[Eeglablist] Call for internship in computational neuroscience

Cartik Sharma cartik_sharma at yahoo.com
Thu Dec 14 10:13:49 PST 2017

Dear All,
I'm interested in filling an opening for Computational Neuroscience at Neuromorph, a spin off from the Quantum machine learning stream at the University of Toronto, Rotman School of Management.
Core skills include:EEG data visualizationOptimizationStatistical Machine LearningComputer GraphicsSignal processing
If you match these skills, please email me at cartik.sharma at gmail.com, CTO of Neuromorph.
Looking forward to receiving highly motivated and dedicated candidates. Please note: Candidates should have capability to work in Canada on full time or part time basis.
Best regards, Cartik Sharma "There is plenty of room at the bottom." - Richard Feynman 

    On Monday, December 11, 2017, 1:53:45 PM EST, <eeglablist-request at sccn.ucsd.edu> wrote:  
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Today's Topics:

  1. Neuroscience data analysis summer-school announcements
      (Mike X Cohen)
  2. disinfection of caps? (Clayton Hickey)
  3. Post-doc position (Elisa Tatti)
  4. PhD position on the neurocognitive mechanisms of    conscious
      access. (Ian Charest (School of Psychology))
  5. Working with components (Ahmad, Jumana)
  6. post-doctoral fellowship position at OHSU (Ram?n Martinez)
  7. Re: Not sure where the bug is (Tarik S Bel-Bahar)
Dear colleagues,
I am happy to announce two week-long neuroscience data analysis courses at the Radboud University in Netherlands in August 2018: One about time-frequency/synchronization /statistics, and one about linear algebra and source-separation.
Below are the direct links to the course pages with application information. You can also find more information, including syllabi, on mikexcohen.com (scroll down to "In-vivo teaching"). Please pass these links around to your colleagues/students who might be interested in one or both of these courses!
Analyzing neural time series data (6-10 August). Fourier transform, convolution, time-frequency analysis, synchronization, nonparametric statistics, simulating time series data.
Linear algebra for neuroscientists (13-17 August). Matrix algebra, least-squares model fitting, eigendecomposition, multivariate source separation, state-space analyses, simulating multicomponent and multichannal time series data.
Please note that applications, if approved, are selected on a first-come-first-serve basis, and that the number of participants for each course is limited.
If you have questions about the courses, please feel free to contact me.
Mike X Cohen, PhD
New online courses: mikexcohen.comHi All, 

This isn’t an eeglab specific question… apologies if I’m stretching list rules. 

Do you disinfect your EEG cap? 

I’m talking about the cap, not the electrodes themselves, and in the context of standard University research use (ie. undergrads, not patients). 

I’ve worked in institutions that do, and in institutions that don’t. Some manufacturers appear to take it for granted (eg. ECI), others suggest avoiding it (eg. Biosemi). 

I get the impression that disinfectant reduces the life of the cap by breaking down the elasticity. Much more than that, though, I really dislike having to deal with glutaraldehyde solution. It’s nasty stuff, it has a short shelf life, and I expect that we as a community put a fair amount of it in our local water supplies (probably a drop in the proverbial bucket when one considers the medical system as a whole, but still). 

In your opinion, is it necessary? Does anyone know of any university / medical / governmental regulations that require it? 


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Dear all, 

there is a Post-Doc position available at the Neuroplasticity Lab at the City College of New York. Successful applicant will work with Dr. M. Felice Ghilardi and her team on a NIH-funded project investigating the functional significance of local sleep in humans. Our project, in partnership with the University of Wisconsin-Madison, is aimed to determine if sleep in humans occurs locally, in small-circumscribed regions of the cerebral cortex, during normal waking hours and if it is related to intense practice.
Requirements: PhD or equivalent degree in neuroscience, psychology, engineering or a related discipline is required. Ideal candidates would have extensive experience in HD-EEG data analysis and be proficient in Matlab programming. 
Preference will be given to candidates with experience in sleep research; background in cognitive neuroscience and experimental psychology; interest/experience with clinical populations; experience in task design and analysis for cognitive experiments.
Position available from January 2018.  Interested applicants should email: (a) CV, (b) statement of post-doctoral and career goals, and (c) letters and/or contact information for two references to Dr. Elisa Tatti <etatti at ccny.cuny.edu>. 

Stipend levels are in line with experience and NIH.  A two-year commitment is required.


 #yiv8992402943 P {margin-top:0;margin-bottom:0;}Dear EEGlab list, 

see below for details of a fully funded PhD position in Birmingham.

Best wishes,

Ian Charest
Lecturer, School of Psychology,
University of Birmingham, UK


The School of Psychology at the University of Birmingham is looking for a bright and motivated PhD student to join the Charest Laboratory (iancharest.com). The PhD position to be filled is part of a project recently funded by a European Research Council Starting Grant entitled: "Spatio-Temporal Attention and Representation Tracking: the precise neural architecture of conscious object perception" (START). 

The Project: 
START is an ambitious programme of work that will make use of cutting-edge multivariate pattern analyses (MVPA) techniques to reveal the brain mechanisms that are critical for consciously perceiving visual objects in tasks that manipulate conscious access to visual information. The ability to consciously recognise faces, objects, or sounds is crucial for adaptive behaviour and survival. Yet, how our conscious experience of the world emerges in our brain remains unknown. The overall aim of the START programme is to fill an important gap in our understanding of consciousness by elucidating the neural underpinnings of conscious access. How does the brain select relevant information among distractors, and keep this information in mind? Why does our ability to consciously recognise salient objects sometimes fail under pressure and exhibit variability across days and individuals? START will try to address these important questions by precisely tracking where in the brain and when in time the representations critical for conscious access are established, by using novel approaches of Representational Similarity Analyses which combines the strengths of EEG, fMRI, and Deep Convolutional Neuronal Networks. This project will provide new insights on the precise spatio-temporal dynamics of conscious access, the mechanisms governing it, and the idiosyncratic subtleties behind the meanderings of consciousness. 

The candidate: 
The successful candidate will have (or be in the process of obtaining) a Masters degree in cognitive neuroscience or a related field. Previous experience with psychophysical tasks that manipulate conscious access in vision is desirable. Given the nature of the project, good understanding of and experience with fMRI, EEG/MEG and data analysis is desirable. Experience in using matlab or python (and Psychtoolbox or PsychoPy) is a requirement. The successful applicant will have experience with multivariate pattern analyses (Representational Similarity Analysis, Fisher linear discriminants, etc) of neuroimaging data. This post will require designing experiments, collecting and analysing data associated with the project, preparing manuscripts for publication, presenting results at national and international conferences and the possible supervision of research assistants and students. 

The School: 
The School of Psychology at the University of Birmingham (http://www.birmingham.ac.uk/schools/psychology/index.aspx) is one of the largest and most successful in the UK, currently ranked in the top 5 Schools in the country (REF 2014). The School is soon to move to new accommodation in the form of a fully refurbished, purpose-designed space and a new-build Centre for Human Brain Health that will house our new MRI, MEG, EEG, NIRS, sleep lab, and the recently appointed Chair in Translational Neuroscience. The University of Birmingham is an equal opportunities employer. The School of Psychology has a Bronze Athena SWAN award and strives to maintain a flexible and supportive environment that enables its staff to flourish. 

For informal enquiries about the project please contact Dr. Ian Charest (i.charest at bham.ac.uk). Formal applications must be made via the postgraduate admissions system in the School of Psychology. Applicants are encouraged to attach to their application a short and original project proposal (500 words).


Full advert of the position on find a phd:

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Dear EEG list,
Using code, I want to work on the component level. I have interpolated X number of electrodes, but reduced the rank of the data with PCA before ICA to total number of electrodes – X.
I now want to perform analysis on the components, but I am wondering how to use the following structs to calculate a matrix of ICA components, and how to link this to topographic information (I know it cannot map to channels anymore).
I am aware of the following fields.
                          EEG.data with channel level data (some channels interpolated).
Best wishes,
Jumana Ahmad
Post-Doctoral Research Worker in Cognitive Neuroscience 
EU-AIMS Longitudinal European Autism Project (LEAP) & SynaG Study
Room M1.09. Department of Forensic and Neurodevelopmental Sciences (PO 23) | Institute of Psychiatry, Psychology & Neuroscience | King’s College London | 16 De Crespigny Park | London SE5 8AF
Phone: 0207848 0260| Email: jumana.ahmad at kcl.ac.uk | Website: www.eu-aims.eu | Facebook: www.facebook.com/euaims
We are currently looking for volunteers with mild intellectual disability to be part of our exciting and world-leading European project into brain development and social behaviour. Please, do get in touch if you know of anyone who may be interested in taking part.

Post-doctoral fellowship position

Oregon Health & Science University (OHSU) has an ongoing NIH-funded T32 fellowship for postdoctoral fellows with an interest in complementary medicine and neurological disorders or stress and a career goal in academic medicine (http://www.ohsu.edu/xd/research/centers-institutes/neurology/orccamind/academics/fellowships.cfm ). While complementary medicine is a broad area applicants for this posting will be doing research on meditation involving physiological signal analysis, including EEG. Applicant should have knowledge of EEG signal analysis and classification beyond typical signal averaged event-related potentials or EEG frequency analysis, e.g., machine learning using convolutional neural networks or other approaches and phase locking. Programming is required and should extend to Python as well as Matlab/EEGlab. Their primary mentor will be Dr. Barry Oken. The fellowship is generally for two years with the possibility of extending it one additional year depending on the fellow’s success and funding availability. Fellows conducting clinical research will be expected to participate in the Human Investigations Program at OHSU http://www.ohsu.edu/xd/education/schools/school-of-medicine/academic-programs/hip/


Eligibility: Applicants must have a doctoral degree and be a US citizen or have been lawfully admitted for permanent residence. 


Application process: Applicants should send a letter of interest expressing what they would like to accomplish over the fellowship-training period. The applicant should also describe their long-term career interests and how this post-doctoral fellowship will help them. The letter of interest and CV should be sent to: 

Barry Oken, MD, PhD, (oken at ohsu.edu) Oregon Health & Science University, CR-120, 3181 SW Sam Jackson Pk Rd, Portland, OR  97239.


OHSU is an Equal Opportunity/Affirmative Action Employer
Hello Tyler, not sure if this helps: it's totally possible that eeg_lat2point removes or discounts 2 data points. It's unclear whether clean_windows can or should accomodate the changes made by eeg_lat2point. As this is unlikely to lead to a major issue, you could modify the sample_mask (inside the code) to take 2 less datapoints, although this might lead to several changes that one would need to make. Another option is to contact the developer Dr.Kothe? directly. Thanks very much for letting the list know when you have a solution, as it would benefit other users to learn from your experience.
On Sun, Dec 3, 2017 at 8:34 PM, Tyler Grummett <tyler.grummett at flinders.edu.au> wrote:


Im having a great time using the clean_rawdata toolbox, however, I ran into a bug recently which is preventing me from using the function vis_artifacts. The bug occurs after Ive used clean_windows and try to compare the output data to the input data. The following error occurs:

Subscripted assignment dimension mismatch.
Error in vis_artifacts/expand_ rejections (line 334)        tmpdata(EEG.etc.clean_channel_ mask,EEG.etc.clean_sample_ mask)        = EEG.data;
Error in vis_artifacts (line 101)    new = expand_rejections(to_ continuous(new));

Digging into the code I find out that the number of true logicals in EEG.etc.clean_sample_mask is equal to 2449098, whereas the number of data points in my 'cleaned' data is 2449096. Returning to the clean_windows function, I get the following warning:

Warning: eeg_lat2point(): Points out of range detected.Points replaced with maximum value > In eeg_lat2point (line 101)  In pop_select (line 534)  In clean_windows (line 136)  In clean_artifacts (line 226)  In clean_rawdata (line 83)  In mcgurk_clean_data (line 187) 

This suggests to me that eeg_lat2point may have removed some data points? Or do you think that clean_windows should accommodate for changes made my eeg_lat2point? Like the subject of this email suggests, I dont know where the bug is.

I can confirm that I am using clean_rawdata version 0.32


Tyler Grummett ( BBSc, BSc(Hons I))PhD CandidateBrain Signals LaboratoryFlinders UniversityRm 5A301Ext 66125
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