, ~3- 4ppm from water; imino, ~5-7ppm from water). The main compounds are carbohydrates (sugars), peptides and proteins, and nucleic acids, which is important to mention because these are natural bio-organic substances. MRI is an insensitive method and, contrary to PET and optical approaches, the application of contrast agents often requires physiologically incompatible (micromolar-millimolar) concentrations. Unlike paramagnetic metallic contrast agents, diaCEST provides natural, non-metallic labels. As a consequence, this methodology has already allowed the use of many agents in vivo in animals, while endogenous markers such as cellular peptides and sugar derivatives are even been studied in humans. Recent data suggest that amide proton transfer (APT) may provide a biomarker for separating tumor recurrence from treatment necrosis in the brain. ^3 In this presentation, an overview will be given of current diaCEST agents as well as of their applications and pitfalls. Based on its non-invasive character, diaCEST is expected to revolutionize the rapid translation of contrast agents to the clinic. The field is evolving rapidly and many novel exogenous agents and endogenous markers are expected to be discovered in the near future. Reference: 1) Ward KM et al. J Magn Reson 2000;143:79–87. 2) van Zijl PC, Yadav NN. Magn Reson Med. 2011;65(4):927-48. 3) Zhou J. et al. Nat Med. 2011;17(1):130-4. -- ************************************************************************ Dr. Rebecca E. Millman Science Liaison Officer York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 567614 Fax: +44 (0) 1904 435356

1 0

YNiC seminar 24th August
by rem 22 Aug '11

22 Aug '11

Dear Users This *Wednesday* (4-5 pm in YNiC) there will be a talk by Dr. Peter van Zijl from Johns Hopkins University and the Kennedy Krieger Institute. http://www.kennedykrieger.org/kki_staff.jsp?pid=1064 The title of Dr van Zijl's talk is "Chemical Exchange Saturation Transfer (CEST) contrast agents". Please see below for the talk abstract. Everyone is welcome to attend and refreshments will be provided after the talk. Best wishes Rebecca Abstract: CEST agents^1,2 exploit exchangeable protons to achieve contrast in MRI. This can be accomplished by using radiofrequency saturation at the NMR frequency of these protons and monitoring of the transfer of this saturation to the water protons imaged in MRI. When continuous saturation is applied, strong sensitivity enhancements (factors of hundred to hundreds of thousands depending on the protons) can be attained to image micromolar compounds. CEST agents have been broadly classified in terms of containing paramagnetic metals (paraCEST) or not (diaCEST). The main characteristic of diaCEST agents is that the chemical shift range of their exchangeable protons is limited to a range of approximately 6-7 ppm positive with respect to the water signal, which can be extended by another 6-7 ppm through hydrogen bonding of the exchangeable site. Currently, protons used for diaCEST include OH (hydroxyl, ~0-3ppm from water), NH2 (amine ~0-3 ppm from water), NH (amide, ~3- 4ppm from water; imino, ~5-7ppm from water). The main compounds are carbohydrates (sugars), peptides and proteins, and nucleic acids, which is important to mention because these are natural bio-organic substances. MRI is an insensitive method and, contrary to PET and optical approaches, the application of contrast agents often requires physiologically incompatible (micromolar-millimolar) concentrations. Unlike paramagnetic metallic contrast agents, diaCEST provides natural, non-metallic labels. As a consequence, this methodology has already allowed the use of many agents in vivo in animals, while endogenous markers such as cellular peptides and sugar derivatives are even been studied in humans. Recent data suggest that amide proton transfer (APT) may provide a biomarker for separating tumor recurrence from treatment necrosis in the brain. ^3 In this presentation, an overview will be given of current diaCEST agents as well as of their applications and pitfalls. Based on its non-invasive character, diaCEST is expected to revolutionize the rapid translation of contrast agents to the clinic. The field is evolving rapidly and many novel exogenous agents and endogenous markers are expected to be discovered in the near future. Reference: 1) Ward KM et al. J Magn Reson 2000;143:79–87. 2) van Zijl PC, Yadav NN. Magn Reson Med. 2011;65(4):927-48. 3) Zhou J. et al. Nat Med. 2011;17(1):130-4. -- ************************************************************************ Dr. Rebecca E. Millman Science Liaison Officer York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 567614 Fax: +44 (0) 1904 435356

1 0

Jump to page:

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

ynic-users