ynic-users July 2008

ynic-users@ynic.york.ac.uk

10 participants
9 discussions

printer at YNiC
by Gary Green 28 Jul '08

28 Jul '08

I am sorry to have to report that the printer at YNiC (Canon) has jammed and is out of operation until an engineer can visit. I will inform you when it becomes available again Gary -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

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Interesting paper
by Michael Simpson 24 Jul '08

24 Jul '08

Dear all, an interesting and brief article on the relationship between fMRI and electrophysiology. http://dx.doi.org/10.1016/j.cub.2008.03.042 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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MRI setup change - Mirror for visual stimuli
by Andre Gouws 24 Jul '08

24 Jul '08

Dear users TAKE HOME MESSAGE: A FRONT-SILVERED MIRROR HAS NOW BEEN MOUNTED IN MRI IMPROVING IMAGE QUALITY Many of you will be aware that the visual stimulus delivery setup in MRI relies on back-projection onto a screen which the participant then views via a mirror mounted in front of their face. We have always been aware that standard mirrors are sub-optimal for this type of setup: as soon as a standard mirror is tilted internal reflection and refraction of light causes slight blurring of the image .. sometimes this is perceived as a 'double edge' when viewing object binocularly. This effect can be minimised by using a minimum glass thickness in front of the reflective surface of the mirror. Thus, to date, we have used a 2mm thick mirror to aid image quality. Unfortuantely many of you have expressed concerns that this is still not as good as you would like. We have thus decided to fit a custom cut front-silvered mirror in place of the previous setup. These mirrors have effectively no glass thickness since it is the front surface of the mirror that is the reflective one. This (for the money) is as close as we can get to perfect reflection and should resolve your problems. Unlike standard mirrors, front-silvered ones have no protection of the reflective surface and are highly sensitive to scratching and marking. The mirror can only be cleaned of dust with special products and oily stains may be impossible to remove. As such all users / operators must avoid handling the mirror surface directly and should place the mirror array in place / store with care to avoid scratching of the mirror surface by other objects. We hope the improved quality will benefit us all. Contact me if you have any queries. Kind regards, Andre' -- ************************************************************************ Andre Gouws User Support Manager York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 435328 Fax: +44 (0) 1904 435356

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questions about freesurfer
by Jing Kan 16 Jul '08

16 Jul '08

Dear users, Thanks for reading! I am a new user about freesurfer, after learning it a little while, I have got some problems: 1. I have used "recon-all" successfully to process the sMRI data, which generated the "lh.pial". And, I used "mris_convert lh.pial lh.pial.asc", get text mesh "lh.pial.asc". May I ask how can I view this with visible mesh associated with the vertices and triangle? 2. I have read the Manual v 0.8. It seems all of the interface has not supported in our new Freeserfer version...do you have some good suggestion about the materials for beginner to learn? I really appreciate your help!Looking forward to your reply! Kind regards, Jing

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Ole Jensen seminar TODAY
by rem 10 Jul '08

10 Jul '08

*N.B. Today's seminar will be held in A202 in Psychology and not in YNiC* Dear Users Today's seminar (Thursday 4 pm in the Venables room, A202 ) will be given by Ole Jensen from FC Donders. http://oase.uci.ru.nl/~olejen/ The title of his talk will be "How slow event-related fields are created from cognitive modulations in oscillatory brain activity". Everyone is welcome to attend and there will be wine and soft drinks available after the talk. 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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Call for expertise: across session fMRI analyses
by andre＠ynic.york.ac.uk 09 Jul '08

09 Jul '08

Dear Users, Concatenation or higher level stats? We would value the input of any users who have experience of 'combining' fMRI data across multiple runs for more robust averaging. The issue arises when trials of an experient are acquired in different data blocks due to technical limitations of scan scquisition protocols or often to reduce the strain on participants in a single session. I have searched many available resources. There are well documented routines for (1) analysinng the sessions individually and then compring them with a higher level analysis or (2) demeaning the two timeseries and combining them into a single one .. then following the standard analysis individual subject routine. Comments would be appreciated (especially from anyone has first hand experience of doing this). Thanks Andre'

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Ole Jensen seminar
by rem 07 Jul '08

07 Jul '08

Dear Users Please note that, contrary to the email I sent this morning, this week's YNiC seminar will be held in Psychology i.e. *NOT YNIC*. Ole's talk will be in the Venables room (A202) since B020 is being used for a graduation party. 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 10th July
by rem 07 Jul '08

07 Jul '08

Dear Users This week's seminar (Thursday 4 pm at YNiC) will be given by Ole Jensen from FC Donders. http://oase.uci.ru.nl/~olejen/ The title of his talk will be "How slow event-related fields are created from cognitive modulations in oscillatory brain activity". Everyone is welcome to attend and there will be wine and soft drinks available after the talk. 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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Computing service maintenance
by Gary Green 02 Jul '08

02 Jul '08

Dear Colleagues Computing Service have asked us to take our machines down for a period of three hours on Wednesday evening. This will allow us to take advantage of a change in the University network architecture and will provide more resilience in our connections to the University. Please can everyone stop submitting cluster jobs that will not be complete by 5pm on Wednesday. To be on the safe side I would suggest not submitting jobs after 3pm on Wednesday. Even then jobs may be lost if they are still running at 5. During the downtime, mail and web services will also be interrupted but for a shorter period. Thanks -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

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ynic-users July 2008