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2780 discussions

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

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

[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

[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

[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

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

[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

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, 2 months

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, 2 months

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, 2 months

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