ynic-users

ynic-users@ynic.york.ac.uk

2 participants
2841 discussions

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/ =====================================================================

1 0

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

1 0

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

1 0

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

1 0

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

1 0

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

1 0

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

1 0

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/> .

1 0

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

1 0

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

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

ynic-users