ynic-users April 2011

ynic-users@ynic.york.ac.uk

5 participants
6 discussions

Niedermeyer's Electroencephalography
by michael＠ynic.york.ac.uk 19 Apr '11

19 Apr '11

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

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[Fwd: [megcommunity] Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School]
by Gary Green 13 Apr '11

13 Apr '11

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

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Beamforming questions
by Luis Peraza 07 Apr '11

07 Apr '11

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

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Questions about beamforming
by Luis Peraza 07 Apr '11

07 Apr '11

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

1 0

Beamforming files
by Luis Peraza 07 Apr '11

07 Apr '11

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

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Beamforming files
by Luis Peraza 07 Apr '11

07 Apr '11

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ynic-users April 2011