Dear all,
when new users arrive at YNiC, some would like to practice using data
analysis scripts before they record their own data. As such, we would
like to document some of the paradigms that have already been recorded.
We would not want to know in detail the specifics of your project, just
the basics to allow for a sensible analysis.
For example, the following may be enough:
"In the data for project Pxxxx, responses were recorded in continuous
mode to visual stimuli. There were four conditions which had the
respective trigger codes 4150, 4152, 4154 and 4156. Triggers 4150 and
4152 had a group code of 2, and triggers 4154 and 4156 had group codes
of 4. Participants made responses to some trials, which have a response
code of 32. Suggested epochs for data analysis are 150ms pre-trigger and
900ms post-trigger. Data was recorded for participants Rxxxx, Rxxxy ...
Rxyyx."
With this information new Users could run a trial analysis without any
necessary knowledge of your hypothesis, but enough information about
your stimulus parameters to run practice analyses on your data.
If you we be happy to provide this information about your data we would
be most grateful. We would then put this in some shared space for all
Users to access. If however you would like to give a more detailed
account of your experiment, then this could contribute towards the
initiative that Tony prompted in the email copied below.
With thanks,
Michael
--
Dr Michael Simpson
Science Liaison Officer
York Neuroimaging Centre
Innovation Way
York
YO10 5DG
Tel: 01904 567614
Web: http://www.ynic.york.ac.uk
*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_
Copy of mail from Tony Morland date 25th October.
Dear All,
Since the first beamforming course a number of people have been asking
questions like;
What can beamforming really do?
If I do this and get that, what does it mean?
Is beamoforming precise enough to distinguish between activity in brain
area A and B?
If I do X will it result in data that can be analysed with beamforming?
Can virtual electrode traces allow latencies to be measured in brain areas
A and B and do they make sense?
If I filter in this frequency band rather than that band why do I get this
result?
The answers to many of these questions are empirical and although Will et
al have been striving to test, retest and validate the methods, there will
always be questions that can't quite be answered unless more data is
acquired/analysed. It appears necessary therefore to start bench marking
the beamforming methods that are available. The aim is to undertake a
series of empirical studies that will reflect, in broad terms, the types
of paradigm used by investigators. My personal preference would be for a
set of basic experiments to be devised for which results are predictable
and could be compared with previous research. I accept that this is a
conservative aim, but the data sets acquired are likely to be the most
informative about the capabilities of the beamforming analysis tools. The
data acquired would also offer us an excellent resource for training any
researchers wishing to undertake investigations using beamforming.
Before devising new experiments it would be worth reviewing previous
studies undertaken at YNiC to see whether they can be used to bench mark
the beamforming methods. To this end, I would be grateful if you could
provide me with details of data that you think are suitable for bench
marking beamforming. The most helpful form for the information would be
the following:
Project Number and Title
Number of participants and their registered numbers
Paradigm used
Relevant research (the study replicated)
Predicted outcome
What you want to test with beamforming
Ethical concerns/limitations concerning use of the data
I will review the forthcoming information and after that will arrange a
brainstorming session on how best to move things forward.
Thanks
Tony
Dear Users,
further to the email sent recently about the format of booking requests,
Users may book scan time via a new on-line booking form.
https://www.ynic.york.ac.uk/user-resources/booking
However to cancel a booking please send the following request to
bookings(a)ynic.york.ac.uk :
CANCEL
Date: 31st October 2006
Time: 00.00
Type of Scan: structural MRI
Project ID: P0666
Participant ID: R0000
Unfortunately, verbose requests can lead to ambiguities and increase the
chances of errors. Please avoid the following style of request:
"This is just a request to cancel the time for one subject on Monday of
this week (my subject is on holiday LOL!) and then re-book them in to
another slot next Friday, for some time in the afternoon (don't mind
when), with all the same information, but an amendment to the Stimulus
Code from P0666et to P0666aa."
Should you need to re-schedule a subject, please simply send a CANCEL
request as shown above, and then re-book some new time via the website.
Thanks,
Michael
Dear All,
Since the first beamforming course a number of people have been asking
questions like;
What can beamforming really do?
If I do this and get that, what does it mean?
Is beamoforming precise enough to distinguish between activity in brain
area A and B?
If I do X will it result in data that can be analysed with beamforming?
Can virtual electrode traces allow latencies to be measured in brain areas
A and B and do they make sense?
If I filter in this frequency band rather than that band why do I get this
result?
The answers to many of these questions are empirical and although Will et
al have been striving to test, retest and validate the methods, there will
always be questions that can't quite be answered unless more data is
acquired/analysed. It appears necessary therefore to start bench marking
the beamforming methods that are available. The aim is to undertake a
series of empirical studies that will reflect, in broad terms, the types
of paradigm used by investigators. My personal preference would be for a
set of basic experiments to be devised for which results are predictable
and could be compared with previous research. I accept that this is a
conservative aim, but the data sets acquired are likely to be the most
informative about the capabilities of the beamforming analysis tools. The
data acquired would also offer us an excellent resource for training any
researchers wishing to undertake investigations using beamforming.
Before devising new experiments it would be worth reviewing previous
studies undertaken at YNiC to see whether they can be used to bench mark
the beamforming methods. To this end, I would be grateful if you could
provide me with details of data that you think are suitable for bench
marking beamforming. The most helpful form for the information would be
the following:
Project Number and Title
Number of participants and their registered numbers
Paradigm used
Relevant research (the study replicated)
Predicted outcome
What you want to test with beamforming
Ethical concerns/limitations concerning use of the data
I will review the forthcoming information and after that will arrange a
brainstorming session on how best to move things forward.
Thanks
Tony
Dear Users,
Can Users who wish to book MRI / MEG please use the
bookings(a)ynic.york.ac.uk email address. This address can in theory be
checked by all staff, and hence always monitored.
If you have made any bookings to an address other than the
bookings(a)ynic.york.ac.uk email, please re-send your booking to the
correct address.
To make things more efficient, and enable the Operator to set up you
recording preferences in advance, could your booking include the
following (preferably in the following format - see example in post script):
Date:
Time:
Type of scan: (MEG / structural MRI / fMRI)
Your Name:
Project ID:
Participant ID: (If your participant needs to be registered on the
database, please attach their registration form).
Stimulus Code*:
Stimulus Presentation software / apparatus*: (e.g. E-Prime, screen and
etymotics)
MEG position (Seated / Supine):
* Contact your SLO if you don't know what a / your Stimulus Code is.
with thanks,
Michael
P.S.
Example booking -
Date: 31st October 2006
Type of Scan: structural MRI
Project ID: P0666
Participant ID: R0000
Stimulus Cods: P0666et
Stimulus Presentation software / apparatus: Visage and Phantom
MEG position (Seated / Supine): N/A
--
Dr Michael Simpson
Science Liaison Officer
York Neuroimaging Centre
Innovation Way
York
YO10 5DG
Tel: 01904 567614
Web: http://www.ynic.york.ac.uk
Procedures for applying for ethical approval to conduct research at YNiC
have been revised. Details of the new arrangements, along with guidance
on how to prepare an application, can be downloaded from the YNiC
website at:
https://www.ynic.york.ac.uk/information/application/so-you-want-to-use-the-…
Please could all new applications for research ethics approval conform
to the revised instructions.
Thank you.
--
Gary Green
Director
York Neuroimaging Centre
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5DG
tel. 01904 435349
fax 01904 435356
mobile 07986 778954
Due to the fact that user's Trash folders are growing in size again, we
have taken the decision that we will start automatically emptying the
trash directories at least once a week (initially on Friday evenings).
Please note that we do not backup Trash directories at all and any file
placed in there should be regarded as deleted. As from next week, we may
also decide to empty Trash directories without notice should we need to
(for instance we have seen 15G trash directories this week). To assist
with this, please empty your Trash directory manually as often as you
can (preferably as soon as you've placed anything in it).
Mark
--
Mark Hymers
York Neuroimaging Centre
Dear fellow ynic-users,
You may notice some difficulty removing non-brain tissue from structural MR
images obtained at YNiC when using the brain extraction tool (bet - a part
of FSL) with its default parameters. Symptoms are that tissue around the
brainstem, mouth and throat is not removed. This might adversely affect
coregistration.
One workaround I know some people have used is to coregister the
"unstripped" brain to the "unstripped" reference volume (which seems to work
quite well). However, the FSL help strongly recommends removing non-brain
tissue, so this might not be the best solution.
Bet uses an estimate of the centre of the image to begin the process of
finding the inner and outer scalp and brain boundaries. The default estimate
doesn't seem to be right for out structural scans. I have had more success
using the following from the command line:
bet myinfileroot myoutfileroot -c 87 108 165
Where you replace myinfileroot and myoutfileroot with the names of your
input and output files (without .hdr or .img on the end).
The coordinates 87 108 165 may not be quite right for the centre of your
image but the bet algorithm seems to work much better with these values.
Best wishes,
Tom Hartley
===================================
Dr Tom Hartley
Dept. of Psychology,
University of York
Heslington,
YO10 5DD
UK.
t.hartley(a)psychology.york.ac.uk
http://www-users.york.ac.uk/~th512
tel: +44 (0)1904 432903
