- ynic-users

This Week at YNiC
by Lauren Welbourne 11 Nov '19

11 Nov '19

Hi everyone Thank you to all those who came along to the Science Social last week, we had a great turn-out, learnt about DTI scans, and had enough pizza for everyone! This week we have a guest speaker at YNiC - Dr Melanie Burke from the University of Leeds will be presenting at our Thursday seminar, at 4pm in YNiC open plan. Refreshments will be provided after the talk. Please find the title and abstract below: Dr Melanie Burke - Thursday 14th November, 4pm, YNiC open plan *Title:* “Inducing neuroplasticity in the prefrontal cortex: a preliminary investigation into the effects on the brain and cognition.” *Abstract:* Theta burst stimulation (TBS) is a form of repetitive transcranial magnetic stimulation (rTMS) that can be used to increase (intermittent TBS) or reduce (continuous TBS) cortical excitability. The current study used iTBS in 18 adults, to investigate the causal role of the dorsolateral prefrontal cortex (DLPFC) during the performance of four cognitive functions: attention, inhibition, sequence learning and working memory. Participants performed the cognitive tasks both before and after iTBS stimulation and functional near infra-red spectroscopy (fNIRS) was monitored throughout. Preliminary findings of brain activity before, during and after TBS, alongside eye movements responses to the cognitive tasks will be presented. Additional notices: *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 date will be Wednesday 13th November at 2pm. Please ask them to contact support(a)ynic.york.ac.uk to sign up. *GE Projector* We have updated the projector in the GE scanner. If you are using this scanner please refer to the instructions on the wall above the stimulus PC for information on turning the projector on/off. The instructions for the projector in the Siemens scanner remain the same (for reference, see the instructions sheet above the stimulus PC, or the information on the website https://www.ynic.york.ac.uk/docs/MRIFrontPage). Hope you have a great week! Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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Fwd: [ML-news] Modeling shift from efficient to inefficient divided attention using EEG/fMRI/MEG
by Antony Morland 08 Nov '19

08 Nov '19

Job opportunity ---------- Forwarded message --------- From: Dimitar Kazakov <dimitar.kazakov(a)york.ac.uk> Date: Fri, 8 Nov 2019, 16:17 Subject: Fwd: [ML-news] Modeling shift from efficient to inefficient divided attention using EEG/fMRI/MEG To: <arm501(a)york.ac.uk> FYI Dimitar www.cs.york.ac.uk/~kazakov Disclaimer: http://www.york.ac.uk/docs/disclaimer/email.htm ---------- Forwarded message --------- From: Nicolas Drougard <drougardn(a)gmail.com> Date: Fri, 8 Nov 2019 at 15:01 Subject: [ML-news] Modeling shift from efficient to inefficient divided attention using EEG/fMRI/MEG To: Machine Learning News <ml-news(a)googlegroups.com> *Modeling shift from efficient to inefficient divided attention using EEG/fMRI/MEG * *Advisor(s): * Frederic Dehais, https://personnel.isae-supaero.fr/frederic-dehais/ Caroline Chanel, https://personnel.isae-supaero.fr/caroline-chanel/ Daniel Callan, https://cinet.jp/english/people/2014898/ *Net salary:* 2700e per month with some teaching *Duration:* 2 years *DESCRIPTION * Optimal distribution of attention is a key issue in our everyday-life multitasking activities. It relies on a tradeoff between exploration and exploitation attentional policies to select and maintain attentional focus on the relevant streams of information while remaining alert to unexpected changes. Several studies have identified some neural correlates supporting such attentional dynamics. For instance, top-down and bottom-up types of attention are respectively delineated by the dorsal and ventral neural networks that are in close interaction with the anterior cingulate cortex for resource allocations. Efficient divided attention results in an enhancement of task relevant networks activity via cross frequency coupling in the theta and gamma band and enhancement of secondary task networks activity at different phase to that of primary task networks. However, when task demand exceeds mental capacity, the homeostasis between the ventral and dorsal pathways is disrupted, leading to the suppression of non-primary task relevant network (via increased alpha oscillations) and decreased frequency coupling between theta and gamma in primary task networks. Although this shielding mechanism can prevent from mental overload and distractions, missing critical information can have devastating consequences in real-life scenarios such as driving or operating an aircraft (eg. auditory alarms). The candidate is expected to design and conduct experiments to investigate the shift from efficient to non-efficient divided attention between the visual and the auditory modality. These experiments will be conducted 1) in the lab using fMRI and high-density 2) under highly ecological conditions with portable EEG. The candidate is expected to perform state-of-the-art analyses including effective connectivity and to apply inverse reinforcement learning (IRL) technics to 1) estimate the efficient (optimal) and non-efficient (sub-optimal) policies with respect to best expected distribution of attention. 2) to predict long-term attentional efficiency. The ideal candidate will have a strong background in Neurosciences, brain imaging (EEG or/and fMRI/MEG), signal processing, artificial intelligence for automated learning and planning. She/he will have to work in strong collaboration with the three other researchers (2 PhD students, 1 post doc) funded by the ANITI program. This research will be conducted within the stimulating environment of Neuroergonomics lab at ISAE-SUPAERO (25 researchers), the Artificial and Natural Intelligence Toulouse Institute. The candidate will have the opportunity to have a long stay in Cinet (Osaka/Japan) at Daniel Callan’s research department to conduct the fMRI or MEG experiment. *References* • Durantin, G., Dehais, F., Gonthier, N., Terzibas, C., & Callan, D. E. (2017). Neural signature of inattentional deafness. Human brain mapping, 38(11), 5440-5455. • Dehais, F., Rida, I., Roy, R. N., Iversen, J., Mullen, T., & Callan, D. A pBCI to Predict Attentional Error Before it Happens in Real Flight Conditions. • Tombu, M. N., Asplund, C. L., Dux, P. E., Godwin, D., Martin, J. W., & Marois, R. (2011). A unified attentional bottleneck in the human brain. Proceedings of the National Academy of Sciences, 108(33), 13426-13431. • Doesburg, S. M., Roggeveen, A. B., Kitajo, K., & Ward, L. M. (2007). Large-scale gamma-band phase synchronization and selective attention. Cerebral cortex, 18(2), 386-396. • Arora, Saurabh and Doshi, Prashant (2018). A survey of inverse reinforcement learning: Challenges, methods and progress. arXiv preprint arXiv:1806.06877 *APPLICATION PROCEDURE* Formal applications should include detailed cv, a motivation letter and transcripts of bachelors' degree. Samples of published research by the candidate and reference letters will be a plus. Applications should be sent by email to first_name.name(a)isae.fr More information about ANITI: https://aniti.univ-toulouse.fr/ -- You received this message because you are subscribed to the Google Groups "Machine Learning News" group. To unsubscribe from this group and stop receiving emails from it, send an email to ml-news+unsubscribe(a)googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/ml-news/5799d6d7-59b4-449d-80eb-de0d553d1… <https://groups.google.com/d/msgid/ml-news/5799d6d7-59b4-449d-80eb-de0d553d1…> .

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YNiC Science Social today 4pm
by Lauren Welbourne 07 Nov '19

07 Nov '19

Hi everyone This is a reminder that our first Science Social will be happening today at 4pm in YNiC Open Plan. Come and play with some diffusion data, and we'll provide pizza! Hope to see you later, Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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This Week at YNiC
by Lauren Welbourne 04 Nov '19

04 Nov '19

Hi everyone Here's what's going on this week: *YNiC Monthly Science Social:* We're kicking off the first Science Social session with a talk by Andre on DTI scanning; this should be a really interesting introduction to this type of scan, plus we'll be providing pizza, so we hope to see many of you there! The session will be held in YNiC open plan this *Thursday 7th Nov at 4pm*. For a list of the upcoming Thursday sessions, please visit https://www.ynic.york.ac.uk/events/thursday-sessions. *Level 0 operator training:* The upcoming Level 0 training session this week is now fully booked. Our next scheduled training session will take place on *Wednesday 11th December at 2pm-4pm*. 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, and include which scanner you wish to be trained on. *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.* *It is recommended that all Level 0 operators attend an 'Emergency First Aid at Work' one-day training course.* This is currently a requirement for Level 1 operators, and will also be required for Level 0 operators soon - we will enforce this requirement from March 2020, to give current Level 0 users time to arrange the training course. Courses should be organised by the project PI with a relevant training provider (e.g. St Johns Ambulance, Red Cross); these providers can also run group training sessions (8 or more people) on-site, so labs may wish to coordinate their operators to all attend training on the same day, at a location of your choice. *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 date will be Wednesday 13th November at 2pm. Please ask them to contact support(a)ynic.york.ac.uk to sign up. *Christmas Closure:* We'd like to give you advance warning that YNiC will be closed to users from the week commencing 16th December, and will re-open in the New Year, on the 3rd of January. Hope you have a great week. Cheers Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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YNiC Halloween 'Scary Slice' Game
by Lauren Welbourne 31 Oct '19

31 Oct '19

Hi everyone Happy Halloween! Today is your last chance to have a go at our 'Scary Slice' game. Come down to YNiC and try match the staff member to the scary MRI slice. The person with the most correct answers will win a bottle of wine! Deadline is 4pm, and the winner will be announced before the end of the day. Cheers Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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This Week at YNiC
by Lauren Welbourne 28 Oct '19

28 Oct '19

Hi everyone We have quite a few notices for you today, including a chance to *win a bottle of wine* if you read until the end! *Level 0 training:* We have reviewed the Level 0 training process, and now, in addition to the training session, Level 0 trainees will also be observed for a minimum of 3 scan sessions, until we are satisfied that they meet operator requirements (these scans must be booked in operator-covered slots). We therefore recommend that you only book onto a training session when you have ethical approval for a project, and intend on scanning within the next couple of months. Our next scheduled *Level 0 training session *is at *2pm on 6th November*, please email support(a)ynic.york.ac.uk to book on to this session, and include which scanner you wish to be trained on. Training will take up to two hours. *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.* *First Aid Training for Level 0 operators:* It is recommended that all Level 0 operators attend an 'Emergency First Aid at Work' one-day training course. This is currently a requirement for Level 1 operators, and will also be required for Level 0 operators soon - we will enforce this requirement from March 2020, to give current Level 0 users time to arrange the training course. Courses should be organised by the project PI with a relevant training provider (e.g. St Johns Ambulance, Red Cross); these providers can also run group training sessions (8 or more people) on-site, so labs may wish to coordinate their operators to all attend training on the same day, at a location of your choice. *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 date will be Wednesday 30th October at 2pm. Please ask them to contact support(a)ynic.york.ac.uk to sign up. *Monthly Science Social Seminars:* On the first Thursday of every month YNiC will be hosting a 'Science Social' at 4pm in YNiC open plan. This will include a talk or discussion on topics that will include imaging methods, software, and analysis techniques. We also encourage users to volunteer to present if they would like to share something that they think may be of interest to other users. Pizza and drinks will be provided! *Halloween 'Scary Slice' Game:* This week at YNiC you will have a chance to win a bottle of wine by correctly matching the staff member to the MRI slice (a coronal slice of the face that is suitably scary and Halloween-y). Images will be up on the white board in open plan until the end of the day on Thursday. The person that correctly matches the most images will be awarded the bottle of wine - good luck! Hope you have a great week! Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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Reminder: YNiC Project Presentation 4pm today Inbox
by Richard Aveyard 24 Oct '19

24 Oct '19

Hi all This is a reminder that we have a project presentation from Martin Scott *Today at 4pm* in YNiC open plan, titled: "Effects of 670nm photobiomodulation on mitochondrial function in the human brain". Talks are followed by refreshments. We hope to see you there. Cheers, Rich -- Richard Aveyard, Senior Research Technician York NeuroImaging Centre University of York, UK

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Siemens Update
by Lauren Welbourne 23 Oct '19

23 Oct '19

Hi everyone I'm pleased to announce that the Siemens mechanical fault has now been fixed - the drive that moves the table into the scanner has been replaced, and everything is running smoothly now. Scanning will continue as normal from tomorrow. Apologies for any inconvenience caused. Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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This Week at YNiC
by Lauren Welbourne 21 Oct '19

21 Oct '19

Hi everyone This week we have a few notices to communicate with you. *Siemens Bed Repair:* We are currently experiencing a mechanical fault with the Siemens table. Engineers are due to attend Tuesday AM to resolve the issue. Users affected by this fault today and tomorrow have already been contacted, and we will keep YNiC-users updated via this mailing list. *Project Presentation - Thursday 4pm:* This week we have a project presentation from Martin Scott on *Thursday at 4pm* in YNiC open plan, titled: "Effects of 670nm photobiomodulation on mitochondrial function in the human brain". Talks are followed by refreshments. *Safety Screening Form:* Further to Tony's announcement last week, we would like to remind all operators (and users who may be involved in screening participants) that the following text now appears on YNiC safety forms: "It is essential that all questions on this sheet are answered truthfully. This information is essential in order to ensure your safety and will be kept completely confidential. If you do not want to answer any question(s) on this form you are free to withdraw from this scanning session without any prejudice." Please read this text to potential participants *before* you ask the questions on the form, some of which can be personal in nature and which some individuals may not wish to answer. Copies of the safety forms can be found on the YNiC website (https://www.ynic.york.ac.uk/forms), please familiarise yourself with all text on these forms before your next scanning session. *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 date will be Wednesday 30th October at 2pm. Please ask them to contact support(a)ynic.york.ac.uk to sign up. Hope you have a great week! Cheers Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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Reminder: YNiC Project Presentation 4pm today
by Lauren Welbourne 17 Oct '19

17 Oct '19

Hi all This is a reminder that we have a project presentation from Frida Torkelsen *Today at 4pm* in YNiC open plan, titled: "Diffusion Weighted functional brain imaging: investigating cellular swelling as a potential direct measure of neuronal activity". Talks are followed by refreshments. We hope to see you there. Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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This Week at YNiC
by Lauren Welbourne 14 Oct '19

14 Oct '19

Good morning everyone This week we have a project presentation from Frida Torkelsen on *Thursday at 4pm* in YNiC open plan, titled: "Diffusion Weighted functional brain imaging: investigating cellular swelling as a potential direct measure of neuronal activity". Talks are followed by refreshments. 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 date will be Wednesday 30th October at 2pm. Please ask them to contact support(a)ynic.york.ac.uk to sign up. Hope you have a great week! Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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Screening Form
by Antony Morland 14 Oct '19

14 Oct '19

Hello All, I wanted to highlight the following text that now appears on YNiC MRI safety screening forms: "It is essential that all questions on this sheet are answered truthfully. This information is essential in order to ensure your safety and will be kept completely confidential. If you do not want to answer any question(s) on this form you are free to withdraw from this scanning session without any prejudice." Please read this text to potential participants before you ask the questions on the form, some of which can be personal in nature and which some individuals may not wish to answer. Thank you Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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YNiC Seminar today 4pm
by Lauren Welbourne 10 Oct '19

10 Oct '19

Hi everyone This is a reminder that Mark Hymers will be running a seminar this afternoon at 4pm in the YNiC open plan, on how to use the YNiC cluster for processing data. It will be worthwhile for new or existing YNiC users that haven't previously used the cluster, and may need to make use of it for upcoming data analysis. We hope to see you this afternoon. Cheers Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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This Week at YNiC
by Lauren Welbourne 07 Oct '19

07 Oct '19

Good afternoon everyone We have a few notices for you today: *Thursday Seminar - Using the Cluster:* Mark Hymers will be running a session this Thursday on how to use the cluster at YNiC. We encourage users to attend if they are unfamiliar with how to send jobs to the cluster for processing. The session will be held at *4pm on Thursday 10th October in YNiC open plan*. *Remote Desktop:* We have made some configuration changes to the remote desktop, so if you are experiencing any issues please follow these steps on the wiki: https://www.ynic.york.ac.uk/docs/ITPages/RemoteDesktop#FAQ_and_errors Please note that you must be connected to the University of York VPN, and should also have followed the latest remote desktop server setup guidelines (https://www.ynic.york.ac.uk/docs/ITPages/RemoteDesktop). *YNiC User Inductions:* Hopefully everyone that needed an induction was able to attend the two large sessions we put on last week, but if there are any other students/staff that will require an IT account for YNiC, our next induction date will be Wednesday 30th October at 2pm. Please ask them to contact support(a)ynic.york.ac.uk to sign up. Hope you all have a great week. Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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YNIC Science Comittee
by Jonny Smallwood 07 Oct '19

07 Oct '19

Hello everyone, Next week on Monday is the next meeting of the YNIC Science committee. Please let me know if there is any issues you would like me to raise with the other members. Thanks Jonny -- Jonathan Smallwood, Professor in Psychology / Cognitive Neuroscience Room E008, Department of Psychology, University of York, England. YO10 4PH. Telephone: 01904 324651

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Open plan teaching times
by Mark Hymers 30 Sep '19

30 Sep '19

Dear all, Over this term, Open plan will be used for teaching on a number of occasions. We will be asking everyone who is not taking part in the class to leave the open plan area at these times. The times for this term are: Week 1: Thursday 3rd October: 0900-1300 Friday 4th October: 0900-1300 Week 2: Tuesday 8th October: 1200-1600 Week 4: Tuesday 22nd October: 1200-1600 Week 7: Tuesday 12th November: 1200-1600 Week 9: Tuesday 26th November: 1200-1600 These times can be found on the University timetable http://www.york.ac.uk/viewtimetables by choosing YNiC as the room and clicking "View Room" Thanks, Mark

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This Week at YNiC
by Richard Aveyard 23 Sep '19

23 Sep '19

Hi Everyone, As of Monday 23rd of September, *YNiC has reopened.* Following the closure *we strongly recommend that users visit YNiC to test their stimulus presentation scripts before their next scanning session.* YNiC staff will provide support in modifying scripts, but this *must* be done prior to scanning. During the closure, IT updates described in the email from the 30th of August were implemented. However, *FSL 6 will not be available* due to compatibility issues. The upgraded YNiC MEG suite is now in testing. *We are inviting informal discussions of prospective MEG studies.* During the closure the facility was re-decorated and *we welcome contributions of A0 posters for display*. The next *user inductions will take place on Thursday 3rd October* at 9am and 11am. New students will be contacted about these sessions, and any additional staff or existing PhD students that require an induction should contact us to book onto one of these sessions. There will be project *proposal presentations on Thursday the 26th of September at 15:30* in open plan: - "Pattern extraction and memory-guided decision-making" by Jamie Cockcroft - "Using intersubject correlations during movie-watching to assess the neural basis of mind wandering" by Adam Turnbull. There will be a talk by* guest speaker, Dr Ed Silson on Thursday the 26th of September at 16:00* in open plan, on the subject of: - "Scene perception, memory and the functional organisation of human medial parietal cortex." Cheers, Rich -- Richard Aveyard, Senior Research Technician York NeuroImaging Centre University of York, UK

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Posters
by Antony Morland 18 Sep '19

18 Sep '19

Hello All, We have been revamping the poster displays at YNiC during the summer closure. We are a bit short of posters showcasing areas other than vision, so would be delighted to receive any A0 (landscape or portrait) posters that we can display. A broad cross-section of topics that reflects research opportunities for the incoming MSc cohorts would be greatly appreciated. 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 Closure - IT updates
by Lauren Welbourne 30 Aug '19

30 Aug '19

Hi everyone During the YNiC closure the following updates and changes will be made to the available software: *FSLView* - This will be the last YNiC desktop build which contains FSLView. It is deprecated and we are already pulling various tricks to make it work. We had initially scheduled its removal for Summer 2018 but we have managed to keep it going. We now intend to remove it in Summer 2020. This really is the end of fslview, so please migrate to FSLeyes. *FSL* - FSL 5 has been updated from 5.0.9 to 5.0.11 with all new tools also added (bianca, mist, surface-based tools, film_cifti). - FSL 6 is now installed (version 6.0.1) but version 5 will remain the default. - We will review the default FSL version in Summer 2020 and decide whether to switch the default to FSL-6 at this time. *Freesurfer*. - This will be the last YNiC desktop build which contains Freesurfer 5.3. All projects should now be using 6.0. Please let us know if you are still using 5.3. *AFNI* - AFNI is being reintroduced after a several year absence. We will be using the latest stable release (20190220), but will configure AFNI in such a way that multiple versions can be supported at once. Details of how to use AFNI at YNiC will be added to the documentation pages. *MATLAB* - The available versions of Matlab will be 8.5 and 9.6 - Matlab 9.0, 9.2 and 9.4 are no longer available. - Note that we will not retain 8.5 beyond Summer 2021, so if you are still using it, you need to migrate your tools as soon as possible. Please let us know if you are still using 8.5 for some reason. *SPM* - SPM 12 has been updated to the latest patch release. - SPMs 5 and 8 have been removed from the system. These versions are over a decade old, are not supported upstream, and building them is becoming harder as compilers become more pedantic about code quality. - We have retained SPM 2 as it is still buildable and has historically been used by a couple of other packages (for co-registration etc). SPM 2 will be removed in Summer 2021. If you still have a real need for SPM 2, 5 or 8, please get in touch as soon as possible. - All new projects should be using SPM 12. *Connectome Workbench* - This has been upgraded from 1.2.3 to 1.3.2 *Python 2 / 3* - This will be last build of the YNIC desktop where Python 2 is fully supported as it is now deprecated upstream. - All new code should be written using Python 3. We plan to run a workshop in the first weeks of term to assist people in migrating code from Python 2 to 3; this will be especially relevant for those who use Psychopy. - Python 3.7.3 is now installed, upgraded from 3.5.3. - We are aware of the following modules used under Python 2 which are not currently available for python 3: *python-mvpa2:* Upstream are working on porting this; we will make it available as soon as possible. *python-pymc: *We are currently working on python3 compatible packages for this Major module updates: - numpy 1.16.2 (from 1.12.1) - scipy 1.1.0 (from 0.18.1) - matplotlib 3.0.2 (from 2.0.0) - h5py 2.8 (from 2.7) - mdp is no longer available: you should use sklearn instead - mpi4py 3.0.2 (from 2.0.0); note that this is a newer version than in Debian Buster by default - nibabel 2.3.2 (from 2.1.0) - nifti -> this is a python 2 module and is deprecated; use nibabel instead - pil 5.4.1 (from 4.0) - pyglet 1.4.1 (from 1.1.4); note that this is a newer version than in Debian Buster by default - scikits.audiolab is replaced by soundfile 0.10.1 - sounddevice 0.3.13 is the supported sound presentation module - vtk: version 7 for Python 3; version 6 for Python 2 - wxpython 4.0 (from 3.0); note that this is a major version change - Psychopy has been updated to 3.1.5 (from 1.90.0). This involves changing from Python 2 to Python 3. We recommend that people attend the Python 2 to 3 migration workshop which will provide a good opportunity for people to get assistance in updating scripts (where necessary). *Mathematica* - Version 10 is no longer available; you should use Mathematica 11. *Shutter (the screenshot app)* - This application is no longer available. We recommend Flameshot as the replacement. YNiC will be closed from 5pm today (Friday 30th Aug), and will re-open on Monday 23rd September. Please note that there will be no access to YNiC open plan, remote desktops, or support, during the closure period. I hope you all have a pleasant YNiC break, and we'll see you again in a few weeks! Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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This Week at YNiC
by Lauren Welbourne 27 Aug '19

27 Aug '19

Hi everybody I hope you all enjoyed the record-breaking temperatures this weekend! This is the final week that YNiC is open before the closure; we will send out a separate email to let you know exactly what IT upgrades will be happening during the closure period. YNiC will be closed from Monday 2nd until Friday 20th September, there will be no remote access or support during this period. Please be aware that on Wednesday 28th August, PAT testing will be carried out in open plan. Each PC will need to be turned off for approximately 10 minutes for the testing to be done - if you are in open plan during the time the testing occurs you will be given advanced warning of when we'll need to turn off your PC. We apologise for any inconvenience this will cause. Hope you all have a great week. Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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This Week at YNiC
by Lauren Welbourne 20 Aug '19

20 Aug '19

Hi everyone There's nothing new to report this week, so here's a reminder of the upcoming closures again: - Monday 26th August (Bank Holiday) - Monday 2nd September - Friday 20th September (YNiC Closure) Don't forget that during the YNiC Closure in September we will be performing essential IT upgrades and maintenance, and therefore there will be no access to the centre (including remotely), and no support will be provided over this period. Hope you have a great week! Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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This Week at YNiC
by Lauren Welbourne 12 Aug '19

12 Aug '19

Hi everyone Our final YNiC user induction for the summer will take place this *Thursday 15th August at 2pm*. If you are aware of any students/staff that will require an IT account for YNiC, they must complete a User Induction first. Please ask them to contact support(a)ynic.york.ac.uk to sign up for this next induction date. Any new staff or students that start after this final summer induction can join the group induction sessions for new MSc and PhD students. These will take place on Thursday 3rd October at 9am and 11am. New students will be contacted about these sessions, and any additional staff or existing PhD students that require an induction should contact us to book onto one of these sessions. Finally, please note the upcoming closures: - Monday 26th August (Bank Holiday) - Monday 2nd September - Friday 20th September (YNiC Closure) Hope you have a great week, Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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This Week at YNiC
by Lauren Welbourne 05 Aug '19

05 Aug '19

Hi everyone *YNiC Closures* I wanted to remind you all of the upcoming bank holiday and the YNiC closure dates. The Centre will be closed on the following: - Monday 26th August (Bank Holiday) - Monday 2nd September - Friday 20th September (YNiC Closure) During the YNiC closure we will perform essential IT upgrades and maintenance. There will be no access to the centre (including remotely), and no support will be provided over this period. *User Inductions* Our final YNiC user induction for the summer will take place on *Thursday 15th August at 2pm*. If you are aware of any students/staff that will require an IT account for YNiC, they must complete a User Induction first. Please ask them to contact support(a)ynic.york.ac.uk to sign up for the next induction date. Any new staff or students that start after the final summer induction can join the group induction sessions for new MSc and PhD students. These will take place on Thursday 3rd October at 9am and 11am. New students will be contacted about these sessions, and any additional staff or existing PhD students that require an induction should contact us to book onto one of these sessions. Hope you have a great week! Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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Request for example Psychopy stimulus presentation scripts
by Mark Hymers 29 Jul '19

29 Jul '19

Hi all, We are currently preparing a large software update for YNiC. This update will be applied during YNiC's closure in September. To assist us in our testing, we would like to request that labs provide us with example stimulus code which you have used at YNiC. This will help us build up a repository of stimulus code for regression test purposes. Please email me directly (mark.hymers(a)ynic.york.ac.uk). The easiest way to do this is for you to send a path to your code on the YNiC system along with a note that you are happy for us to copy the code and us it in our tests. More details about the upgrade work will follow over the next few weeks. Thanks, Mark -- Mark Hymers, Lecturer in Neuroimaging Methods York NeuroImaging Centre and Department of Psychology University of York, UK Please note that my email address is: mark.hymers(a)ynic.york.ac.uk Responses to messages sent to other addresses may be delayed

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This Week at YNiC
by Lauren Welbourne 29 Jul '19

29 Jul '19

Hi all The only update I have for you this week is to remind you that our next YNiC user induction is provisionally planned for this *Thursday 1st August *(time TBC). If you are aware of any students/staff that will require an IT account for YNiC, they must complete a User Induction first. Please ask them to contact support(a)ynic.york.ac.uk to sign up for the next induction date. Hope you have a great week! Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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