Hello Everyone,
Andre Gouws will be telling us how to script FSL analyses today, allowing
for more efficient data processing. We willkick off a little later than
4pm to allow colleagues, who have commitments in Psychology, to get over
to YNiC.
Cheers
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hello Everyone,
I am having trouble finding someone to act as a level 0 operator at 9am on
Friday (I know it is the morning after Richard's viva celebrations so the
Morland lab group won't be feeling too fresh).
If anyone is available to help out then please let me know. Otherwise I
will have to cancel this scan with one of my ASD participants.
Thanks,
Ellie
Dear All,
Sorry to report that MEG is proving to be unreliable at present. We hope
to be able to re-establish service as soon as possible. In the meantime,
please don't book the MEG scanner.
Thanks
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hello everyone,
The next meeting for the YNIC Science committee is on the 23rd of January.
Please send me an email describing any issues you would like me to raise,
ideally by the end of tomorrow.
Thanks,
Jonny
--
Jonathan Smallwood, Reader in Psychology / Cognitive Neuroscience
Room C023, Department of Psychology, University of York, England. YO10 4PH.
Telephone: 01904 324651
Hello all,
Kirstie Wailes-Newson will be giving a project presentation at 4pm at YNiC
today.
Best wishes
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hi all,
As usual, YNiC open plan will be used for teaching over the Spring term.
During this times, the open plan area will be unavailable to anybody
not involved in teaching.
The times at which teaching will occur are:
Week 2:
* Monday 16th January 1200-1600
* Tuesday 17th January 1100-1500
Week 3:
* Friday 27th January 1200-1600
Week 4:
* Monday 30th January 1200-1600
* Friday 3rd February 1200-1600
Week 5:
* Tuesday 7th February 1200-1600
Week 7:
* Monday 20th February 1200-1600
* Tuesday 21st February 1200-1600
Week 8:
* Friday 3rd March 1200-1600
Week 9:
* Monday 6th March 1200-1600
* Friday 10th March 1200-1600
Week 10:
* Friday 17th March 1200-1600
If you have a University of York account, the teaching timetable can
also be accessed by going to https://www.york.ac.uk/viewtimetables ,
choosing YNiC as a room and choosing View Room.
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
Hello YNIC Users
As part of the new schedule for YNIC we thought it might be helpful to
provide sessions in which users of the centre provide information on (i)
the methods that they use and (ii) the research questions that these are
helpful in addressing. The next available slot will be in mid March. Please
get in contact if you are interested in giving one of these talks.
Thanks
--
Jonathan Smallwood, Reader in Psychology / Cognitive Neuroscience
Room C023, Department of Psychology, University of York, England. YO10 4PH.
Telephone: 01904 324651
Hello Everyone,
This Thursday (12th Jan) I'll be giving a talk about 'People and Procedures
at YNiC'. It's targeted at introducing the YNiC staff, new and old, and
how investigators can use the centre. Refreshments will be provided. The
talk will be held at YNiC.
I'll also be sending out a programme for this term's seminars soon. We are
hoping to follow a scheme whereby we alternate between talks that cover
what is provided at YNiC and talks that share research being undertaken on
labs that use YNiC. The aim is to have short talks (30mins of so) to allow
for project presentations to be made at the same sessions as the need
arises.
Cheers
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hello All,
Happy New Year!
2017 is kicking off with a seminar from Matthew Brett, who will be talking
about neuroimaging methods at YNiC tomorrow at 4pm.
Best wishes
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hello Everyone,
We are fortunate to have Matthew Brett coming through York in January and
he will be giving a talk 4pm, 5th January at YNiC. Details to follow.
Best wishes
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hi all,
This Friday evening from 9pm we will be upgrading several parts of key
infrastructure at YNiC. During the work no YNiC services will be
available. We expect the maintenance to be completed by the early hours
of Saturday morning.
Thanks, Paul.
--
Paul Elliott, UNIX Systems Administrator
York Neuroimaging Centre (YNiC), University of York
Hello All,
We have a project presentation by David O'connor this week. He will
present his project 'Exploring the impact of environmental factors on
impulsive choice and impulsive action'.
The presentation will be at YNiC.
Best wishes
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hi all,
Those of you who use NAF or the python-megdata module may have noticed
that the online documentation has been unavailable for a couple of weeks.
For technical reasons, we've had to move the location of the
documentation. This can now be found at:
https://www.ynic.york.ac.uk/code-docs/
Please update any bookmarks or other references to the old URL
(https://vcs.ynic.york.ac.uk/docs)
Sorry for the inconvenience,
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
Dear All,
We are not aware of anyone needing Presentation software and we are
therefore planning to discontinue with providing it from August 2017
onwards.
Best wishes
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hello Everyone,
This one is important. In recent weeks we have found that safety screening
forms and consent forms are not being returned appropriately to ynic in all
cases. That is, the personal information on these documents is not being
kept confidential.
Please ensure that after scanning has finished, participant's forms are
returned to YNiC reception. You MUST either hand the forms personally to a
member of YNiC staff or place the forms in the secure gray post-box behind
the reception desk.
During the period of time you are responsible for the forms do not leave
them in open site anywhere in the building and do note take them away from
the building.
Thank you
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hello All,
We've had reports of intermittent loss of access to some files and folders.
We are investigating. We may have to reboot some servers controlling our
storage arrays in the near future without notice. More to follow.
Bw
Tony
Dear all,
We have made a small change to the YNiC cluster configuration.
Until now, each cluster job could use as much memory as they wanted.
This has been known to cause problems for users when they submit jobs
which require a large amount of RAM. If multiple jobs which require
large amounts of RAM are put onto the same machine, the jobs may run out
of memory. More problematically, it was sometimes the case that jobs
which did not require much RAM were the ones which failed.
To prevent this, we have added a default RAM limitation to the cluster.
Each "slot" is allocated 8G by default. If the job uses more than this,
it will be killed.
Jobs which require more RAM can still be run on the cluster. To do
this, you will simply need to tell the cluster how much memory to
reserve for your job - this will prevent your job from running out of
RAM by reserving enough for you. This can be done using the -l
h_vmem=xxG argument to the qsub command. We have documented this on the
wiki at:
https://www.ynic.york.ac.uk/docs/ITPages/IT/ClusterScripts
under the "Resource Limitations" section.
We estimate that this will not affect many users. For anybody who is
affected and are using qsub directly, the instructions above provide
information on how to request more RAM to be made available. If you are
find that you are getting memory allocation errors when using any of the
YNiC provided cluster commands (clusterFeat, clusterR, clusterMatlab,
clusterReconAll), or when using NAF, please contact
it-support(a)ynic.york.ac.uk and we will make sure that we adapt the
scripts to use the correct arguments with the qsub command.
If you have any questions, please contact it-support(a)ynic.york.ac.uk
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
Hello All,
A gentle reminder that we mechanisms in place to allow you to provide MRI
images to those participants that request them. Please use this process
rather than printing out 'pictures' of brains.
Many thanks
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Many of you will be aware that we have recently experienced a few
hardware failures on the YNiC computing cluster. We have now escalated
these issues and the manufacturer has committed to attend on site to
attempt to resolve the existing issues. Without being too technical,
this process is essentially an overhaul of the current cluster and
requires two engineers.
Obviously, we are doing out utmost to get your cluster up and running
again but, considering the scale of the job, please be patient. We will
keep you updated.
Thanks,
--
André
************************************************************************
André Gouws
York Neuroimaging Centre
University of York
The Biocentre
York Science Park
Heslington
YO10 5NY
Tel: +44 (0) 1904 435327
Fax: +44 (0) 1904 435356
Dear All,
We have a system for providing CDs at YNiC. However, such is the number of
requests we have to deal with, we now need to rethink how to provide the
anatomical scan data to participants. What’s even more frustrating, is
that although we have a system that alerts participants that their CD is
ready, 58 remain uncollected. We are therefore being asked to allocate
considerable resource to generating CDs that the participants subsequently
have little or no interest in.
Rethink: Moving forward, we will allow researchers to create data CDs for
their participants. The researcher will need to provide their own CD and
execute a script. The script, 'Create subject CD', can be run from the
'Applications' menu under 'YNiC Utilities'. Please follow the instructions
given by the script and note that you (1) have to have the permission of
the participant (2) make sure that the participant receives the CD [you may
want to record their signature] and (3) you record who you have sent CDs to.
Andre is also putting a webpage together to give guidance.
https://www.ynic.york.ac.uk/information/mri/MakeASubjectCD
Requests to YNiC for data CDs will no longer be met after 1/11/2016.
Thank you
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Dear Users,
Today we will be graced with the presence of Dr Helen Nutall from the
Psychology Department at Lancaster University. She will be giving a talk
entitled:
"Sensorimotor processing in perception of degraded speech"
The talk will be held in room B020 in the Psycholgy Department, at 4pm.
All are welcome and refreshments will be served afterwards.
Best,
Junior
--
Junior Whiteley
York Neuroimaging Centre
junior.whiteley(a)ynic.york.ac.uk
Hello All,
It has been noted that investigators are sometimes asking potential
participants screening questions in reception and other areas where
confidential answers may be overheard. Please make appropriate
arrangements to ensure the confidentiality of your participants responses.
Many thanks
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hello everyone,
To avoid confusion for those recently joining the ynic user community,
Thursday seminars are announced, usually early in the week. This week there
is no seminar.
Best wishes
Tony
Hi all,
At the following times during this term, YNiC open plan will be closed
for teaching.
Please note that if any YNiC open plan computers have been left logged
on at the start of the teaching sessions, they will be automatically
logged out.
Week 2:
* Tuesday 4th October 1200-1600
* Thursday 6th October 0900-1300
Week 3:
* Monday 10th October 1200-1600
Week 4:
* Monday 17th October: 1200-1600
Week 7:
* Monday 7th November: 1200-1600
Week 9:
* Monday 21st November: 1200-1600
Timings for the Spring term will be sent around in December.
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
