November 22nd
1. Update on analysis tools at YNiC
2. MRI
FSL
2.1 Features: Atlases, Bedpostx and FIRST, avw2fsl
2.2 Scripts and batch processing (python demo)
2.2 Higher level analyses (?)
2.3 Cluster Feat and Cluster Other
OTHER (Freesurfer, SPM, mrVista)
3. MEG tools
3.1. Beamforming and permutation statistics
4. Visualisation tools at YNiC
4.1 FSLVIEW
4.2 YNICDV3D
5. Support & Documentation at YNiC
6. Users' requests and what we can do better
All welcome, refreshments will be provided afterwards.
--
Will Woods
York Neuroimaging Centre
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5DG
http://www.ynic.york.ac.uk
Hi Laura,
Rapid event-related fMRI has many advantages for cognitive neuroscience
research. However, the main problem with this technique is that the
signal is very small compared to a block design. One way to increase
the signal-to-noise ratio is to increase the number of trials. This
typically means using a short ISI (otherwise your subjects could be in
the scanner for a long time!). It is also good to vary the ISI to avoid
expectation effects (i.e the subject predicting when the next event is
likely to occur). However, the problem with a short ISI is that the
response to one stimulus will likely overlap with the response to the
next. This is not a problem if the BOLD response is linear (i.e. the
response to two successive stimuli is the same as adding the response to
two independent stimuli with an appropriate temporal offset). However,
a number of studies have found that there are significant
non-linearities when the ISI is less than ~5sec (eg Dale and Buckner,
1997; Huetell and McCarthy, 2000). So, varying ISI can have positive
and negative effects on the BOLD signal. I haven't used the programs
that Claire and Silvia are using, but I assume they are trying to find
an optimum balance between these effects.
Users - please feel free to correct or comment!
Tim
Laura Lee wrote:
> Hi MRI-support,
>
> I'm struggling along trying to work out how to create a 'stochastic'
> event-related design for fMRI. Claire Moody has passed on a program
> that searches for the optimum stimulus schedule (she & Silvia used it
> for their last project). I've read over all the bumpf but am still
> quite confused by all the new concepts. I think I know roughly what I
> want but then there are some parameters I am unsure about and don't
> really understand the implications of the settings. I'd be really
> grateful if you could give me a hand.
>
> This is the programme I downloaded...
> http://surfer.nmr.mgh.harvard.edu/optseq
> And there's a pretty comprehensive help page here...
> http://surfer.nmr.mgh.harvard.edu/optseq/optseq2.help.txt
>
> Thanks, Laura
>
>
>
>
>
--
Dr Tim Andrews
Department of Psychology
University of York
York, YO10 5DD
UK
Tel: 44-1904-434356
Fax: 44-1904-433181
http://www-users.york.ac.uk/~ta505/http://www.york.ac.uk/depts/psych/www/admissions/cns/
Dear all,
there is another interesting paper in the 'Articles of interest' section of:
https://www.ynic.york.ac.uk/doc/Miscellaneous
This one is on combined MRI / MEG, which may or may not be of interest you.
If you have any papers to add to this section, forward them to me and
I'll make them globally available.
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
Elena Solesio has been visiting YNiC from the imaging centre in Madrid.
Today, Thursday lunchtime, at 1:00pm, Elena will be giving a talk in
YNiC open plan on some of the work she's been doing, entitled:
Retroactive Interference Modulates Magnetic Brain Activity In Normal
Aging: A Magnetoencephalography Study.
All are welcome to come along.
-----------
At 4pm today, there is a YNiC update seminar
1. update on MEG
2. recap of MEG facilities at YNiC
3. what is new and what has changed
4. sensor space and source space
5. beamforming update
6. minimum norm and dipoles
7. Users' requests and what we can do better
All welcome
Refreshments will be served after the seminar
--
Gary Green
York Neuroimaging Centre
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5DG
http://www.ynic.york.ac.uk
tel. 01904 435349
fax 01904 435356
mobile 07986 778954
Hello all,
Elena Solesio has been visiting YNiC from the imaging centre in Madrid.
This Thursday lunchtime, at 1:00pm, Elena will be giving a talk in YNiC
open plan on some of the work she's been doing, entitled:
Retroactive Interference Modulates Magnetic Brain Activity In Normal
Aging: A Magnetoencephalography Study.
As ever all are welcome to come along.
Thanks,
Sam
Dear All,
I would really like to see a Thursday session on connectivity -
dynamic causal modelling, diffusion tensor imaging, etc. Is this
interesting to anyone else?
Best,
Johan Carlin
Dear All,
Recently, we have had some problems with registration using FSL. Some
of the registrations, particularly with the standard brain appear to be
quite poor. Jodie, Claire and Andre have done some work on this
recently and found that the best combination of registrations in FSL is
Initial Structural: 15 degree search, 6 DOF
Main Structural: 15 degree search, 6 DOF
Standard Brain: 15 degree search, 12 DOF
If you have any views on this, could you let us know. We have also
noticed that the brain extraction tool, which is set as default on FEAT
has not always been removing the skull from the EPI images. If you have
been doing FEAT analysis, I would be grateful if you could let us know
whether BET has been working for you. If this hasn't been happening, it
could affect your registrations. A related issue, is that although
structural brain images are automatically skull stripped using BET,
FLAIR images are not. However, I believe that BET may be automatically
applied to FLAIR images in the near future. :-)
Cheers,
Tim
--
Dr Tim Andrews
Department of Psychology
University of York
York, YO10 5DD
UK
Tel: 44-1904-434356
Fax: 44-1904-433181
http://www-users.york.ac.uk/~ta505/http://www.york.ac.uk/depts/psych/www/admissions/cns/
"Off-line consolidation during sleep and wakefulness"
Dr Penny Lewis
Psychology Department, University of Liverpool
Date: 16:00. Thursday 01 November 2007
Location: YNiC Open Plan
Host: Gary Green
Programme: York Neuroimaging Centre Seminars
All welcome
Refreshments will be served after the seminar
Penny Lewis will be in YNiC this afternoon if individuals would like to
meet her.
We will be taking Penny out to dinner after the seminar. If you would
like to join us for dinner please contact Gary Green.
--
Gary Green
York Neuroimaging Centre
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5DG
http://www.ynic.york.ac.uk
tel. 01904 435349
fax 01904 435356
mobile 07986 778954
