- ynic-users

"Cogs" discussion group
by Tom Hartley 01 Nov '23

01 Nov '23

Hi everyone, As you may already know we are organizing a new cognitive science group "Cogs" that will take place at YNiC with the aim of generating informal and lively discussion about topics that excite and inspire us. It's open to undergrads, academics, masters students, postdocs, research staff, PhD students, YNiC staff and basically anyone with an interest in cognitive neuroscience at the University of York. This semester the* meetings are taking place on alternate Friday lunchtimes at 12:15*, the next ones being: *10th Nov Tom Hartley, Space and Concepts <https://uniofyork.padlet.org/tomhartley/cogs-7svj1mgvsc2jq2yp/wish/27644611…>* *24th Nov leader TBC* *8th Dec Beth Jefferies, Spiral Waves in the Brain <https://uniofyork.padlet.org/tomhartley/cogs-7svj1mgvsc2jq2yp/wish/27644691…>* *We have a padlet (https://cogs.ynic.york.ac.uk/ <https://cogs.ynic.york.ac.uk/> bookmark it)* where you can find out more, read and post papers/preprints <https://uniofyork.padlet.org/tomhartley/cogs-7svj1mgvsc2jq2yp/wish/27644996…> and suggest your own topics for discussion <https://uniofyork.padlet.org/tomhartley/cogs-7svj1mgvsc2jq2yp/wish/27644962…>, raise questions or even volunteer to lead a session. And you can "like" posts, so we know which topics and ideas generate the greatest appetite. You can also *email the organizers (Tom Hartley, Beth Jefferies) by email at cogs(a)ynic.york.ac.uk <cogs(a)ynic.york.ac.uk>*. I've attached my powerpoint slides from last week's inaugural meeting. See you all at Cogs! Tom ============ Dr Tom Hartley (Senior Lecturer) Dept. of Psychology, University of York, Heslington, York, YO10 5DD, UK +44 1904 322903 https://www-users.york.ac.uk/~th512 <http://www-users.york.ac.uk/~th512> https://www.york.ac.uk/psychology/staff/faculty/th512/ <http://www.york.ac.uk/psychology/staff/faculty/th512/>

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"Cogs": YNiC's new Cognitive Neuroscience Discussion Group
by Tom Hartley 27 Oct '23

27 Oct '23

On Friday October 27th at 12:15 we are launching the “Cogs” discussion group at YNiC. Cogs runs alongside existing YNiC events and is intended to help build an inclusive research culture by welcoming people to the centre and talking about new and exciting ideas in cognitive neuroscience. This could include talking about recent papers or new tools, but beyond that we’re pretty open-minded, so the first meeting will be a chance to share your thoughts on the format and what we can do to make it work best for you. Cogs is open to everyone with an interest in cognitive neuroscience research, whether that’s undergraduates or masters students running projects at YNiC, PhD students, postdocs, academic staff and the YNiC team. This semester Cogs sessions will start at 12.15 on alternate weeks Semester 1, Week 5, October 27th 12.15 Inaugural welcome and discussion Further dates this semester - presenters/topics to be announced in due course (let us know if you want to present, now or in the future) Semester 1, Week 6, November 10th 12.15 Semester 1, Week 8, November 24th 12.15 Semester 1, Week 10, December 8th 12.15 This timetable will be reviewed at the end of the semester, so let us know if it works/doesn't work for you and we'll try to take that into account. Tom (YNiC Community Coordinator) & Beth (Co-Director, YNiC) Email cogs(a)ynic.york.ac.uk with your thoughts and suggestions for topics/presenters. ============ Dr Tom Hartley (Senior Lecturer) Dept. of Psychology, University of York, Heslington, York, YO10 5DD, UK +44 1904 322903 https://www-users.york.ac.uk/~th512 <http://www-users.york.ac.uk/~th512> https://www.york.ac.uk/psychology/staff/faculty/th512/ <http://www.york.ac.uk/psychology/staff/faculty/th512/>

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YNiC Seminar Tomorrow 4pm!
by Jennifer Ashton 24 Oct '23

24 Oct '23

Hi Everyone, We have our YNiC seminar tomorrow at 4pm. *Dr Arianna Moccia *will be presenting her talk titled: *How do we select memories? Goal-states and consequences of the pre-retrieval control of episodic memory.* We really hope to see everyone at YNiC! If you are unable to attend the talk in person, you can catch it on zoom using the following link: https://york-ac-uk.zoom.us/j/96762553290?pwd=UEluT1lMd3V5azY5YzNmWkJCV1VTdz… <https://www.google.com/url?q=https://york-ac-uk.zoom.us/j/96762553290?pwd%3…> . We look forward to seeing you tomorrow! Many thanks, Jennifer -- Jennifer Ashton, PhD Senior Research Technician York Neuroimaging Centre Working days: Monday, Tuesday and Wednesday

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Fwd: Making your MATLAB Code faster • Wednesday 1 November • 1pm to 4.30pm • AEW/004 PC Room
by Joe Lyons 24 Oct '23

24 Oct '23

There's a MATLAB workshop bring run next week by the Research Coding Club just round the corner from YNiC. It will be presented by Mike Croucher, Customer Success Engineer at MathWorks. You can register using the Google Form below if you'd like to attend. Thanks Joe ---------- Forwarded message --------- From: Philip Harrison <philip.harrison(a)york.ac.uk> Date: Tue, 24 Oct 2023 at 11:35 Subject: Making your MATLAB Code faster • Wednesday 1 November • 1pm to 4.30pm • AEW/004 PC Room To: viking-users <viking-users-group(a)york.ac.uk> Hello everyone The first Research Coding Club session of the semester is happening next *Wednesday 1st November from 1pm to 4:30pm*, in-person in PC Room AEW/004 <https://www.york.ac.uk/map/#locidaew-004> and it's all about Making your MATLAB Code faster. Do you write MATLAB code and wish it went a little faster? In this hands-on workshop, you will learn a range of techniques in how to make MATLAB go faster including modern MATLAB programming techniques, GPU and parallel computing. For more information, please visit the sign-up form <https://docs.google.com/forms/d/e/1FAIpQLSebNWCu_fvgApUo71PD5mGcNmYyZHYyoDO…>. Please share these details with students and colleagues. Get in touch if you have any questions and hope to see you there. Phil -- Dr Philip Harrison Research Software Engineer Team Lead Research IT Team, IT Services University of York V/B/115 - 01904 32 2668 Email disclaimer <https://www.york.ac.uk/about/legal-statements/email-disclaimer/> -- You received this message because you are subscribed to the Google Groups "viking-users" group. To unsubscribe from this group and stop receiving emails from it, send an email to viking-users-group+unsubscribe(a)york.ac.uk. To view this discussion on the web visit https://groups.google.com/a/york.ac.uk/d/msgid/viking-users-group/CAAPyAr7D… <https://groups.google.com/a/york.ac.uk/d/msgid/viking-users-group/CAAPyAr7D…> . -- Thanks Joe Lyons, Systems Administrator York Neuroimaging Centre (YNiC), University of York joe.lyons(a)york.ac.uk 01904 325949 | 01904 325940

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DPIA_183_v3 and university servers
by Fiona McNab 20 Oct '23

20 Oct '23

Hi All, In DPIA_183, we now have approval to store YNIC data on University servers (not just YNIC servers). Version 3 (attached) replaces version 2, and it will appear on the YNIC forms website <https://www.york.ac.uk/psychology/research/york-neuroimaging-centre/forms/> shortly. Best wishes, Fiona

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YNiC Seminar next Wednesday!
by Rebecca Lowndes 19 Oct '23

19 Oct '23

Hi all, Dr Arianna Moccia will be presenting her talk entitled: *How do we select memories? Goal-states and consequences of the pre-retrieval control of episodic memory* We really hope to see everyone at YNiC! The talks will take place *next Wednesday (the 25th of October) at 4pm*. If you are unable to attend the talk in person, you can catch it on zoom using the following link: https://york-ac-uk.zoom.us/j/96762553290?pwd=UEluT1lMd3V5azY5YzNmWkJCV1VTdz… <https://www.google.com/url?q=https://york-ac-uk.zoom.us/j/96762553290?pwd%3…> . Quick reminder that all our upcoming seminar talks are on our YNiC seminar calendar: https://calendar.google.com/calendar/u/0?cid=Y19mZDNiNjNhY2Y4NzNiZDVkYzhhZD… We look forward to seeing you then! Becky Selective retrieval means picking specific memories out of many encoded traces to inform present actions. To do so, control processes need to act prior to the point of retrieval. Neuroimaging has shown that we can select memories in this way, but little is known about the factors and mechanisms that enable pre-retrieval selection in episodic memory. We tested this in a first set of electrophysiological studies. Results showed that internal control modified recollection-related ERPs – the left parietal old/new effects – when the external retrieval cues overlapped with targeted traces. Goal-related effects arising from comparing ERPs elicited by the new items also tracked cue overlap before recollection was complete, indicating that control was engaged prior to retrieval. But how is selection achieved during retrieval? Using multivariate pattern analysis in these two datasets, we showed that study phase neural patterns matching the current retrieval goal were reinstated before the retrieval cues were presented, indicating that study context was reinstated in preparation to retrieve targeted information. A final study using fMRI to investigate selective retrieval in the brain showed that internal goals alone modified activation and neural representations of task-relevant features in content-specific regions. Goal- directed preparatory reinstatement of study context was detected in both domain-general control regions and content-specific regions. However, while activation in domain general areas predicted subsequent memory performance, goal-directed reinstatement did not do so significantly, suggesting that further, generic control mechanisms may support readiness to remember sought-for episodic information. -- Rebecca Lowndes Research Technician York Neuroimaging Centre

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YNiC - Changes to booking system & operator cover
by Aidan Horner 17 Oct '23

17 Oct '23

Dear all, Beth, myself, and all the YNiC staff are working hard to ensure YNiC is an open and inclusive environment to conduct amazing cognitive neuroscience research. Part of that is reviewing a lot of our current policies and making changes where we think it will help. One current bottleneck for accessing the MRI scanner is the need for all "operator-covered", bookable slots to have two YNiC staff acting as operators. This severely limits the number of hours we can make available on the booking system. When YNiC provides both operators, groups do not need to provide an operator but many groups already have someone who is at least level 0 trained. We are looking to get even more YNiC researchers trained up to reduce this bottleneck and thus make more "operator-covered" bookable slots available. To increase bookable hours, we are moving to a system where YNiC ensures one YNiC staff as operator. This means, by default, you will be expected to provide one level 0 trained individual (usually the person running the study), to ensure we have at least one level 0 and one level 1 individual present at all scans (in line with existing policy). This will increase the number of operator-covered bookable hours per week from ~10 - ~16hours. Note, if your lab can provide at least a level 1 and level 0 operator, you are still able to book the MRI scanner outside of these hours. We believe this shouldn't affect any projects that are currently running, but please get in touch if this is not the case. For future projects, you will be expected to provide a level 0 trained individual by default. If you cannot do this, then this shouldn't prevent you from scanning - get in contact with us and we can work something out. The only real change is we are moving from two YNiC staff by default (with exceptions when the researcher is level 0 trained) to one YNiC staff by default (with exceptions when the researcher isn't level 0 trained). Finally, all supervisors of MSci projects that are about to start scanning will be emailed directly by a YNiC staff member to ask what support they need. Please respond to this email as soon as possible so that we can ensure these projects run as smoothly as possible. I hope this change, and the rationale for making the change, are clear. Please get in contact with me and Beth if this is not the case, or you have specific concerns about how this change might impact your research. Best wishes, Aidan -- ===================================================================== York Neuroimaging Centre (YNiC) Directors Prof Beth Jefferies - Co-Director for Research Dr Aidan Horner - Co-Director for Strategy & Operations https://www.york.ac.uk/psychology/research/york-neuroimaging-centre/ =====================================================================

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Building work disruption next week
by Rebecca Lowndes 28 Sep '23

28 Sep '23

Hi all, There will be some disruptive building work in the MRI corridor next week (w/c 2nd Oct). The Siemens scanner will be up and running, data quality will not be affected, and the Siemens control room will not be affected. However, the work may be noisy in the MRI corridor at times and participants will have to walk past construction barriers to access the SIemens scanner. Please bear this in mind when booking any scans next week. If you already have slots booked for next week, you can keep them as is, or let us know if you would prefer and we will remove them free of charge in this instance. Thanks Becky -- Rebecca Lowndes Research Technician York Neuroimaging Centre

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YNiC seminar 4pm today!
by Rebecca Lowndes 28 Sep '23

28 Sep '23

Hello, Don't forget our new semester of seminars kicks off today at 4pm with two exciting talks! We will be hearing from Dr Lauren Welbourne with a short talk titled "*Measuring binocular combination of luminance and chromatic stimuli using fMRI"* and Dr David Watson with a talk titled *"Mapping the connectivity of the scene network in the human brain"* (see abstract below). We really hope to see everyone at YNiC! The talks will take place *today (Thursday the 28th) at 4pm*. If you are unable to attend the talk in person, you can catch it on zoom using the following link: https://york-ac-uk.zoom.us/j/96762553290?pwd=UEluT1lMd3V5azY5YzNmWkJCV1VTdz… <https://www.google.com/url?q=https://york-ac-uk.zoom.us/j/96762553290?pwd%3…> . We look forward to seeing you then!! Many thanks, Becky *Dr David Watson* *Mapping the connectivity of the scene network in the human brain* The perception of places has been linked to a network of scene-selective regions in the human brain (OPA: occipital place area; PPA: parahippocampal place area; RSC: retrosplenial complex). However, the connectivity of these regions to each other and the rest of the brain remains poorly understood. Here, we measured the functional and structural connectivity of the scene network. Functional connectivity, measured at rest and during movie watching, revealed a bias between posterior and anterior scene regions that have been implicated in perceptual versus mnemonic aspects of scene perception. For example, OPA and posterior PPA showed greater connectivity with visual and dorsal attention networks, which may play a role in the visual representation of scenes. In contrast, anterior PPA and RSC showed preferential connectivity with default-mode and frontoparietal control networks and the hippocampus, which may reflect our memory for places. We also measured the structural connectivity of the scene network using diffusion tractography. This indicated both similarities and differences with the functional connectivity, highlighting distinctions between posterior and anterior but also ventral and dorsal scene regions. These findings provide a map of the connectivity of the scene network, informing possible roles for scene-selective regions in brain function and human behaviour. -- Rebecca Lowndes Research Technician York Neuroimaging Centre

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YNiC Seminar this Thursday!!
by Jennifer Ashton 27 Sep '23

27 Sep '23

Hello, We have a new semester of YNiC Seminars kicking off this week!! We will be hearing from Dr Lauren Welbourne with a short talk titled "*Measuring binocular combination of luminance and chromatic stimuli using fMRI"* and Dr David Watson with a talk titled *"Mapping the connectivity of the scene network in the human brain"* (see abstract below). We really hope to see everyone at YNiC! The talks will take place *tomorrow (Thursday the 28th) at 4pm*. If you are unable to attend the talk in person, you can catch it on zoom using the following link: https://york-ac-uk.zoom.us/j/96762553290?pwd=UEluT1lMd3V5azY5YzNmWkJCV1VTdz… <https://www.google.com/url?q=https://york-ac-uk.zoom.us/j/96762553290?pwd%3…> . We look forward to seeing you then!! Many thanks, Jennifer *Dr David Watson* *Mapping the connectivity of the scene network in the human brain* The perception of places has been linked to a network of scene-selective regions in the human brain (OPA: occipital place area; PPA: parahippocampal place area; RSC: retrosplenial complex). However, the connectivity of these regions to each other and the rest of the brain remains poorly understood. Here, we measured the functional and structural connectivity of the scene network. Functional connectivity, measured at rest and during movie watching, revealed a bias between posterior and anterior scene regions that have been implicated in perceptual versus mnemonic aspects of scene perception. For example, OPA and posterior PPA showed greater connectivity with visual and dorsal attention networks, which may play a role in the visual representation of scenes. In contrast, anterior PPA and RSC showed preferential connectivity with default-mode and frontoparietal control networks and the hippocampus, which may reflect our memory for places. We also measured the structural connectivity of the scene network using diffusion tractography. This indicated both similarities and differences with the functional connectivity, highlighting distinctions between posterior and anterior but also ventral and dorsal scene regions. These findings provide a map of the connectivity of the scene network, informing possible roles for scene-selective regions in brain function and human behaviour. -- Jennifer Ashton, PhD Senior Research Technician York Neuroimaging Centre Working days: Monday, Tuesday and Wednesday

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Door fobs plea
by Jacqueline Mayhew 21 Sep '23

21 Sep '23

Hi all If you have a YNiC door fob that you no longer require, we would appreciate them being returned so that we can reuse them. They can either be returned to YNiC directly or you could return them to Psychology reception and they can forward them to us by internal mail. Best wishes Jackie Jackie Mayhew York Diagnostic Imaging The BioCentre York Science Park Heslington York YO10 5NY

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Stimuli scripts after YNiC systems upgrade
by Richard Aveyard 21 Sep '23

21 Sep '23

Hi All, I am writing to remind everyone that, following our recent operating system upgrade,* it is important to check that your stimuli scripts are running as intended before resuming scanning*. There are testing PCs available in YNiC for this purpose, and in many cases we can help to resolve issues you might have difficulties with. *Psychopy users* Our testing has highlighted that *some psychopy scripts will be susceptible to inaccurate timing* issues with the new psychopy version (2023.2.0). We now strongly recommend that when initialising your visual window you set waitBlanking=False, or that you ensure your script runs at 120 Hz, and the monitor is adjusted accordingly using the Applications>>Settings>>Display menu. In addition, the event.getkeys() function is deprecated, an example update to fix this can be found here: https://wiki.pages.ynic.york.ac.uk/IT/summer_2023_upgrade.html#psychopy Please remember that it is your responsibility to thoroughly test your stimuli scripts and ensure that everything is working as intended. Cheers, Rich -- Dr Richard Aveyard Senior Technical Specialist York NeuroImaging Centre University of York, UK

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This Week at YNiC
by Jennifer Ashton 20 Sep '23

20 Sep '23

Hello, Please find details about Open Plan availability and the next inductions and training sessions. *Open Plan Availability* MSc inductions will be taking place at YNiC this *Friday (22nd of September) 13:00 - 15:00*. Due to the number of students attending, Open Plan will not be available to users during this time. *YNiC User Inductions* If you are aware of any new students/staff that will require access to YNiC and/or an IT account, they must attend a YNiC user induction. Our next induction will be on *Friday the 13th of October, at 13:00*. Please ask them to contact support(a)ynic.york.ac.uk to sign up. *Level 0 operator training*The next L0 training session will be held on *Friday the 20th of October, 13:00-15:00.* Please note that users requesting Level 0 training should be a PhD, RA/Postdoc, or staff, and should already have a project proposal submitted to YNiC. Please email support(a)ynic.york.ac.uk if you have any questions or wish to book on to this session. Please note that sessions are limited to 4 trainees, which will be allocated on a first-come first-served basis. *YNiC Seminar* If you would like to give a talk at our YNiC seminar, please get in touch. There are no specific requirements; presentations can include previously collected data, new data, pilot data and/or study plans and ideas. This is a great way to get feedback in a relaxed and friendly environment, please message support(a)ynic.york.ac.uk. Many thanks, Jennifer -- Jennifer Ashton, PhD Senior Research Technician York Neuroimaging Centre Working days: Monday, Tuesday and Wednesday

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Important information for everyone using YNIC
by Fiona McNab 15 Sep '23

15 Sep '23

Dear All, As you know, most of the imaging data we collect at YNIC is potentially biometric. As well as making sure we have appropriate consent from participants, we have to abide by certain legislative requirements relating to collecting, storing and sharing personal data. We've put in place some procedures to make things easier. What you need to know is summarised below and there's a diagram attached (it contains the same information but with boxes and arrows!) Any questions, please ask. Please also be aware that we have a new page for YNIC forms <https://www.york.ac.uk/psychology/research/york-neuroimaging-centre/forms/>, where you will find new versions of the participant information sheet and study-specific consent form (we're now on version 9 for both). Best wishes, Fiona and Andre *Collecting data at YNIC and keeping it at YNIC* - Before submitting your ethics application, you need to check whether your study needs a separate *Data Protection Impact Assessment (DPIA)*, or whether it is covered by DPIA_183 v2 <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/YNICDPIA183.pdf> (found on the new YNIC forms webpage <https://www.york.ac.uk/psychology/research/york-neuroimaging-centre/forms/>). If it is not covered by DPIA_183 v2, there's a DPIA screening tool here <https://www.york.ac.uk/records-management/dp/dataprivacyimpactassessments/> . - If it is covered by DPIA_183 v2 <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/YNICDPIA183.pdf>, make sure you follow the procedures outlined in that document. - Make sure everyone with access to the data has signed and submitted the *Appropriate Data Usage Declaration* <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/AppropriateDataU…> . *Bringing into YNIC data that were collected elsewhere* - You will need to complete and submit your own DPIA, but we have had one of these approved already, so contact Andre and he will provide you with a template. - If there are any agreements to sign, you will need to get HOD approval before signing. *Transferring data collected at YNIC to external collaborators* - You will need to complete and submit your own DPIA, but we have had one of these approved already, so contact Andre and he will provide you with a template. - You will also need an external collaborator agreement. We have had one approved already. Andre can provide a template and let you know the procedure for obtaining approval from the HOD and the contracts office. - Make sure everyone with access to the data has signed and submitted the *Appropriate Data Usage Declaration* <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/AppropriateDataU…> . *Transferring data collected at YNIC to former staff or students* - You will need to complete and submit your own DPIA, but we have had one of these approved already, so contact Andre and he will provide you with a template. (It's the same template as used for sharing data with external collaborators). - You will also need a data sharing agreement. This is not the same as the one used for external collaborators. We'll have a template soon, which Andre will be able to provide. The procedure for obtaining approval from the HOD and the contracts office will be the same. - Make sure everyone with access to the data has signed and submitted the *Appropriate Data Usage Declaration* <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/AppropriateDataU…> . *Making data collected at YNIC publicly available* (many thanks to Angela for this) - Make sure that this is covered by DPIA_183 v2 <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/YNICDPIA183.pdf> and you abide by the procedures outlined in that document. This includes making sure you use version 9 of the information sheet <https://www.york.ac.uk/psychology/research/york-neuroimaging-centre/forms/>and version 9 of the consent form <https://www.york.ac.uk/psychology/research/york-neuroimaging-centre/forms/>. There is a guidance document here <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/Open_Data_Sharin…> . - If it is not covered by DPIA_183 v2, you will need to complete and submit your own DPIA <https://www.york.ac.uk/records-management/dp/dataprivacyimpactassessments/> .

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This Week at YNiC
by Jennifer Ashton 13 Sep '23

13 Sep '23

Hello, Please find details about Open Plan availability, the next inductions and training sessions and an upcoming workshop. *Open Plan Availability* MSc inductions will be taking place at YNiC on *Friday the 22nd of September, 13:00 - 15:00*. Due to the number of students attending, Open Plan will not be available to users during this time. *YNiC User Inductions* If you are aware of any new students/staff that will require access to YNiC and/or an IT account, they must attend a YNiC user induction. Our next induction will be on *Thursday the 21st of September, at 10:00*. Please ask them to contact support(a)ynic.york.ac.uk to sign up. *Level 0 operator training*The next L0 training session will be held on *Tuesday the 19th of September, 13:00-15:00.* Please note that users requesting Level 0 training should be a PhD, RA/Postdoc, or staff, and should already have a project proposal submitted to YNiC. Please email support(a)ynic.york.ac.uk if you have any questions or wish to book on to this session. Please note that sessions are limited to 4 trainees, which will be allocated on a first-come first-served basis. *YNiC Seminar* If you would like to give a talk at our YNiC seminar, please get in touch. There are no specific requirements; presentations can include previously collected data, new data, pilot data and/or study plans and ideas. This is a great way to get feedback in a relaxed and friendly environment, please message support(a)ynic.york.ac.uk. *Upcoming Workshops* The first *Environmental Impacts of Computing in Health & Life Sciences Research workshop <https://www.eicworkshop.info/> *will be taking place on November 7th in London, and online. This will be a great opportunity to learn about the carbon footprint of high-performance computing, in neuroimaging research and beyond. Find more information on the workshop website <https://www.eicworkshop.info/>, and register for attendance here <https://www.tickettailor.com/events/universityofsussex/986909>. Many thanks, Jennifer -- Jennifer Ashton, PhD Senior Research Technician York Neuroimaging Centre Working days: Monday, Tuesday and Wednesday

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YNiC Cluster: now available
by Joe Lyons 13 Sep '23

13 Sep '23

Good Morning The cluster is now back up and online. The upgrade has now been completed. There are a few small changes to some software packages so please check the upgrade notes wiki page if you have any queries. https://wiki.pages.ynic.york.ac.uk/IT/summer_2023_upgrade.html Any other issues not covered in the wiki page, please email support(a)ynic.york.ac.uk. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

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Update: Remote Desktops are now up
by Joe Lyons 11 Sep '23

11 Sep '23

The remote desktops are now stable. We're still waiting on a few jobs running on the cluster before it's available for use. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

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Update: YNiC partially open after systems maintenance
by Joe Lyons 11 Sep '23

11 Sep '23

Good Morning. We're still having some issues from the upgrade last week. The desktops in Openplan are up and running. The cluster is currently down as we're debugging an issue with the new OS. The remote desktops are also down as we're seeing problems with some of the nodes. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

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Reminder: YNiC Closed for systems maintenance
by Joe Lyons 05 Sep '23

05 Sep '23

YNiC is closed for the week while we perform some essential systems maintenance. All remote desktops and cluster services will be down. We'll update you once services are back up and running. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

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Test your stimuli on new PC in YNiC
by Rebecca Lowndes 30 Aug '23

30 Aug '23

Hi all Just reminding you all that there is a new stim PC with new software available in OpenPlan to test scripts/stimuli. All the desktops will move over to this software when we are closed next week Thanks Becky -- Rebecca Lowndes Research Technician York Neuroimaging Centre

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YNiC Desktop Upgrades
by Joe Lyons 23 Aug '23

23 Aug '23

Hello As mentioned in the "This Week at YNiC" email, we'll be doing our annual software upgrades on the YNiC desktops w/c 4th September. The centre will be closed while we undertake the upgrades. A wiki page has been setup with details of the changes. https://wiki.pages.ynic.york.ac.uk/IT/summer_2023_upgrade.html A desktop with the new software is available in OpenPlan to test scripts/stimuli. Please email support if you have any questions. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

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IT closure this weekend
by Rebecca Lowndes 18 Aug '23

18 Aug '23

Hi all, Due to emergency power testing at the Science Park, the remote desktop may not be accessible or reliable on Saturday and Sunday. While the remote desktop machines may be intermittently available they may shut down without notice, so we strongly advise you do not attempt to work on the remote desktop this weekend. Open Plan will also be unavailable. Thanks Becky -- Rebecca Lowndes Research Technician York Neuroimaging Centre

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This Week at YNiC
by Richard Aveyard 17 Aug '23

17 Aug '23

Hello, Please find details about a change to the YNiC phone system, an upcoming summer closure, and the next scheduled induction and training sessions below. *YNiC phone number change* Due to an update to phone systems throughout the science park, unfortunately YNiC can no longer be contacted using our long-standing number. *You can now reach us on 01904 325940. *Please update our contact details anywhere you hold them, and in particular,* please update any material provided to participants.* As part of the upgrade to the science park phone system, we have new phone hardware. As these phones serve an important part of our safety procedures,* we encourage all operators to familiarise themselves with the new phones.* *YNiC summer closure* *YNiC will be closed to users for the week commencing Monday the 4th of September. *This is necessary for us to undertake vital updates to our computing systems. More details will be provided by email shortly. We apologise for any inconvenience this may cause. Please let us know if there are any mitigations we may be able to provide. *YNiC User Inductions* If you are aware of any new students/staff that will require access to YNiC and/or an IT account, they must attend a YNiC user induction. Our next induction will be on *Thursday the 14th of September, at 13:00*. Please ask them to contact support(a)ynic.york.ac.uk to sign up. *Level 0 operator training* *The next L0 training session will be held on Monday the 11th of September, 13:00-15:00. *Please note that users requesting Level 0 training should be a PhD, RA/Postdoc, or staff, and should already have a project proposal submitted to YNiC. Please email support(a)ynic.york.ac.uk if you have any questions or wish to book on to this session. Please note that sessions are limited to 4 trainees, which will be allocated on a first-come first-served basis. Training must be booked at least a week before the session date, in order to reserve the scanner booking. *YNiC Seminar* If you would like to give a talk next term, please get in touch, there are no specific requirements; presentations can include previously collected data, new data, pilot data and/or study plans and ideas. This is a great way to get feedback in a relaxed and friendly environment. Please message support(a)ynic.york.ac.uk. Cheers, Rich -- Dr Richard Aveyard Senior Technical Specialist York NeuroImaging Centre University of York, UK

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Useful dataset
by Aidan Horner 16 Aug '23

16 Aug '23

Hi all, A big new data set has just been published that could be useful for many of us, particularly for those interested in hippocampal subfields (who isn't?!): https://www.nature.com/articles/s41597-023-02449-9 Best wishes, Aidan -- *I work 0.8FTE and my working days are Monday-Wednesday and Friday* ======================================================= Dr Aidan J Horner Associate Professor (Senior Lecturer) in Psychology Department of Psychology University of York York YO10 5DD Mastodon: @aidanhorner@fediscience.org Twitter: @aidanhorner Lab website: http://www.aidanhorner.org/ =======================================================

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Fwd: Green Computing Paper
by Beth Jefferies 08 Aug '23

08 Aug '23

Here's an interesting paper from Nick about how we can reduce the carbon footprint of fMRI analysis. https://osf.io/7q5mh/ Let me know what you think :) Cheers Beth ---------- Forwarded message --------- From: Nick Souter <nes522(a)york.ac.uk> Date: Tue, 8 Aug 2023 at 17:00 Subject: Green Computing Paper To: FLEXSEM <flexsem-group(a)york.ac.uk> Hi all, Hope you're all doing well :) I've just released the preprint for my first post-doc paper <https://osf.io/7q5mh/>! It's a short perspective piece focusing on 10 steps neuroimagers can take to reduce the carbon footprint of their research computing (preprocessing and analysis). Thought I would share here in case there is anything actionable you could take away from it. In particular, there is stuff about long term data storage and data cleaning which might be relevant to issues with freeing up space on the FLEXSEM drive at YNiC. As part of this, we've developed a tool called fMRIPrepCleanup <https://github.com/NickESouter/fMRIPrepCleanup> specifically designed to comb over fMRIPrep output and delete all the junk files (although take caution using it, as covered in the readme!!). Thanks! Nick Nick Souter, PhD Department of Psychology University of York nes522(a)york.ac.uk -- You received this message because you are subscribed to the Google Groups "FLEXSEM" group. To unsubscribe from this group and stop receiving emails from it, send an email to flexsem-group+unsubscribe(a)york.ac.uk. To view this discussion on the web, visit https://groups.google.com/a/york.ac.uk/d/msgid/flexsem-group/CACz3qpZwiMMdG… <https://groups.google.com/a/york.ac.uk/d/msgid/flexsem-group/CACz3qpZwiMMdG…> . -- Beth Jefferies Department of Psychology, University of York, UK +44 01904 324368

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