ynic-users March 2010

ynic-users@ynic.york.ac.uk

6 participants
13 discussions

Software updates
by Mark Hymers 30 Mar '10

30 Mar '10

Hi, Some small software updates were pushed out to the YNiC systems this afternoon: Visualization: -------------- * mricron was added to all machines. Python related: --------------- * python-pymc and python-h5py were added to the supported modules list. * winpdb (a debugging tool) was added to the system. Matlab: ------- * Matlab 7.10 (2010a) was added to the system but has *not* been made the default (which remains at 7.8). We encourage people to try out the new release which will be made the default (unless problems are encountered) in September as explained at: https://www.ynic.york.ac.uk/doc/ITPages/FAQ/Misc/SupportedVersions#Matlab All toolboxes which are available in 7.8 should also be available in 7.10. * cbinifti and mlpipe (from http://www.pc.rhul.ac.uk/staff/J.Larsson/software.html ) have been made available to make dealing with nifti files in Matlab simpler. As usual, we rely on users to let us know if they encounter any issues, so if you do, please email it-support(a)ynic.york.ac.uk . Thanks, Mark -- Mark Hymers York Neuroimaging Centre

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Science Trail - Monday 29th March
by Michael Simpson 23 Mar '10

23 Mar '10

Dear all, As usual, YNiC will be one of the venues for the UoY Science Trail, which is a day for groups of local secondary schools pupils to sample the many areas of scientific research in the university. Therefore, YNiC Open Plan will be very busy with enthusiastic school children between 10.00 and 15.00 on Monday 29th March. Although the pupils will not be using I.T. workstations, it may be preferable for you to not use the six workstations nearest the projector, nor to try and have a lab meeting in Open Plan until after 15.00 on Monday 29th March. However, in general, access to the Open Plan workstations will not be affected by this event. Only the level of background noise is anticipated to be affected ... Thanks, Michael -- Dr Michael Simpson Science Liaison Officer York Neuroimaging Centre Innovation Way York YO10 5DG Tel: 01904 567614 Web: http://www.ynic.york.ac.uk

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Will Woods
by Gary Green 23 Mar '10

23 Mar '10

Dear Users You may have already heard that Will Woods will be leaving us this summer. He will be moving to Australia to take up a new position in Melbourne. Before he leaves, he has agreed to give a seminar presentation. It will be on the 22nd of April at 4pm in YNiC. This gives us an excellent opportunity to express our gratitude for the major role that Will has played in establishing YNiC. Therefore, we will hold a reception for him immediately after the seminar. If you would like to contribute to a gift to mark this occasion, then please could you contact Jo Saunders in YNiC. All are welcome Gary -- 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 (Sara Narayan) +44 (0) 1904 435329 fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004

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YNiC seminar TODAY
by rem 18 Mar '10

18 Mar '10

Dear Users Today (4-5 pm in YNiC open plan), there will be a YNiC project proposal given by Matt Speed (Department of Electronics) on imaging the vocal tract. Title: MRI capture of the vocal tract. Abstract: Acoustic modelling research in the AudioLab in the Department of Electronics focuses on the synthesis of “natural” human voice through the computer simulation of the acoustic properties of the vocal tract. This study aims to generate accurate 3D acoustic models of the vocal tract based on MRI scans of trained speakers/singers for particular phonemes/vowel-based utterances. From this data, new detailed 3D models of the vocal tract will be produced, leading to more accurate simulation of its acoustic characteristics, and the potential for new developments in the field of speech synthesis. A particular challenge is the recording of the audio speech signal during the MRI capturing process, with a view to providing a benchmark against which sound synthesised using the resulting 3D acoustic model can be compared. The preferred approach has not yet been determined, but will be discussed during the project presentation (18th March). Additionally we hope to use our same subjects to capture different styles of singing with a view to identifying and characterising “ringing” qualities of vocal sounds. This is a secondary study that we will brief our subjects on and carry out if time is remaining once appropriate source data for our primary study has been obtained. Everyone is welcome to attend. Best wishes Rebecca -- ************************************************************************ 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

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YNiC seminar 18th March
by rem 15 Mar '10

15 Mar '10

Dear Users This week (4-5 pm in YNiC open plan), there will be a YNiC project proposal by Matt Speed (Department of Electronics) on imaging the vocal tract. Title: MRI capture of the vocal tract. Abstract: Acoustic modelling research in the AudioLab in the Department of Electronics focuses on the synthesis of “natural” human voice through the computer simulation of the acoustic properties of the vocal tract. This study aims to generate accurate 3D acoustic models of the vocal tract based on MRI scans of trained speakers/singers for particular phonemes/vowel-based utterances. From this data, new detailed 3D models of the vocal tract will be produced, leading to more accurate simulation of its acoustic characteristics, and the potential for new developments in the field of speech synthesis. A particular challenge is the recording of the audio speech signal during the MRI capturing process, with a view to providing a benchmark against which sound synthesised using the resulting 3D acoustic model can be compared. The preferred approach has not yet been determined, but will be discussed during the project presentation (18th March). Additionally we hope to use our same subjects to capture different styles of singing with a view to identifying and characterising “ringing” qualities of vocal sounds. This is a secondary study that we will brief our subjects on and carry out if time is remaining once appropriate source data for our primary study has been obtained. Everyone is welcome to attend. Best wishes Rebecca -- ************************************************************************ 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

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YNiC seminar this week
by rem 09 Mar '10

09 Mar '10

Dear Users There is no planned YNiC seminar this week. Unless someone is keen to give a talk this Thursday (11th), there will not be a seminar this week. The last seminar for this term will take place next week (18th March). Best wishes Rebecca -- ************************************************************************ 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

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VC visit tomorrow
by Gary Green 09 Mar '10

09 Mar '10

Dear colleagues The Vice-Chancellor will be bringing a visitor to YNiC tomorrow afternoon at 2.55pm. The visitor is Nicola Dandridge who is the Chief Executive of Universities UK. The VC has asked whether Users might be available in case the visitor wishes to ask about their work. We will be taking the VC and his visitor to the open plan area, MEG and then MRI. If you are working in YNiC tomorrow afternoon then I would be very grateful if you could be prepared to briefly speak about your research. Thank you and apologies for any inconvenience caused -- 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 (Sara Narayan) +44 (0) 1904 435329 fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004

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YNiC seminar TODAY
by rem 04 Mar '10

04 Mar '10

Dear Users Today (4-5 pm in YNiC open plan), Gary Green will give an update on the hyperpolarisation project. Everyone is welcome to attend. Best wishes Rebecca -- ************************************************************************ 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

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FW: [BIC-announce] Symposium: Dysfunctional Imaging: Advances in lesion-function mapping of the human brain
by Ekaterini Klepousniotou 03 Mar '10

03 Mar '10

FYI **************************************************************** Dr. Ekaterini Klepousniotou Lecturer in Cognitive Neuroscience & Neuropsychology Institute of Psychological Sciences University of Leeds Leeds LS2 9JT UK Tel: +44 (0)113 3435716 Fax: +44 (0)113 3435749 From: bic-announce-bounces(a)bic.mni.mcgill.ca [mailto:bic-announce-bounces@bic.mni.mcgill.ca] On Behalf Of Jennifer Chew, Ms. Sent: 01 March 2010 16:38 To: bic-announce(a)bic.mni.mcgill.ca Subject: [BIC-announce] Symposium: Dysfunctional Imaging: Advances in lesion-function mapping of the human brain FOR YOUR INFORMATION. Jennifer ________________________________ From: arlene.berg(a)muhc.mcgill.ca [mailto:arlene.berg@muhc.mcgill.ca] Sent: Monday, March 01, 2010 11:28 AM To: Anna Maria Rossi; Carolina Oyarzun, Ms.; Enza Ferracane, Ms.; Monique Ledermann, Ms.; Terry Kaluta, Ms.; Jennifer Chew, Ms.; Adele D'Amato, Mrs.; Luisa Birri, Ms. Subject: request Good morning, I'm attaching two posters (English & French), along with the description below, of an upoming symposium that Dr. Fellows is organizing. We would be grateful if you could distribute/email this to the people on your mailing list. I will also send you a color poster as soon as I have them. Thank you so much for your help. Arlene Berg for Dr. Fellows (See attached file: Dysfunctional Imaging Poster-English.jpg)(See attached file: Dysfunctional Imaging Poster-Fre.pdf) Dear Colleagues, I'm writing to invite you to a symposium discussing the latest methods in lesion-symptom mapping to be held April 17, 2010, at the Montreal Neurological Institute: 'Dysfunctional Imaging': Advances in lesion-function mapping of the human brain This one day meeting and think-tank will bring together leaders in cognitive neuroscience, neuroimaging methods, and experimental neuropsychology to discuss methodological advances in structure-function mapping in the human brain. Technical and conceptual advances in characterizing lesions, measuring behavioral changes, and linking the two through voxel-based, region-of-interest, and network lesion-symptom mapping approaches will be presented. This informal meeting will be of interest to experts working in these areas, and to researchers and cognitive neuroscience trainees who would like to know more about these new methods. Please post the enclosed poster at your centre or department to help us advertize this event. Please see the meeting website for the preliminary program and registration details. http://neuroevents.mcgill.ca/index.php?page=dysfunctional-imaging-symposium If you have questions, feel free to contact me, or Arlene Berg (arlene.berg(a)muhc.mcgill.ca). See you in Montreal! Lesley Fellows _______________________________ Lesley Fellows, MD CM, DPhil Associate Professor Department of Neurology & Neurosurgery McGill University Montreal Neurological Institute, Rm. 276 3801 University St. Montreal QC H3A 2B4 lesley.fellows(a)mcgill.ca 514 398 8980 (o) 514 398 1338 (fax)

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[Fwd: Multimodal Neuroimaging Postdoctoral Fellow at MGH / Harvard Medical School]
by Gary Green 03 Mar '10

03 Mar '10

FYI ---------------- Multimodal Neuroimaging Postdoctoral Fellow (posted 2/19/10) Responsibilities: Emphasis will be on MRI (DTI, spectroscopy, morphometry, ASL) and additionally on EEG and MEG. This position will involve analysis of existing multimodal imaging data and collection of new data. It will also involve some research oriented analysis of imaging data collected for clinical purposes. The age range of our subjects is primarily from early infancy to mid-adolescence, with some additional studies including young adults. Requirements: Applicants must have a PhD. or equivalent and an extensive background in cognitive neuroscience and/or neuroimaging (MEG, EEG, fMRI, MRI, or other brain imaging techniques). Experience in computer programming (Linux/Unix shell scripting and MATLAB), neuroimaging analysis methods (FSL, Freesurfer, SPM), signal processing and advanced statistical analyses would be a plus. The position is for two years, available immediately may have the option of extension. Salary will be consistent with the NIH levels in accordance with the Massachusetts General Hospital, Harvard Medical School policies for Postdoctoral trainees. Compensation includes full staff benefits, including health insurance, and vacation time. Contact: Martha Herbert: transcend(a)partners.org; cc mherbert1(a)partners.org

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ynic-users March 2010