- ynic-users

by Mark Hymers

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

14 years, 1 month

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Tonight in YNiC

by Gary Green

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

14 years, 1 month

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YNiC seminar today

by Rebecca E Millman

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

14 years, 1 month

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[Fwd: [SPM] Vacancy for one postdoc and one PhD student in Leuven, Belgium]

by Gary Green

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

14 years, 1 month

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YNiC seminar 26th May

by Rebecca E Millman

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

14 years, 1 month

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YNiC Closed 27th May

by Jen Downing

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

14 years, 1 month

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Lies and statistics?

by Philip Quinlan

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

14 years, 1 month

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smoking

by Gary Green

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

14 years, 1 month

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[Fwd: Re: poststats inquiry pls]

by Gary Green

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

14 years, 1 month

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External Seminar Today

by Julian Oldmeadow

Dear All, Today's external seminar will be delivered by Prof. Michelle Ryan from Exeter. Her talk will follow on nicely from last wednesday's Athena Swan talk, as she will be presenting her research on the "Glass Cliff", a precarious and obscured obstacle faced by women in leadership. As usual there will be drinks in the foyer afterwards. 4:15 in B020. Please come. Julian Julian Oldmeadow, PhD Department of Psychology University of York York, YO10 5DD julian.oldmeadow(a)york.ac.uk

14 years, 1 month

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[Fwd: Neuroimaging post]

by Gary Green

FYI ---------------------------------- Applications are invited for a position at a Hospital Research Center in Barcelona, Spain. The position is full-time for 15 months (with a probable extension to 18 months). It entails working mainly on neuroimaging data. The postholder will help in analyzing functional, structural, and diffusion tensor data. Essential skills include knowledge of fMRI and/or structural MRI techniques, a proficient management of SPM and programming skills in MATLAB. The position is available to start 1st of September 2011. Annual salary will be around €26,000 (plus social security, health and unemployment benefits). Please send enquiries or applications (which must include a covering letter detailing professional objectives and interests, CV, all in one pdf file) to cenicogni(a)gmail.com, with the subject line "Neuroimaging position". -- Gary

14 years, 1 month

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[Fwd: Postdoctoral fellowships at Oxford University on brain basis of visual attention and associative processing and disruption and retraining of these mechanisms in anxiety]

by Gary Green

FYI ----------------------- Positions to be based at The Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB), Oxford University. From June 2011 part of my lab (primarily at UC Berkeley) will be based at The Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB), Oxford University. I am looking for two postdoctoral researchers to join the group there. The positions are to play a key role in a programme of research aimed at identifying and retraining the brain mechanisms underlying disrupted attentional and associative processing in anxiety. The research is supported by funding from the European Research Council and conducted in collaboration with Drs K Weich, I Tracey and E Holmes. Candidates are sought with a doctorate in a relevant discipline and research experience in neuroimaging and programming (ideally in matlab or python). Employment is for an initial period of 1 year with the possibility of extension for an addition 2-4 years. Salary is from £33084. Start date is flexible between July 1 and Dec 1 2011. Further details can be obtained from sbishop(a)berkeley.edu <mailto:sbishop@berkeley.edu>. Prof. Sonia Bishop Assistant Professor Dept Psychology & Helen Wills Neuroscience Institute, UC Berkeley; visiting Senior Researcher, FMRIB, Oxford University

14 years, 1 month

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[Fwd: PostDoc- and PhD-positions at the Central Institute of Mental Health in Germany (ZI Mannheim)]

by Gary Green

FYI -------------------------------------------------------------------------------------------------------------- The Central Institute of Mental Health in Mannheim, Germany, is an internationally renowned research institute in the field of psychiatry and neuroscience, home of the Department of Psychiatry and Psychotherapy of the Medical Faculty Mannheim of the University of Heidelberg, and a psychiatric hospital with 255 inpatient and 52 day-clinic beds. To strengthen our recently established independent neuroscience research group funded by the Federal Ministry of Education and Research (BMBF), the Clinic for Psychiatry and Psychotherapy (Medical Director: Prof. Dr. med. Andreas Meyer-Lindenberg) offers * * *1 PostDoc and 1 PhD-Student Position* * * in the area of functional and structural magnetic resonance imaging (MRI). Positions are initially limited to 2 years, a prolongation is intended. The Central Institute of Mental Health is equipped, among others, with two Siemens 3 Tesla research MR scanners. Our research group consists of an interdisciplinary team of psychologists, psychiatrists, neurologists, biologists and technical assistants (http://www.zi-mannheim.de/ag_imaging.html). The main goal of the international research project is to examine fronto-striatal plasticity processes and their molecular genetic basis in healthy individuals and psychiatric patients using multimodal magnetic resonance imaging techniques (fMRI, morphometry, DTI, spectroscopy). Ideally, potential applicants will have previous experience with the acquisition, processing and analysis of MRI data, as well as a strong interest in the application of systems neuroscience methods in the context of neuropsychiatric research questions. We offer an interesting job in a pleasant working environment at a leading German research institute. Salary is according to the German TV-L pay scale, including the social benefits of the German public service sector. For further information please contact Dr. Dr. Heike Tost, Tel. +49 621 1703-6508, E-Mail heike.tost(a)zi-mannheim.de <mailto:heike.tost@zi-mannheim.de>. ____________________________________ Maria Zangl, PhD-Student Central Institute of Mental Health Research Group Imaging in Psychiatry J5, 68159 Mannheim, Germany Phone: +49-621-1703-6514 Email:maria.zangl@zi-mannheim.de <mailto:maria.zangl@zi-mannheim.de>

14 years, 1 month

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Niedermeyer's Electroencephalography

by michael＠ynic.york.ac.uk

Dear all, does anyone have a recent edition of Niedermeyer's Electroencephalography: Basic Principles, Clinical Applications and Related Fields? If so, would I be able to borrow it? Thanks, Michael

14 years, 2 months

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[Fwd: [megcommunity] Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School]

by Gary Green

FYI ---------------------- Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School Job Description A postdoctoral position is available with the TRANSCEND Research Program (www.transcendresearch.org <http://www.transcendresearch.org/>) at the Martinos Center for Biomedical Imaging in Charlestown, MA (www.martinos.org <http://www.martinos.org/>) which is affiliated with the Massachusetts General Hospital, Harvard Medical School and MIT. We are seeking a candidate with a strong basis in magnetic resonance imaging. Emphasis will be on MRI (DTI, spectroscopy, morphometry, ASL as well as resting state fMRI), and on co-registering MEG with MRI. This position will involve analysis of existing multimodal imaging data and collection of new data. The emphasis of the postdoctoral fellowship will be analysis of existing datasets with secondary activity in piloting data for new studies. It will involve working closely with a multidisciplinary team and with children, and will also involve some research oriented analysis of data collected for clinical purposes. After initial phase-in, ample opportunity will also be provided to the candidate to self-explore and lead research. Datasets to be analyzed include: MRI (including DTI and 1H-spectroscopy) and MEG data on 6-12 and teenage matched autism spectrum and control subjects with phenotyping data MRI data ( (morphometry, DTI, spectroscopy) plus laboratory and phenotyping data) on 70 children with autism plus epilepsy and/or mitochondrial dysfunction, along with one or more overnight EEGs on each patient data from children ages 2-10 with and without autism. Overall objectives: To perform multimodal analyses of research and clinical research data, to develop new approaches for performing these analyses, and to design pipelines for data analysis. To write papers and grants which will be high priorities all along the way and will be actively supported by senior faculty. To take advantage of the world class faculty and facilities of the Martinos Center for Biomedical Imaging to perform the above activities to their maximal potential. The program’s emphasis is on pathophysiologically grounded brain research and application of advanced imaging acquisition and analysis techniques to neurological and sensory aspects of autism spectrum disorders. Requirements: Candidates must have PhD in neuroscience, physics, biomedical engineering, electrical engineering, computer science or other related fields. Prior experience in MRI analysis is required. Experience with EEG will be an added advantage. Salary will be consistent with Massachusetts General Hospital, Harvard Medical School policies for Postdoctoral trainees and will range between $45,000 to $55,000 depending upon qualifications and experience. Compensation also includes full staff benefits, including health insurance, and vacation time. Contact: Interested applicants may send a CV and statement of interest addressing background and specific pertinence of the candidate’s interest to Dr. Martha R. Herbert at mherbert1(a)partners.org <mailto:mherbert1@partners.org> and cc transcend(a)partners.org <mailto:transcend@partners.org>. Applications will be considered until the position is filled. -- 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

14 years, 2 months

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Beamforming questions

by Luis Peraza

More about Beamforming files In a previous mail-list I was told that the *spheres.txt and *transform.txt file are obtained after coregistration of the MEG data to the MRI structural before beamforming. So I imagine that transform.txt matrix takes the NAI voxel values to the MNI space with a 5mm or 2mm volume grid, from the individual/subject brain to the MNI standard. Am I right? Is it MNI standard or the MNI space of the individual structural MRI? But anyway, (and this is a supposition) coregistration should be done first between MEG and the individual MRI structure to perform Beamforming in world/real or physical coordinates (right?). So there should be a previous space transform in world coordinates to perform beamforming, then the NAI values are obtained in world coordinates and finally transformed to MNI space together with the individual structural MRI. Am I right about this? The reason why I am to eager to know this, is because I am doing Beamforming for my project using python-vtk, and so far I have learned how to extract the cortical voxels of individual structrual MRI using BET-FAST from FSL. But in order to run my beamforming I need to transform the structural voxels (in MNI) to world coordinates and also do coregistration between the fiducial skin points, which I imagine were obtained using the stylus pen for 3D modelling during the MEG acquisition with the surface of the subject skin from the MRI. I was wondering if the transform.txt file does the coregistration skin-points-to-skin-surface for the Beamforming, Now I know that it does not. Maybe I will have to program my own coregistration algorithm anyway. I only wanted to know If there were a less painful way to do it. My fifth question is the following. According to the ynic-wiki, it says that I am able to define any voxel in MNI coordinates to define virtual electrodes using the Beamforming functions. The problem is that the wiki does not say how to define this coordinates. From where can I take them? > From the structural MRI or from the MRI standard? Can they be only the cortex or any voxel inside the brain? And my last question is about the sphere.txt file. It is composed of 248 lines, they should be the MEG coils, but I can not imagine the meaning of the rest of the four columns. I was thinking they where x,y,z coordinates, but there is a fourth one that tells me I am wrong. Many thanks, Luis R. Peraza

14 years, 3 months

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Questions about beamforming

by Luis Peraza

More about Beamforming files In a previous mail-list I was told that the *spheres.txt and *transform.txt file are obtained after coregistration of the MEG data to the MRI structural before beamforming. So I imagine that transform.txt matrix takes the NAI voxel values to the MNI space with a 5mm or 2mm volume grid, from the individual/subject brain to the MNI standard. Am I right? Is it MNI standard or the MNI space of the individual structural MRI? But anyway, (and this is a supposition) coregistration should be done first between MEG and the individual MRI structure to perform Beamforming in world/real or physical coordinates (right?). So there should be a previous space transform in world coordinates to perform beamforming, then the NAI values are obtained in world coordinates and finally transformed to MNI space together with the individual structural MRI. Am I right about this? The reason why I am to eager to know this, is because I am doing Beamforming for my project using python-vtk, and so far I have learned how to extract the cortical voxels of individual structrual MRI using BET-FAST from FSL. But in order to run my beamforming I need to transform the structural voxels (in MNI) to world coordinates and also do coregistration between the fiducial skin points, which I imagine were obtained using the stylus pen for 3D modelling during the MEG acquisition with the surface of the subject skin from the MRI. I was wondering if the transform.txt file does the coregistration skin-points-to-skin-surface for the Beamforming, Now I know that it does not. Maybe I will have to program my own coregistration algorithm anyway. I only wanted to know If there were a less painful way to do it. My fifth question is the following. According to the ynic-wiki, it says that I am able to define any voxel in MNI coordinates to define virtual electrodes using the Beamforming functions. The problem is that the wiki does not say how to define this coordinates. From where can I take them? >From the structural MRI or from the MRI standard? Can they be only the cortex or any voxel inside the brain? And my last question is about the sphere.txt file. It is composed of 248 lines, they should be the MEG coils, but I can not imagine the meaning of the rest of the four columns. I was thinking they where x,y,z coordinates, but there is a fourth one that tells me I am wrong. Many thanks, Luis R. Peraza

14 years, 3 months

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Beamforming files

by Luis Peraza

After doing beamforming there are two files besides the NAI ones, a *spheres.txt and *transform.txt files. My question is which is the purpose of these files. What do they represent? Many thanks. Luis Peraza

14 years, 3 months

1
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Beamforming files

by Luis Peraza

After doing beamforming there are two files besides the NAI ones, a *spheres.txt and *transform.txt files. My question is which is the purpose of these files. What do they represent? Many thanks. Luis Peraza

14 years, 3 months

1
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MRI help

by Philip Quinlan

Are there any useful rules of thumb about what the critical cluster size should be in reporting results. I have a results with a cluster size of 1 that reaches the 2.3 threshold. (i) this cant be a real ROI - can it? (ii) why is the critical z val set at 2.3 anyway? Any help gratefully received. Thanks Philip. ******************************************************************** 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. ********************************************************************

14 years, 3 months

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[Fwd: [megcommunity] MEG Research Associate - University of Cambridge]

by Gary Green

FYI Research Associate *University of Cambridge, Department of Experimental Psychology* *Vacancy Ref: PJ07992* * * *Salary: £27,428 - £35,788 pa* Applications are invited for a post-doctoral researcher to develop, implement, and analyse MEG studies investigating cognitive and motor abilities across the adult life-span for an interdisciplinary BBSRC funded research project (Cambridge Centre for Ageing and Neuroscience (Cam-CAN) www.cam-can.com). This collaborative project involves researchers in a number of University of Cambridge Departments and at the MRC-Cognition and Brain Sciences Unit. The applicant will be based in the Centre for Speech, Language and the Brain, Department of Experimental Psychology, led by Professor Lorraine K Tyler. The post-holder will be expected to interact frequently with members of the CSLB and other members of the Cam-CAN team. The Centre has access to a research-dedicated 3T Siemens MR scanner, EEG and MEG facilities housed at the MRC-CBU. Applicants must have a PhD in a relevant discipline and experience in MEG imaging analysis, particularly connectivity in both sensor and source space. Excellent computer programming (MATLAB and/or Python) and MEG analysis (SPM, Fieldtrip) skills are essential. A background in cognitive neuroscience, particularly ageing, would be beneficial. /Closing date: 4 May 2011, Start date: 1 October 2011/ /Limit of tenure: The funds for this post are available for one year in the first instance, with a possibility to extend for a further two-three years./ / / For further details, please see our website at http://csl.psychol.cam.ac.uk/vacancies.html or http://www.cam-can.org/vacancies/index.html Applications should include a covering letter, CV, publications list and a completed form CHRIS/6 Parts I and III (downloadable from http://www.admin.cam.ac.uk/offices/hr/forms/chris6), and should be sent to Mrs M Dixon at csladmin(a)csl.psychol.cam.ac.uk <mailto:csladmin@csl.psychol.cam.ac.uk> or by post to Mrs M Dixon, Centre for Speech, Language and the Brain, Department of Experimental Psychology, University of Cambridge, Downing Street, Cambridge, CB2 3EB. /The University values diversity and is committed to equality of opportunity./ /The University has a responsibility to ensure that all employees are eligible to live and work in the UK./

14 years, 3 months

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post-doc positions

by Gary Green

FYI -------- Original Message -------- Date: Tue, 22 Mar 2011 16:53:49 +0000 (GMT) From: Klaas Enno Stephan <klaasenno(a)yahoo.de> Reply-To: Klaas Enno Stephan <k.stephan(a)fil.ion.ucl.ac.uk> To: Klaas Enno Stephan <klaasenno.stephan(a)econ.uzh.ch> Dear colleagues, The Max-Planck Society and University College London recently launched a joint initiative in Computational Psychiatry & Aging. This program currently offers a number of open postdoctoral positions (application deadline: 31 March 2011). We would be grateful if you could forward the information below to students in your department who may have an interest in applying for these positions. With many thanks and my very best wishes, Klaas Max Planck Society – University College London Joint Initiative in Computational Psychiatry and Aging The Max Planck Society (MPS) and University College London (UCL) are launching a joint initiative, funded by contributions from MPS and UCL, commencing in May 2011 (for details, see www.mpib-berlin.mpg.de/research-initiative-mps-ucl <http://www.mpibberlin.mpg.de/research-initiative-mps-ucl>). The initiative will involve laboratories including the Max Planck Institute for Human Development (Berlin) and the Max Planck Institute for Cognitive and Brain Sciences (Leipzig), in Germany, and the Wellcome Trust Centre for Neuroimaging (London) and the Gatsby Computational Neuroscience Unit (London) in the UK. The goal of the initiative is to develop novel neuroscience approaches to understanding psychopathology and cognitive aging that exploit computational and mechanistic perspectives. We are seeking applicants for a number of post-doctoral positions with an interest or background in computational neuroscience who would like to use such approaches to understand psychiatric disorders and cognitive aging. The applicants should forward their CVs to Helena Maravilla (MPSUCL(a)mpib-berlin.mpg.de), Max Planck Institute for Human Development, Lentzeallee 94, 14195 Berlin, Germany. The deadline for the first round of applications is March 31, 2011. For further information, please see http://www.mpib-berlin.mpg.de/en/research/research-initiative-mps-ucl http://www.mpib-berlin.mpg.de/sites/default/files/media/pdf/25/mps-ucl-anno… __________________________________________________ Prof. Klaas Enno Stephan, MD Dr.med. PhD Laboratory for Social and Neural Systems Research, Dept. of Economics, University of Zurich Tel. +41-44-6343799/-6345520 http://www.socialbehavior.uzh.ch/stephan.html Wellcome Trust Centre for Neuroimaging, Institute of Neurology, University College London Tel. +44-207-8337472 http://www.fil.ion.ucl.ac.uk/Staff/

14 years, 3 months

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Science Trail

by Michael Simpson

Dear all, The university Science Trail will be on tomorrow. As per usual, YNiC will be taking part. Availability of Open Plan will not be affected, however, there may be background noise from excitable secondary school students between 10 am and 3 pm. 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

14 years, 3 months

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Useful Tool for Meta-analysis and Functional Anatomy

by Tom Hartley

I've just come across pubbrain.org. It looks like a fantastic tool for cognitive neuroscience. Search for a term (e.g. "working memory") and find out how many PubMed papers have referred to different brain regions (a "heat map" is provided), together with a list of citations. For example, Pubmed find 161 papers linking "working memory" and "inferior frontal gyrus". Of course this is only the first step in understanding the brain basis of a given function, but I think it should be very useful for gaining a quick overview. Tom

14 years, 3 months

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YNiC seminar today

by rem

Dear Users Today (4.30-5.30 pm in YNiC) there will be a YNiC project proposal presentation given by Koulla Mikellidou. The title of Koulla's talk is "Neural correlates of the Helmholtz's squares illusion". Everyone is welcome to attend. Best wishes Rebecca -- ************************************************************************ 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

14 years, 3 months

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