Dear Users
This Thursday (4-5 pm in YNiC) there will be a talk on "Measuring the
spatial resolution of MEG beamformers" given by Sam Johnson.
Everyone is welcome to attend.
Best wishes
Rebecca
--
Dr. Rebecca E. Millman
York Neuroimaging Centre
The Biocentre
York Science Park
York
YO10 5DG
Email: rem(a)ynic.york.ac.uk
Tel: 01904 435 5373
Hi,
FreeSurfer has recently announced a new version (5.1.0) where they've
finally sorted out the license issues after several years.
We don't have packages built for it yet, but will be looking at it very
soon (in conjunction with the neurodebian team) to replace the
semi-working 4.5.0 packages we have now.
Release notes can be found at:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
Thanks,
Mark
--
Mark Hymers
York Neuroimaging Centre
This evening we are hosting a visit from members of the York
Philosophical Society. They will be in YNiC from 6-8pm.
If anyone would like to help us show people around, please contact me
Gary
--
Gary Green
York Neuroimaging Centre
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5DG
http://www.ynic.york.ac.ukhttps://www.ynic.york.ac.uk/about-us/people/ggrg
tel. +44 (0) 1904 435349
PA +44 (0) 1904 435329 or reception(a)ynic.york.ac.uk
fax +44 (0) 1904 435356
mobile +44 (0) 788 191 3004
Dear Users
Today (4-5 pm in YNiC) there will be a YNiC project proposal
presentation given by Chris Racey.
The title of the talk is "The effects of parametrically manipulating view
exposure range on representational invariance in object selective
cortex". Please see the abstract below.
Everyone is welcome to attend.
N.B. The starting time of the YNiC seminars will be 4 pm this term.
Best wishes
Rebecca
*Abstract*
Previously we have carried out two experiments in which view shift
of objects and landscape scenes was parametrically manipulated. In both
experiments participants viewed blocks of stimuli changing in view by 0,
5, 10, and 15°. Different levels of adaptation across these view
shift conditions allow us to derive a measure of view sensitivity for any
given voxel or region. We were able to show variation in the degree of
view sensitivity between category selective regions for both objects and
landscape stimuli. Our previous work has shed new light on how category
specific visual information is processed and represented during
perception. However, it is not yet clear what the effect of object
learning and long term storage is on these ventral stream
representations. Previous research on this issue is limited, and there
have been few studies investigating the effects of prior learning on
neural adaptation.
We aim to apply our parametric manipulation of view shift paradigm
during an encoding experiment with unfamiliar objects prior to scanning.
Participants will under training, and learn to recognise objects where
their range of view exposure will vary parametrically, from 0°,
10°, and 20°. In the scanner, all of the stimuli will be
presented from previously unseen views in an fMR-adaptation block design,
with blocks of images shifting in view in 10° steps. For each
pre-exposure condition, the presentation conditions in the scanner will
be identical, and any differences across conditions must be due to
differences during the encoding of items. We predict that objects learned
with a greater range of views will be associated with richer, more
invariant, representations, and show greater degrees of invariant
adaptation than objects learned under a narrower range of views.
--
Dr. Rebecca E. Millman
York Neuroimaging Centre
The Biocentre
York Science Park
York
YO10 5DG
Email: rem(a)ynic.york.ac.uk
Tel: 01904 435 5373
FYI
---------------------
We are looking for two bright and motivated researchers to work on a
research project in which we will use *brain imaging and advanced brain
decoding methods to investigate the neural basis of deviant mental
representations in neurodevelopmental disorders such as autism,
dyslexia, and dyscalculia*. This project is an interdisciplinary
collaboration between the Laboratory of Biological Psychology (Hans Op
de Beeck), the Parenting and Special Education Research Group (Bert De
Smedt), and Child Psychiatry (Jean Steyaert, Bart Boets), all part of
the University of Leuven (K.U.Leuven) in Belgium.
We offer one PhD position and one Post-doc position. Eligible candidates
should have or should soon obtain a master’s degree (for the PhD
position) and a PhD (for the postdoc position) in a relevant field such
as neuroscience, psychology, psychiatry, neurobiology, or medical
engineering. Specific positive points for the evaluation will be
experience with brain imaging (in particular functional magnetic
resonance imaging), a computational background in a relevant field
(e.g., brain imaging data analysis, neural networks, etc.), and good
computer skills (e.g., Matlab). A background in neurodevelopmental
disorders is a plus, but not mandatory. Good English (oral and written)
communicative skills are necessary.
The two positions are full-time, for a period of 4 years (PhD position)
and 2-3 years (postdoc), and start in October 2011. The two positions
are strongly research oriented, and teaching and/or administration load
will be minimal. The research will be embedded in a very stimulating
environment with state-of-the-art technical facilities and with ample
opportunities for interaction with experts on neurodevelopmental
disorders and brain imaging. The K.U.Leuven is consistently ranked
within the top of European Universities and is located in the city of
Leuven, which has an strong international appeal. For more information
about our university, please visit http://www.kuleuven.be/about/
Formal applications should be sent by email to Hans Op de Beeck, and
should include a scientific CV (mentioning past research positions and
education, and publications), motivation letter, and the names and
contact information of 2 senior researchers that are willing to write a
recommendation letter if necessary (no letters have to be sent yet).
Application deadline is June 20^th 2011.
For further information please contact Hans Op de Beeck
(hans.opdebeeck(a)psy.kuleuven.be
<mailto:hans.opdebeeck@psy.kuleuven.be>), Bert De Smedt
(Bert.DeSmedt(a)ped.kuleuven.be <mailto:Bert.DeSmedt@ped.kuleuven.be>), or
Bart Boets (Bart.Boets(a)ped.kuleuven.be
<mailto:Bart.Boets@ped.kuleuven.be>).
Bart Boets, PhD
Postdoctoral fellow of the Research Foundation - Flanders
Leuven Autism Research Consortium
Child and Adolescent Psychiatry
Herestraat 49 - box 7003, B-3000 Leuven, BELGIUM
Tel. +32 (0)16/ 34.22.45
Fax. +32 (0)16/ 34.38.30
Email: bart.boets(a)ped.kuleuven.be <mailto:bart.boets@ped.kuleuven.be>
--
Gary Green
Dear Users
This Thursday (4-5 pm in YNiC) there will be a YNiC project proposal
presentation given by Chris Racey.
The title of the talk is "The effects of parametrically manipulating view
exposure range on representational invariance in object selective
cortex". Please see the abstract below.
Everyone is welcome to attend.
N.B. The starting time of the YNiC seminars will be 4 pm this term.
Best wishes
Rebecca
*Abstract*
Previously we have carried out two experiments in which view shift
of objects and landscape scenes was parametrically manipulated. In both
experiments participants viewed blocks of stimuli changing in view by 0,
5, 10, and 15°. Different levels of adaptation across these view
shift conditions allow us to derive a measure of view sensitivity for any
given voxel or region. We were able to show variation in the degree of
view sensitivity between category selective regions for both objects and
landscape stimuli. Our previous work has shed new light on how category
specific visual information is processed and represented during
perception. However, it is not yet clear what the effect of object
learning and long term storage is on these ventral stream
representations. Previous research on this issue is limited, and there
have been few studies investigating the effects of prior learning on
neural adaptation.
We aim to apply our parametric manipulation of view shift paradigm
during an encoding experiment with unfamiliar objects prior to scanning.
Participants will under training, and learn to recognise objects where
their range of view exposure will vary parametrically, from 0°,
10°, and 20°. In the scanner, all of the stimuli will be
presented from previously unseen views in an fMR-adaptation block design,
with blocks of images shifting in view in 10° steps. For each
pre-exposure condition, the presentation conditions in the scanner will
be identical, and any differences across conditions must be due to
differences during the encoding of items. We predict that objects learned
with a greater range of views will be associated with richer, more
invariant, representations, and show greater degrees of invariant
adaptation than objects learned under a narrower range of views.
--
************************************************************************
Dr. Rebecca E. Millman Science Liaison Officer York Neuroimaging
Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0)
1904 567614 Fax: +44 (0) 1904 435356
Hi Everyone,
Due to an important event taking place, please be aware that YNiC will
be closed all day on Friday 27 May and there will be no scanning or
access to the computers. The centre will be closed on Monday 30th due
to the bank holiday and open again as usual on Tuesday 31st May.
Best Wishes
Jen
http://neuroskeptic.blogspot.com/2009/09/fmri-gets-slap-in-face-with-dead-f…
********************************************************************
Philip Quinlan E-Mail: ptq1(a)york.ac.uk
Department of Psychology FAX: (01904) 323181
The University of York Tel: (01904) 320000 Ext. 3135
Heslington Direct : (01904) 323135
York
YO10 5DD
U.K.
********************************************************************
Dear Users
Please do not smoke just outside the entrance to YNiC.
Thank you
Gary
--
Gary Green
York Neuroimaging Centre
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5DG
http://www.ynic.york.ac.ukhttps://www.ynic.york.ac.uk/about-us/people/ggrg
tel. +44 (0) 1904 435349
PA +44 (0) 1904 435329 or reception(a)ynic.york.ac.uk
fax +44 (0) 1904 435356
mobile +44 (0) 788 191 3004
This email to the FSL mailserver list may be of interest to local YNiC
FSL users
Gary
----------------------------------
Dear David,
The short answer is, no, there is no way to justify Z=1.7 as a
cluster-forming threshold in FEAT.
The problem is that the cluster size P-values are based on Random Field
Theory (RFT), and RFT makes various approximation that are only valid
for high thresholds. While one early reference (Petersson et al, 1999)
specified cluster-forming threshold P=0.01 / Z=2.33 as a practical lower
limit for accurate results, later work (Hayasaka & Nichols, 2003; Silver
et al, 2010; K. Worsley personal communication) found even that level
was unstable, and instead recommended P=0.001 / Z=3.09 as a lower limit
on a cluster-forming threshold to ensure accurate inferences.
On the other hand, if you are using randomise, you can safely use any
cluster-forming threshold (though if you go too low, the clusters might
be too extended and spindly to be interpretable). If using randomise,
though, check out TFCE as away to avoid specifying any particular
cluster-forming threshold.
To answer your second question, the cluster-forming threshold used at
lower-levels is only used to make inferences *at* the lower level, and
is ignored at higher levels. Only the cluster-forming
threshold specified in the top-level FEAT analysis matters for the
top-level results.
-Tom
Petersson, K. M., Nichols, T. E., Poline, J.-B., & Holmes, A. P. (1999).
Statistical limitations in functional neuroimaging II. Signal detection
and statistical inference. /Phil. Trans. R. Soc. Lond. B/, /354/, 1261-1281.
Hayasaka, S., & Nichols, T. (2003). Validating cluster size inference:
random field and permutation methods. /NeuroImage/, /20/, 2343-2356.
Silver, M., Montana, G., & Nichols, T. E. (2010). False positives in
neuroimaging genetics using voxel-based morphometry data. /NeuroImage/.
Elsevier Inc. doi: 10.1016/j.neuroimage.2010.08.049.
On Mon, May 9, 2011 at 1:06 PM, David Soto <d.soto.b(a)gmail.com
<mailto:d.soto.b@gmail.com>> wrote:
Hello,
I am finding that when I use a Z<1.7 to define the cluster size at
he highest level analyses, I am getting some interesting activations
in regions that I don't see when I use Z<2.3. In both cases I use
cluster thresholding and p<0.05 whole brain corrected.....
I know the Z value used to define cluster size prior to correction
for multiple comparisons is arbitrary, but is it there any paper
that I can use to justify
in my study why a Z<1.7 was used instead of Z<2.3?
Would it be right to say that poststat results with a Z<1.7 are more
lenient than with a Z<2.3? I feel it this is not necessarily right
but can you please advise?
A second question I have is about poststats as implemented in FEAT....
Say that I have done a lower level analyses - for session, a 2nd
level -across session within subjects- and 3rd level -across subjects-
do I need to set up the Z<1.7 at the first and second level and
third level analyses - or does FEAT bring the unthresholded data
from lower level analyses to the higher levels and then use the Z
score specified at the highest level analyses? in other words, will
I get the same results if I specify
Z<1.7 across all levels or whether I do Z<2.3 for first and second
level and Z<1.7 at the higher level?
Many thanks,
David
--
____________________________________________
Thomas Nichols, PhD
Principal Research Fellow, Head of Neuroimaging Statistics
Department of Statistics & Warwick Manufacturing Group
University of Warwick
Coventry CV4 7AL
United Kingdom
Email: t.e.nichols(a)warwick.ac.uk <mailto:t.e.nichols@warwick.ac.uk>
Phone, Stats: +44 24761 51086, WMG: +44 24761 50752
Fax: +44 24 7652 4532
