ynic-users October 2017

ynic-users@ynic.york.ac.uk

5 participants
9 discussions

News this week
by Antony Morland 18 Oct '17

18 Oct '17

Hello All, This weeks seminar is 'How to apply to use the centre'. This will be relevant to all newbies, but will also give an overview of updates that are in the pipeline that will affect all applicants. In other news we are continuing with our programme of training for operators of the Siemens and GE scanners. Best wishes Tony Tip of the week: At the command line you can type ls > list.txt it will generate a text file of the files and directories in the current directory (as long as you have write permissions in the current directory) ls *is the 'list' command* > *allows the output of the ls command to be redirected to a file* mylist.txt * is the file name you supply to capture the output of the ls command* Why is this useful? The generation of a file that lists directories or files can be useful when you are writing scripts to perform analysis on multiple directories or files. Note that this help with ls can be obtained by typing man ls -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Updates and news
by Antony Morland 12 Oct '17

12 Oct '17

Hello All, Quite a few things this week: 1) IMPORTANT: Our MRI screening safety screening forms have been updated. The updates are explained in our revised local rules. 2) A reminder: Our training documentation (including the local rules referred to above) is held at the following URL https://www.ynic.york.ac.uk/ docs/forms. A login in required to access the URL. 3) Last weeks seminar, which was postponed, will go ahead this week and will follow the project presentation by Shogo Kajimura entitled '*Decoding contents of mind wandering'*. The seminar series details can be found here: https://www.ynic.york.ac.uk/events/thursday-sessions#preview 4) We are currently training 14 operators at YNiC. Best wishes Tony *Tip of the week* You can control the transparency of your overlays in *fslview *by using the blue transparency slider located a the bottom right of the window - see attached -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Update - GE MRI system repair
by Andre Gouws 09 Oct '17

09 Oct '17

HI all, The GE engineer has attended and diagnosed the fault with the system. A replacement part is required for the Oxygen monitor to work correctly. This part is on express order and we hope to have it installed tomorrow, although it is unclear at what point in the day this will be. We are hoping that normal scanning service will resume by Wednesday (11th), but please keep alert for further updates which we will send once we have more information. Thanks, -- André ************************************************************************ André Gouws PhD York Neuroimaging Centre University of York The Biocentre York Science Park Heslington YO10 5NY Tel: +44 (0) 1904 435327 Fax: +44 (0) 1904 435356

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GE MRI system fault
by Andre Gouws 08 Oct '17

08 Oct '17

Hi all, I am afraid to report that a sensor fault has developed on the GE system over the weekend. This sensor monitors the safe oxygen level in the MRI environment, and thus the scanner cannot be used until the fault is fixed. GE have said the will attend on Monday AM - we hope to have the scanner up and running as soon as possible. Sorry for those affected by the scanner downtime. André ************************************************************************ André Gouws PhD York Neuroimaging Centre University of York The Biocentre York Science Park Heslington YO10 5NY Tel: +44 (0) 1904 435327 Fax: +44 (0) 1904 435356

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Posters
by David Coggan 06 Oct '17

06 Oct '17

Hello all, We are still looking for posters to put up around YNiC open plan. If you would like to contribute one, please get in touch or drop it off at YNiC. Best wishes, Dave

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Postponed: Today's YNiC seminar.
by Andre Gouws 05 Oct '17

05 Oct '17

Hi all, Due to some unforeseen circumstances we have to postpone today's seminar - We will reschedule and update you in next week's update bulletin. Best wishes, -- André ************************************************************************ André Gouws PhD York Neuroimaging Centre University of York The Biocentre York Science Park Heslington YO10 5NY Tel: +44 (0) 1904 435327 Fax: +44 (0) 1904 435356

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Next YNIC Science Meeting
by Jonny Smallwood 03 Oct '17

03 Oct '17

Hello all, We are holding the next meeting of the YNIC Science Committee next Monday. Please send any items you would like me to raise by Thursday so I can add them to the agenda. Thanks Jonny -- Jonathan Smallwood, Reader in Psychology / Cognitive Neuroscience Room C023, Department of Psychology, University of York, England. YO10 4PH. Telephone: 01904 324651

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Disruption
by Antony Morland 03 Oct '17

03 Oct '17

Hello All, We have a Heating and Cooling contractor in attendance today. Alarms may sound. Apologies if they disrupt your work. If an alarm does and stops within 30s there is no need to act. Please be aware that staff may need to ask you to leave at short notice. Thanks Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Weekly update
by Antony Morland 02 Oct '17

02 Oct '17

Hello All, Two things this week 1) The will be a seminar held in the Chemistry Department this week that may interest users: Dr Luisa Ciobanu: Functional MRI at ultra-high magnetic fields Wednesday 4th October 13.00-14.00 In room Chemistry/B101 Abstract Despite the fact that BOLD-fMRI is routinely used to map brain activity and connectivity in preclinical and clinical settings its exact relation with the underlying microscopic changes, either vascular or neuronal, is still not fully elucidated. The development of high magnetic fields promise substantial improvements in the contrast to noise ratio and the spatial resolution with which functional MRI maps are acquired possibly allowing the comparison with other, microscopic, techniques. In the first part of my talk I will review the advantages, but also the challenges, imposed by imaging at ultra-high magnetic fields. Following this, I will present recent results demonstrating that BOLD fMRI faithfully reports microvascular hyperemia, and that the detection of the smallest neuronal activation is limited only by its sensitivity. Beside improved BOLD acquisitions, high magnetic fields allow the development of other alternative ways for studying neuronal activation. In the last part of my presentation, I will describe a novel metabolic imaging approach, based on Chemical Exchange Saturation Transfer (CEST), for assessing the changes induced by neuronal stimulation in rat brains at 17.2T. Specifically, I will present images acquired under glucose-sensitizing conditions showing a significant negative contrast that highlights the same brain regions as those activated in conventional BOLD maps. 2) We are to give 'Tips of the week', hopefully, as the name suggests on a weekly basis. This will largely give advice on IT tricks and work-arounds for commonly occurring analysis tasks. Here's this week's: Scenario: You've submitted a load of jobs to the cluster which you find out will be of no use to you and you want to bring them to a halt. Solution typing: qdel -u <username> into a terminal will stop all cluster jobs submitted by that user, e.g. qdel -u ddc506 Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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ynic-users October 2017