ynic-users

ynic-users@ynic.york.ac.uk

2794 discussions

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

[Fwd: [megcommunity] MEG related positions at the Donders Institute/Nijmegen]
by Gary Green 15 Aug '11

15 Aug '11

FYI --------------------- Dear all, I would like to point your attention to the following MEG related positions at the Donders Institute, Nijmegen, The Netherlands. PhD position: cueing in Parkinson’s disease http://www.umcn.nl/OverUMCstRadboud/werkenbij/Pages/Vacature.aspx?VacatureN… PhD position: Bridging the Gap between Neuronal Activity and Neuroimaging http://www.ru.nl/donders/jobs/vm/vacancies/ Post doctoral fellow in sensorimotor neuroscience http://www.umcn.nl/OverUMCstRadboud/werkenbij/Pages/Vacature.aspx?VacatureN… *** <http://www.ru.nl/publish/pages/605682/phd_position_30_08_111.pdf>*** All the best, Ole -- Ole Jensen http://www.neuosc.com -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk https://www.ynic.york.ac.uk/about-us/people/ggrg tel. +44 (0) 1904 435349 PA - Claire Fox : +44 (0) 1904 435329 or Claire.Fox(a)ynic.york.ac.uk fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004

1 0

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

11 Aug '11

Dear Users Today (4-5 pm in YNiC) there will be a talk by Dr Aneurin Kennerley from the University of Sheffield. http://www.sheffield.ac.uk/psychology/staff/research/aneurin-kennerley The title of Dr Kennerley's talk is "Concurrent 7T fMRI and 2-D Optical Imaging Spectroscopy: Towards building a forward model between neuronal activity and the BOLD signal". Please see below for the talk abstract. Everyone is welcome to attend and refreshments will be provided after the talk. Best wishes Rebecca Abstract: Functional magnetic resonance imaging (fMRI) has become the cornerstone of cognitive neuroscience in recent years. The widely used Blood Oxygenation Level Dependent (BOLD) signal is often used to interpret changes in neuronal activation. However, at present, a biophysical understanding of the neurovascular drivers of the BOLD signal is not clear and thus hinders any quantitative estimation of the underlying neuronal activity. Neuroimaging research at the University of Sheffield drives towards building a forward biophysical model of this complex relationship. As part of this multidisciplinary group my research is aimed at developing a general model of the BOLD signal which can model both intra- and extra- vascular MR signals, across a wide range of imaging parameters, from estimates of the haemodynamic changes. Validation and refinement of the haemodynamic response models underlying fMRI signals, an essential precondition for the correct interpretation of human BOLD data requires invasive multimodal animal imaging. I have developed an innovative in-vivo methodology for concurrent fMRI and 2D optical imaging spectroscopy (2D-OIS) techniques for simultaneous measurement of BOLD signal and underlying haemoglobin changes to neuronal activation in the healthy rodent model. Applications of this technology include: 1) Understanding of the negative BOLD signal (Boorman et al 2010). Most researchers assume a negative BOLD to be a result of either neuronal inhibition or vascular steal. It is only with the simultaneous, independent measurement of haemoglobin changes (with 2D-OIS) that one could disassociate any possible physiological relationships; 2) Refinement of mathematical and biophysical models of both the BOLD signal and optical imaging spectroscopy techniques (Kennerley et.al. 2009); 3) Calibration of non-BOLD fMRI techniques such as VASO and ASL; 4) Interpretation of abnormal BOLD responses; specifically in disease and trauma conditions in which either neuronal or haemodynamic breakdown could be responsible. [1] Boorman, L.W. et.al. (2010) /Journal of Neuroscience/. /30(12): 4285-94;/ [2] Kennerley, A.J. et.al (2009) /NeuroImage 47:1608-1619/; -- ************************************************************************ 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 11th August (external speaker)
by rem 08 Aug '11

08 Aug '11

Dear Users This Thursday (4-5 pm in YNiC) there will be a talk by Dr Aneurin Kennerley from the University of Sheffield. http://www.sheffield.ac.uk/psychology/staff/research/aneurin-kennerley The title of Dr Kennerley's talk is "Concurrent 7T fMRI and 2-D Optical Imaging Spectroscopy: Towards building a forward model between neuronal activity and the BOLD signal". Please see below for the talk abstract. Everyone is welcome to attend and refreshments will be provided after the talk. Best wishes Rebecca Abstract: Functional magnetic resonance imaging (fMRI) has become the cornerstone of cognitive neuroscience in recent years. The widely used Blood Oxygenation Level Dependent (BOLD) signal is often used to interpret changes in neuronal activation. However, at present, a biophysical understanding of the neurovascular drivers of the BOLD signal is not clear and thus hinders any quantitative estimation of the underlying neuronal activity. Neuroimaging research at the University of Sheffield drives towards building a forward biophysical model of this complex relationship. As part of this multidisciplinary group my research is aimed at developing a general model of the BOLD signal which can model both intra- and extra- vascular MR signals, across a wide range of imaging parameters, from estimates of the haemodynamic changes. Validation and refinement of the haemodynamic response models underlying fMRI signals, an essential precondition for the correct interpretation of human BOLD data requires invasive multimodal animal imaging. I have developed an innovative in-vivo methodology for concurrent fMRI and 2D optical imaging spectroscopy (2D-OIS) techniques for simultaneous measurement of BOLD signal and underlying haemoglobin changes to neuronal activation in the healthy rodent model. Applications of this technology include: 1) Understanding of the negative BOLD signal (Boorman et al 2010). Most researchers assume a negative BOLD to be a result of either neuronal inhibition or vascular steal. It is only with the simultaneous, independent measurement of haemoglobin changes (with 2D-OIS) that one could disassociate any possible physiological relationships; 2) Refinement of mathematical and biophysical models of both the BOLD signal and optical imaging spectroscopy techniques (Kennerley et.al. 2009); 3) Calibration of non-BOLD fMRI techniques such as VASO and ASL; 4) Interpretation of abnormal BOLD responses; specifically in disease and trauma conditions in which either neuronal or haemodynamic breakdown could be responsible. [1] Boorman, L.W. et.al. (2010) /Journal of Neuroscience/. /30(12): 4285-94;/ [2] Kennerley, A.J. et.al (2009) /NeuroImage 47:1608-1619/; -- ************************************************************************ 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

[Fwd: [Eeglabnews] EEGLAB multiple subject channel interpolation bug]
by Claire Fox (secretary for Gary Green) 05 Aug '11

05 Aug '11

Some users may need to be aware of this particular bug in EEG. -- Claire Fox PA to Professor Gary Green The York Neuroimaging Centre Innovation Way Science Park York YO10 5DG Tel: 01904 435329 Fax: 01904 435356 Email: Claire.fox(a)ynic.york.ac.uk

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