ynic-users

ynic-users@ynic.york.ac.uk

2 participants
2788 discussions

YNiC Seminar 17th September
by Sarah Finch 16 Sep '15

16 Sep '15

Dear Users This Thursday (4-5 pm in B020), Xiaoqian Yan, will give a project presentation on a new fMRI experiment to investigate the cross-cultural differences in the neural presentation of faces. Everyone is welcome to attend. Refreshments will be available after the seminar. Best wishes -- Sarah Finch | PA to Gary Green, Director York Neuroimaging Centre | The Biocentre | York Science Park | Heslinton | York | YO10 5NY 01904 435329 Working hours are Tues 8.15 -14.45, Weds 8.15-17.15, Thurs 9.30-17.30 and Fri 8.15-14.45

1 0

YNiC Software Upgrade
by Mark Hymers 16 Sep '15

16 Sep '15

Dear all, As announced previously, YNiC staff will be performing a large software upgrade on Monday and Tuesday next week. All systems (including remote desktop) will be unavailable for the duration of the upgrade and the centre itself will be closed to users. An email will be sent to ynic-users once systems are back online and the centre is open. Details of the upgrade can be found at: https://www.ynic.york.ac.uk/docs/ITPages/Summer2015Upgrade **Please note that we are changing default versions of a range of software, including some analysis software - please ensure that you have read this email or the page concerned** A summary of the current version of the page follows: =================================================================================== Operating System ---------------- The primary YNiC operating system will change from Debian 7.0 (wheezy) to Debian 8.0 (jessie). The window system in use will remain as XFCE and we do not expect many major changes in the appearance of the system. General Applications -------------------- The following applications will be replaced: * evince (PDF viewer) will be replaced by atril * eog (Image viewer) will be replaced by eom * File Roller (File compression utility) will be replaced by engrampa * Gedit (Text editor) will be replaced by pluma FSL --- The default version of FSL will change to 5.0.8. This is a major change from 4.1. FSL 4.1.9 is still available on the system. Details of how to use a non-default FSL version can be found at docs/ITPages/FAQ/FSL/Versions. Our advice is not to mix and match versions of FSL within analyses, but to start new projects using 5.0. FSL 5.0 includes new atlases and segmentations - these are all installed in the usual location /usr/share/fsl/data. Python ------ python2.7 and python3.4 are available on the YNiC systems. YNiC still primarily supports python2, however we are aiming for a complete python3 system where possible and will attempt to backport any modules needed to support a full scientific software stack on python3. We aim to change our default version of python to python3 from Summer 2016 (subject to all modules being available in time). Taught courses using Python in 2015/16 will use python2, but will aim to use python3 compatible syntax. Python Modules -------------- The complete list of python module changes is available at the page linked above. Matlab ------ The default version of MATLAB is now 8.5 (R2015a). For backwards compatibility, MATLAB 7.14 (R2012a) is also available. MATLAB Toolboxes ---------------- * SPM 2 and 5 remain available at their existing versions. * SPM 8 has been updated to r6313. * SPM 12 has been updated to r6470. R - * R has been upgraded from 2.15 to 3.1.1. * Rstudio has been upgraded from 0.97.551 to 0.99.484. * Various R libraries have been upgraded. Freesurfer ---------- Only freesurfer 5.3 will now be supported. Freesurfer 5.1 has been removed. The exact revision (CVS date) of freesurfer 5.3 will be confirmed before upgrade. The existing pool of automatic freesurfer extractions was generated using freesurfer 5.1. We intend to archive these and regenerate (over the next few weeks) all of the extractions using the updated freesurfer 5.3. =================================================================================== If you have any queries, please contact myself <mark.hymers(a)ynic.york.ac.uk> or Paul Elliott <paul.elliott(a)ynic.york.ac.uk> Thanks, Mark -- Mark Hymers, York Neuroimaging Centre Please note that my email address is: mark.hymers(a)ynic.york.ac.uk Responses to messages sent to other addresses may be delayed

1 0

Fwd: [BIC-announce] Postdoc, PhD and RA positions available at the BIC
by Jonny Smallwood 12 Sep '15

12 Sep '15

Please find an advert for positions at the Brain Imaging Centre at the MNI.: *From: *"Andrea Bernasconi, Dr." <andrea.bernasconi(a)mcgill.ca> *Subject: **[BIC-announce] Postdoc, PhD and RA positions available at the BIC* *Date: *September 11, 2015 at 4:20:50 PM GMT-4 *To: *BIC-announce <bic-announce(a)bic.mni.mcgill.ca> We are currently looking for *3* enthusiastic and skilled team players (*1 PhD student, 1 Postdoc, 1 RA*) to join the *Neuroimaging of Epilepsy Laboratory* at the Brain Imaging Center (BIC) of the Montreal Neurological Institute (McGill University, Montreal, Canada) http://www.bic.mni.mcgill.ca/~noel Our lab is part of the BIC, an internationally recognized and multidisciplinary centre of neuroimaging, and associated to the Epilepsy Group of the Montreal Neurological Institute and Hospital, a tertiary center that evaluates approximately 200 patients per year for the pre-surgical investigation of drug-resistant seizures. Our group brings together graduate students and postdoctoral fellows in Neuroscience, Cognitive Science, Computer Science, Biomedical Engineering, and Neurology. We use high- and ultra-high field (3 and 7T) structural and functional MRI analysis to characterize cortical architecture, function, metabolism, and networks. We seek to identify novel patient phenotypes and biomarkers of disease. Main topics include automated lesion detection through neuroimage-based machine-learning, surface-based subcortical and cortical modelling, analysis of brain networks using graph-theory. We are interested in tracking disease progression and its consequences on brain plasticity, connectivity, and cognition. The *postdoctoral fellow *will carry our research projects that combine multi-modal neuroimaging with advanced data analysis (graph theoretical network analysis, machine learning, multivariate modeling) in large and well-documented cohorts of patients with drug-resistant epilepsy. Possibility to participate in several multi-centric and longitudinal studies. Requirements: PhD in Neuroscience, Computer Science, Cognitive Science, Engineering, or related fields; experience in neuroimaging, data analysis, programming; strong publication record. The *PhD student* will perform research centered on the development of neuroimaging applications to improve our understanding and diagnostic routines of human epilepsy. The PhD will be carried out within the Integrated Program in Neuroscience at McGill University (IPN, https://www.mcgill.ca/ipn/), the largest inter-disciplinary, inter-departmental graduate program in neuroscience in Canada. Requirements: MSc in Neuroscience, Cognitive Science, Computer Science, Biomedical Engineering, or related fields; solid mathematical and statistical knowledge; previous experience in neuroimaging and data analysis is an asset. The *full-time research assistant (RA)* will help with subject recruitment; administration of questionnaires and neurocognitive tasks; MRI scheduling and data acquisition (with assistance of technician); data quality-control and image processing; database management; technical support. Requirements: BSc/BA in Neuroscience, Cognitive Science, Psychology, or related fields; organizational talent and computer skills; willingness to accept flexible working schedule; knowledge of French (spoken and written). All candidates are expected to show strong communication skills and willingness to learn and help others within a multidisciplinary team. Starting dates are flexible. ** Full applications (cover letter, CV, and names of 2 referees; PhD candidates should also send transcripts) should be sent to: andrea.bernasconi(a)mcgill.ca _______________________________________________ BIC-announce mailing list BIC-announce(a)bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/bic-announce -- Jonathan Smallwood Reader in Psychology / Cognitive Neuroscience University of York, England.

1 0

YNiC Science day tomorrow, 13:30
by James Davey 08 Sep '15

08 Sep '15

Hello Everyone, Just a reminder that the second YNiC science day is tomorrow at 13:30, here in the Psychology department. I have attached the previously circulated flyer as well as the program for this year. YNiC science day 2015 program <https://docs.google.com/a/york.ac.uk/document/d/12OFO2gwpiwWx41jWTM_g6DotsY…> Hope to see you all there! James D

1 0

YNiC annual closure for service upgrades
by Gary Green 08 Sep '15

08 Sep '15

Dear All Every year we perform an overhaul of all of the systems and software within YNiC. Most of the work goes on in the background but for the final part of this we need to close the Centre so that all the software installs can take place and any necessary hardware changes can be made. This year the Centre will be closed on the 21st and 22nd of September. No computer services, including the remote desktop server will be available. An email will be sent to all users when normal service is resumed. The Centre will be physically closed as well to all users on those days Thanks Gary -- --------------- Gary Green York Neuroimaging Centre & Centre for Hyperpolarisation in Magnetic Resonance The Biocentre York Science Park Innovation Way Heslington York YO10 5NY tel +44 (0) 1904 435349 fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004 http://www.ynic.york.ac.uk http://www.york.ac.uk/chym/ https://www.ynic.york.ac.uk/about-us/people/ggrg PA : Sarah Finch tel +44 (0) 1904 435329 fax +44 (0) 1904 435356 Sarah.Finch(a)york.ac.uk

1 0

Remote desktop usage
by Mark Hymers 02 Sep '15

02 Sep '15

Hi all, We've recently started seeing people using the remote desktop server to perform large scale analyses. This is just a reminder that it is not for that sort of work. Performing large scale analysis jobs in this way impacts on other users of the system and has caused us to have to kill jobs. Large scale analysis jobs *must* be submitted to the cluster. This is fairly straightforward for FSL jobs, MATLAB jobs, python scripts and most other general tools. There are some examples on the YNiC wiki: https://www.ynic.york.ac.uk/docs/ITPages/Cluster https://www.ynic.york.ac.uk/docs/ITPages/MRI/FSLCluster https://www.ynic.york.ac.uk/docs/ITPages/IT/ClusterMatlab https://www.ynic.york.ac.uk/docs/ITPages/IT/ClusterScripts We are going to work on improving the documentation regarding use of the cluster. In the meantime, if you have any questions regarding using the cluster for analysis, please contact either myself <mark.hymers(a)ynic.york.ac.uk> or Paul Elliott <paul.elliott(a)ynic.york.ac.uk> Thanks, Mark -- Mark Hymers, York Neuroimaging Centre Please note that my email address is: mark.hymers(a)ynic.york.ac.uk Responses to messages sent to other addresses may be delayed

1 0

This Thursday's ynic project presentation and connectivity club
by Gary Green 02 Sep '15

02 Sep '15

Dear Users This Thursday we will have a shared session with an internal project proposal presentation and a connectivity club session. Both will take place in B020 starting at 15:30 till 17:00. 1) Project proposal by Kay Weibert (15:30-16:00): "Do patterns of response in face-selective regions represent facial identity?" 2) Connectivity club with Dr Boris Bernhardt from the Montreal Neurological Institute (16-17:00). He works with several different methods of brain imaging and uses these tools in both healthy and non healthy populations. Everyone is welcome to attend. Refreshments will be available after the seminar. -- --------------- Gary Green York Neuroimaging Centre & Centre for Hyperpolarisation in Magnetic Resonance The Biocentre York Science Park Innovation Way Heslington York YO10 5NY tel +44 (0) 1904 435349 fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004 http://www.ynic.york.ac.uk http://www.york.ac.uk/chym/ https://www.ynic.york.ac.uk/about-us/people/ggrg PA : Jackie Mayhew tel +44 (0) 1904 435329 fax +44 (0) 1904 435356 Jackie Mayhew <jcm529(a)york.ac.uk>

1 0

YNiC Science Day - 9th September
by James Davey 01 Sep '15

01 Sep '15

Hello everyone, Please find enclosed a program for the upcoming YNiC science day. Please let me know if you wish to attend so that I can make sure we have enough tea/coffee and biscuits! I have also attached the flyer if you missed my previous email. Thanks, James D

1 0

jobs etc
by Gary Green 31 Aug '15

31 Aug '15

1. The Cohen Laboratory in the Department of Psychology and Neuroscience at the University of North Carolina, Chapel Hill, directed by Dr. Jessica Cohen, is seeking a full-time lab manager or research assistant beginning January 2016. We investigate how functional brain networks interact and reconfigure when confronted with changing cognitive demands, when experiencing transformations across development, and when facing disruptions in healthy functioning due to disease. The lab uses behavioral, neuroimaging, and clinical approaches taken from neuroscience, psychology, and mathematics to address our research questions. This is an excellent position for anyone who would like to pursue graduate work in cognitive, developmental, and/or clinical neuroscience. Responsibilities include recruiting and scheduling participants for research studies (healthy adults, typically developing children, and children with ADHD), data collection (MRI and behavioral), data analysis (using neuroimaging software such as FSL, SPM, AFNI), administrative duties, IRB management, and general management of lab operations. Necessary qualifications include: 1) an undergraduate degree in Psychology, Neuroscience, Computer Science, or a related field; 2) prior research experience with human participants; and 3) strong organizational, interpersonal communication, and writing skills, and high motivation and initiative. Preference will be given to applicants who additionally have experience with: 1) unix, python, matlab, or another programming language; 2) neuroimaging analysis software (e.g., FSL, AFNI, SPM); 3) collecting and analyzing fMRI data; and 4) working with children. Commitment must be for at least one year, but position can be extended. Interested applicants should send their CV, at least two letters of reference, transcript with relevant coursework, and a cover letter describing their research interests and career goals to Dr. Jessica Cohen (jrcohen(a)unc.edu <mailto:jrcohen@unc.edu>). Additional information can be found at: http://cohenlab.web.unc.edu/ ========================= 2. Postdoctoral position: MULTIMODAL IMAGING OF NETWORK CONNECTIVITY IN AUTISM Brain Development Imaging Laboratory The Brain Development Imaging Laboratory (BDIL) at the Dept. of Psychology, San Diego State University (SDSU), is offering 1-2 postdoctoral positions in multimodal MRI. Post-doctoral positions will be supported by several newly funded NIH projects examining brain network organization across the lifespan in autism spectrum disorders (ASD). Research at BDIL (www.sci.sdsu.edu/bdil) applies diffusion weighted imaging techniques (tensor-based, multi-fiber, multi-shell imaging), anatomical MRI, fMRI, functional connectivity MRI, MR spectroscopy as well as behavioral and neuropsychological measures to investigate the brain bases of ASD and age-related change across the lifespan (1-65 years). BDIL collaborates with experts in MR physics, radiology, EEG, MEG, and bioinformatics to implement innovative imaging and analysis techniques (e.g., simultaneous fMR/EEG recording, combined MEG and MRI). BDIL researchers have full access to the UCSD Center for Functional MRI (http://fmri.ucsd.edu/), with two 3T human research scanners (32 channel head coils), led by top experts in radiology physics. Applicants should have experience in multimodal MRI (data acquisition, preprocessing, analysis). Experience in other imaging modalities (EEG, MEG) will be relevant, but not indispensable. Applicants with experience in the study of autism or other developmental disorders may be preferred. Please e-mail CV, research statement, reprints, and 3 letters of recommendation to Ralph-Axel Müller at:rmueller@sdsu.edu. ================================ 3. UCL INSTITUTE OF NEUROLOGY Wellcome Trust Centre for Neuroimaging London, UK Research Associate / Senior Research Associate in MRI Physics A postdoctoral position for an expert in MRI physics is available within the Wellcome Trust Centre for Neuroimaging (WTCN), UCL Institute of Neurology, London, UK. The Centre conducts cutting-edge research by means of functional and structural brain imaging, and is equipped with three 3 T MRI scanners (Siemens Tim Trio with 32-ch head coil), an MEG system (CTF/VSM), and MR compatible EEG and TMS systems. One of the MRI systems is equipped with an optical tracking system for prospective motion correction (Kineticor). We are seeking a highly motivated individual to work within the physics group at the WTCN reporting to Prof. Nikolaus Weiskopf, Head of MRI Physics. The group specializes in the development of a broad range of methods, including diffusion, structural and functional imaging, based on understanding the underlying MR physics, to arrive at efficient solutions. Current projects include, but are not limited to, maximizing acquisition efficiency and resolution, artifacts correction including optical prospective motion correction and quantitative MRI (see http://www.fil.ion.ucl.ac.uk/Research/physics.html). As a member of the WTCN Physics Group, the post holder will be expected to support ongoing neuroscience research. The appointee will be engaged in his/her own research projects to improve and develop novel MRI acquisition methods related to the primary projects of the group. Particular emphasis will be placed on fMRI acquisition methods with very high temporal and spatial resolution, to enable unprecedented studies of connectivity and functional microstructure. Applicants must have a PhD or, if not already held (Research Associate applicants only) the PhD must have been obtained by the agreed start-date in physics, biomedical engineering, or a comparable subject. A strong background in MR physics is essential, as is expertise in programming high-level languages (e.g. C/C++, Matlab). Applicants must also be specialized in at least one (Research Associate) or two (Senior Research Associate) of the following areas: pulse sequence programming, Siemens MR scanners and software (IDEA, ICE), MR image reconstruction methods (in particular, parallel imaging and compressed sensing), assessing safety of equipment / implants in the MR environment, time-series analysis, functional MRI or SPM software. Those applying for the Senior Research Associate position will also need to be able to demonstrate an established publication track record and experience of leading a team of researchers. The post is available immediately and is funded by the Wellcome Trust until November 2017, in the first instance. Salary will be in the range of £33,353 - £40,313 pa on UCL Grade 7 (Research Associate) or £41,430-£48,873 pa on UCL Grade 8 (Senior Research Associate) including London Allowance and superannuable. You should apply for this post through UCL's online recruitment http://www.ucl.ac.uk/hr/jobs where you can download a job description and person specification using ref: 1485072. If you have any queries regarding the application process, please contact Samantha Robinson, Personnel Officer, Institute of Neurology, 23 Queen Square, London, WC1N 3BG (email: IoN.HRAdmin(a)ucl.ac.uk <mailto:IoN.HRAdmin@ucl.ac.uk>). *Informal enquiries to Prof Nikolaus Weiskopf (email: **n.weiskopf(a)ucl.ac.uk <mailto:n.weiskopf@ucl.ac.uk>**)*. Further information on the lab: *http://www.fil.ion.ucl.ac.uk/Research/physics.html* ** *Closing date: *20 September 2015 /UCL Taking Action for Equality/ ________________________________ Dr. Martina Callaghan Deputy Head of Physics & Senior Research Associate Wellcome Trust Centre for Neuroimaging Institute of Neurology University College London 12 Queen Square London WC1N 3BG UK Tel: +44-20-344-84383 (internal ext 84383) Email: m.callaghan(a)ucl.ac.uk <mailto:m.callaghan@ucl.ac.uk> ====================================== 4. A new postdoctoral opportunity has arisen here in Cardiff, at the new Cardiff University Brain Research Imaging Centre (CUBRIC -http://sites.cardiff.ac.uk/cubric ). The is is a chance for a smart microstructural imager to get their hands on Cardiff's new 300 mT/m Connectome and 7T systems (seehttp://sites.cardiff.ac.uk/cubric/facilities/mri ) and get involved in an interesting modeling project focused on delivery of drugs / cells. The ad has just been posted here: http://www.ismrm.org/jobs/j05565.pdf and linked here: http://www.ismrm.org/career-center/postdoctoral-positions/ Please drop me a line with any informal enquiries. Thanks for reading! Derek Jones =============================== 5. University of Connecticut College of Liberal Arts and Sciences Postdoctoral Fellow in Cognitive Neuroscience The University of Connecticut’s new Brain Imaging Research Center (BIRC) invites The BIRC is a 3,200 square foot, research-dedicated imaging facility housing a research-dedicated 3T Siemens Prisma scanner and simultaneous high-density EEG/ERP, with a major focus of cognitive neuroscience research. The Postdoctoral Fellow will contribute to multiple funded NIH studies of language processing, reading, word acquisition, and cognition, under PIs Dr. Jay Rueckl and Dr. Peter Molfese. Prior experience in research using MRI/fMRI is required. Responsibilities will include the design and execution of fMRI and behavioral experiments; fMRI data analysis; formulating and participating in writing of scientific papers as part of the research team; participating in grant writing towards the eventual goal of independent funding; and developing independent projects in the areas of speech, reading, and language. Minimum Qualifications: · Ph.D. in Psychology, Cognitive Neuroscience, or Related Field · Experience with fMRI Experimental Design · Experience with MRI/fMRI Data Analysis (e.g. AFNI, FSL, SPM, Freesurfer) Preferred Qualifications: · Strong Analytical & Statistical Skills (e.g. SEM, HLM, Data Mining) · Experience with EEG/ERP Data Collection and Analysis · Programming Skills (e.g. C/C++, Python, R, E-PRIME) · Experience with Computational Modeling The anticipated start date is September 1, 2015, but is negotiable. Salary will be commensurate with qualifications and experience. Interested applicants should send a cover letter describing qualifications, a CV, and any supporting materials to UConn Careers (www.jobs.uconn.edu). Select “Apply Now" to be redirected to Academic Jobs Online to complete your application. Names of three references should be included in the cover letter; letters will be submitted to Academic Jobs Online. Inquiries can be addressed to Peter Molfese, Chair o Screening of applications will begin immediately and continue until the position is filled. The University of Connecticut is an EEO/AA employer. https://academicjobsonline.org/ajo/jobs/5759 =============================== 6. Applications are invited for two Post-Doctoral positions in the Brain and Language Lab (www.brainandlanguagelab.org <http://www.brainandlanguagelab.org>) at the University of Geneva.The positions are for 2.5 years, and will be at the new Biotech Campus (http://www.campusbiotech.ch/en/). 1. For the first position, candidates should have a degree in Cognitive Neuroscience, Biomedical Engineering, Computational Neuroscience or a related field, and should have solid experience in brain imaging data analysis, computational modelling, pattern recognition, machine learning, statistics and programming. The projects will involve the use and development of computational morphometry and of computational modeling to study auditory cortex structure and function in healthy individuals, in experts and in individuals with dyslexia. 2. For the second position, candidates should have a background in Psychology and/or Cognitive Neuroscience, and should have solid experience in functional and structural brain imaging data analysis. The projects will include brain imaging and behavioural studies on multilingualism and expertise, with a focus on executive skills and statistical learning. The salary is competitive, starting salary at 68, 964 CHF/year or more depending on experience. The positions are available immediately, and applications will be considered until the position is filled.Informal inquiries can be addressed to Narly Golestani (Narly.Golestani(a)unige.ch).Applications including a CV, a statement of research interests, and the names and full contact details of three referees should be sent to: Narly.Golestani(a)unige.ch <mailto:Narly.Golestani@unige.ch>. =====================

1 0

YNiC seminar 3rd September
by Rebecca E Millman 31 Aug '15

31 Aug '15

Dear Users This Thursday (4-5 pm in B020), Katja Weibert will give an internal project proposal presentation on "Do patterns of response in face-selective regions represent facial identity?". Everyone is welcome to attend. Refreshments will be available after the seminar. Best wishes Rebecca -- Dr. Rebecca E. Millman York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG Email: rem(a)ynic.york.ac.uk Tel: 01904 435 5373

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