ynic-users May 2011

ynic-users@ynic.york.ac.uk

7 participants
14 discussions

YNiC seminar 2nd June
by Rebecca E Millman 31 May '11

31 May '11

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

1 0

Freesurfer
by Mark Hymers 28 May '11

28 May '11

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

1 0

Tonight in YNiC
by Gary Green 26 May '11

26 May '11

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.uk https://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

1 0

YNiC seminar today
by Rebecca E Millman 25 May '11

25 May '11

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

1 0

[Fwd: [SPM] Vacancy for one postdoc and one PhD student in Leuven, Belgium]
by Gary Green 23 May '11

23 May '11

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

1 0

YNiC seminar 26th May
by Rebecca E Millman 22 May '11

22 May '11

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

1 0

YNiC Closed 27th May
by Jen Downing 19 May '11

19 May '11

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

1 0

Lies and statistics?
by Philip Quinlan 19 May '11

19 May '11

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. ********************************************************************

2 1

smoking
by Gary Green 13 May '11

13 May '11

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.uk https://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

1 0

[Fwd: Re: poststats inquiry pls]
by Gary Green 10 May '11

10 May '11

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

1 0

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

ynic-users May 2011