From psc.dav at gmail.com Thu May 1 15:24:11 2025 From: psc.dav at gmail.com (David Pascucci) Date: Thu, 1 May 2025 15:24:11 +0200 Subject: [FieldTrip] =?utf-8?q?Call_for_Papers_=E2=80=93_Rhythmic_Cogniti?= =?utf-8?q?on_Special_Issue_=28Nature_Portfolio=29?= In-Reply-To: References: Message-ID: Dear colleagues, We are pleased to announce a new *Call for Papers* on the topic of *Rhythmic Cognition*, a cross-journal Collection hosted by *Communications Psychology*, *Nature Communications*, and *Scientific Reports*. This Collection invites contributions that focus on whether and how *endogenous and exogenous rhythms* shape cognitive functions. Relevant topics include, but are not limited to: - Rhythmic attention - Neural entrainment - Oscillatory dynamics in perception, memory, and decision-making - Computational and theoretical models of rhythmic processing - Brain stimulation and neuroimaging studies targeting oscillatory mechanisms - Advanced methods for the analysis of behavioural and neural rhythms We welcome submissions using or combining diverse methodologies, including behavioural experiments, psychophysics, modelling, EEG/MEG and brain imaging. *Submission deadline:* *28 September 2025* *Formats accepted:* Research Articles, Registered Reports, and Resources. If you are interested in submitting a *Review* or *Opinion* piece, please contact the Editors directly to discuss suitability. More information and links to submit can be found on https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nature.com%2Fcollections%2Fjhcjbjgfgj%2Fabout-this-collection&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cccbb4decb1e8431d595908dd88b37d63%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638817026667214496%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=V%2B5ewPWqzRJl7Bq9znb2KhyDpmERWSZujXdP43krBBE%3D&reserved=0. We look forward to your contributions. Please feel free to contact me should you have any questions. *Feel free to share this announcement with colleagues or mailing lists who may be interested.* Best regards, *David Pascucci, PhD* Guest Editor, *Rhythmic Cognition* Collection on behalf of the editorial teams at *Communications Psychology*, *Nature Communications*, and *Scientific Reports* *David Pascucci* Assistant Professor SNSF *Faculty of Biology and Medicine* *Psychophysics and Neural Dynamics Lab*, CHUV-UNIL & Principal Investigator Vision and Sight Recovery Research Unit The Sense Innovation and Research Center Avenue de Provence 82, 00,022 1007 Lausanne david.pascucci at unil.ch david.pascucci at chuv.ch [image: 1746104533665] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Instagram_image-XVYIOG883TZX - Rhythmic Cognition.jpg Type: image/jpeg Size: 235639 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: OutlookEmoji-174610453366505a8b503-f014-4dc6-9b1b-19b51b0c581a.jpg Type: image/jpeg Size: 43302 bytes Desc: not available URL: From npyang at uci.edu Mon May 5 09:11:51 2025 From: npyang at uci.edu (Nathan Yang) Date: Mon, 5 May 2025 00:11:51 -0700 Subject: [FieldTrip] Need Help with Fieldtrip Buffer Interaction with AcqKnowledge Message-ID: To whom it may concern: Hello, I am a college student and I am trying to collect live EMG data from a BIOPAC MP160 using the FieldTrip buffer so I can run the signals through a machine learning model. I went through the tutorials but am still having trouble (I am pretty lost haha). I will give a rundown on the background of my setup. Also if anyone has better ideas of how I can approach this please let me know. I am running AcqKnowledge NDT on TCP port 1972 and I am running buffer.exe on port 1972 as well. Also in my path "fieldtrip/realtime/bin/win64", I did not see "sine2ft" or "viewer" so was unable to further test. This is my matlab code (process1.m): addpath(“fieldtrip-20250106\”); ft_defaults; while true hdr = ft_read_header('buffer://localhost:1972'); disp(hdr); pause(1); end However, when I run it this is what returns. >> process1 Error using buffer ERROR: the buffer returned an error (517) Error in ft_read_header (line 1328) orig = buffer('get_hdr', [], host, port); ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Error in process1 (line 4) hdr = ft_read_header('buffer://localhost:1972'); I will also provide my ports and the IDs so you can see what is happening: netstat -an | Select-String "1972" TCP 0.0.0.0:1972 0.0.0.0:0 LISTENING TCP 0.0.0.0:1972 0.0.0.0:0 LISTENING TCP 127.0.0.1:1972 127.0.0.1:62529 ESTABLISHED TCP 127.0.0.1:62529 127.0.0.1:1972 ESTABLISHED netstat -a -n -o | findstr :1972 TCP 0.0.0.0:1972 0.0.0.0:0 LISTENING 26652 TCP 0.0.0.0:1972 0.0.0.0:0 LISTENING 10956 TCP 127.0.0.1:1972 127.0.0.1:62529 ESTABLISHED 10956 TCP 127.0.0.1:62529 127.0.0.1:1972 ESTABLISHED 6180 tasklist /FI "PID eq 26652" Image Name PID Session Name Session# Mem Usage ========================= ======== ================ =========== ============
AcqKnowledge.exe 26652 Console 1 213,836 K tasklist /FI "PID eq 10956" Image Name PID Session Name Session# Mem Usage ========================= ======== ================ =========== ============
buffer.exe 10956 Console 1 4,768 K tasklist /FI "PID eq 6180" Image Name PID Session Name Session# Mem Usage ========================= ======== ================ =========== ============
MATLAB.exe 6180 Console 1 2,978,264 KPS C:\Windows\System32> Any help would be appreciated thank you! From emma.holmes at ucl.ac.uk Tue May 6 10:44:49 2025 From: emma.holmes at ucl.ac.uk (Holmes, Emma) Date: Tue, 6 May 2025 08:44:49 +0000 Subject: [FieldTrip] Fully-funded PhD studentship at UCL - deadline tomorrow (7th May) In-Reply-To: References: Message-ID: *** Please forward to any potential candidates in your networks who may be interested in this position *** Dear all, I am currently advertising a fully-funded studentship at UCL, open to UK applicants. We'll develop training programmes that aim to help people with hearing loss to listen more easily in noisy environments. The project uses auditory psychophysics and pupillometry. Project: Auditory training interventions to improve speech understanding in noisy environments Supervisors: Emma Holmes & Stuart Rosen Location: UCL, London Funder: RNID The position is open to UK applicants. The application deadline has been extended to 7th May 2025. The full details and job description can be found at the following web page: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ucl.ac.uk%2Fpals%2Fdivisional-vacancies&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cf8f7241697fc4f04b06608dd8c7a4668%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638821179363382219%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=TYH4R5MDYYHc9KSI%2F4lmcbIeqGqLT5fCU%2BDXr1xD9pc%3D&reserved=0 (or downloaded directly from the following link: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ucl.ac.uk%2Fpals%2Fsites%2Fpals%2Ffiles%2Futf-8phd-studentship_ad_20250429.docx&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cf8f7241697fc4f04b06608dd8c7a4668%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638821179363407824%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=FIBrcepNYjthR915Klyxi9MhPeoZdXTXIju%2B%2F5H1nZs%3D&reserved=0). Potential applicants are welcome to get in touch with me (emma.holmes at ucl.ac.uk) for informal queries about the position, or to discuss the position further. Please share this with any students/colleagues in your networks who may be interested. Best wishes, Emma Emma Holmes Associate Professor in Speech and Hearing Science, UCL (she/her) e-mail: emma.holmes at ucl.ac.uk lab website: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcognitivehearinglab.com%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cf8f7241697fc4f04b06608dd8c7a4668%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638821179363431907%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=4xzzBvAybKfNFNTX%2BRjI8Q6weJ0loZxo19xs6tMJSE4%3D&reserved=0 personal website: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Femmaholmes.co.uk%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cf8f7241697fc4f04b06608dd8c7a4668%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638821179363454930%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=dk%2ByRb8RpueA8WSjiyuPHvSw33EiKpFOvFpgQ50J6kM%3D&reserved=0 twitter/X: @Emma_Holmes_90 bluesky: @emmaholmes90.bsky.social Mailing Address: Department of Speech Hearing and Phonetic Sciences Chandler House 2 Wakefield Street London WC1N 1PF United Kingdom Let me know if I can make any adjustments related to disability or neurodivergence to improve how we interact. Please note that I don't expect you to respond to emails outside of your normal working hours. -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.jameshouston81 at gmail.com Thu May 8 15:37:01 2025 From: m.jameshouston81 at gmail.com (Michael Houston) Date: Thu, 8 May 2025 08:37:01 -0500 Subject: [FieldTrip] Help Running ft_postfreesurferscript.sh Message-ID: Hi, everyone! I am trying to create a cortical sheet source model from the standard colin27 brain with accompanying DKT atlas for EEG source reconstruction (single_subj.nii in Fieldtrip template directory). After doing recon-all in FreeSurfer, the resulting meshes are far too large ~160k vertices per hemisphere which is taking too long to run the source analysis on. I followed the instructions according to this tutorial ( https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fsource%2Fsourcemodel%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C95dfd5f11eba45cd573208dd8e357ca4%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638823082693275361%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C60000%7C%7C%7C&sdata=wUJlkWjQA02TxUNt1x89ngMWIqezHUHZWoafJdc51Ts%3D&reserved=0) and set up the HCP-Workbench and copied the requested directory contents to a common folder to use ft_postfreesurferscript.sh to make the lower resolution cortical meshes. While I can get the script to run, I am facing the output and error copied below. If there is any other information I should provide please let me know. I am confused about this output because it looks like the error file is one that should be created by the script however it is not found. I would greatly appreciate any insight on how to fix this.: Command -------------- /mnt/c/Users/mjame/Documents/MATLAB/fieldtrip-20240504/bin/ft_postfreesurferscript.sh /usr/local/freesurfer/7.4.1/subjects single_subj /usr/local/freesurfer/7.4.1/subjects/workbench_freesurfer Output & Error -------------------- START: FS2CaretConvertRegisterNonlinear Saving /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.white.native.surf.gii as a surface in TKREGISTER space Saving /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.pial.native.surf.gii as a surface in TKREGISTER space Saving /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.sphere.reg.native.surf.gii as a surface in TKREGISTER space Saving /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.sphere.native.surf.gii as a surface in TKREGISTER space While running: wb_command -set-structure /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.sulc.native.shape.gii CORTEX_LEFT ERROR: NAME OF FILE: single_subj.L.sulc.native.shape.gii PATH TO FILE: /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench File does not exist. Thanks, Michael -------------- next part -------------- An HTML attachment was scrubbed... URL: From tara.ghafari at gmail.com Fri May 9 16:01:36 2025 From: tara.ghafari at gmail.com (Tara Ghafari) Date: Fri, 9 May 2025 15:01:36 +0100 Subject: [FieldTrip] OPM-MEG FLUX toolkit course, University of Oxford, sign up by 16 May In-Reply-To: <22E4D8B4-70A5-478B-847F-16EC7D0C1F50@gmail.com> References: <22E4D8B4-70A5-478B-847F-16EC7D0C1F50@gmail.com> Message-ID: <903B193F-09BC-4A29-890A-2BB4651E5E54@gmail.com> Dear admin team, We are organising a toolkit for analysing OPM-MEG data at the University of Oxford on June 9th-12th. Could you please send the below email to the mailing list? Thank you, Tara Dear all, We are delighted to announce the first OPM-FLUX toolkit to be held 9th-12th June 2025 at St. Catherine's College at the University of Oxford. The OPM-FLUX toolkit course provides a comprehensive introduction to analysing OPM-MEG data using OPM-FLUX, an advanced analysis pipeline for human electrophysiological data. Originally designed for SQUID-based MEG, the FLUX pipeline has been adapted for OPM-MEG. While OPM-MEG offers exciting opportunities in cognitive and clinical neuroscience, analysing its data can be challenging due to technical complexities and a lack of standardised methods. To meet the increasing demand for accessible training in this area, we have developed the FLUX toolkit, built on MNE-Python, a leading MEG analysis toolbox. Participants will be taught the theoretical foundations of OPM sensors and human electrophysiology and gain practical experience with OPM FLUX. In the mornings we will have lectures on the basics data analysis as well as examples on novel cognitive neuroscience research based MEG or OPM-MEG. In the afternoon we will have hands-on data analysis workshops applying the OPM-FLUX pipeline on a data set collected from the local OPM systems. Will cover the analysis of FieldLine as well Cerca/QuSpin data. The analysis sections will include the BIDS format, preprocessing, event-related fields, spectral analysis, source modelling, and multivariate pattern analysis. We will not provide hands-on training on the actual data acquisition but we will outline the general steps required. For details and registration please see https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.neuosc.com%2Ffluxtoolkit2025&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C402f4bcad03948365e8808dd8f020f23%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638823961192902972%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=j1FuviHm6dAMbMKMe4ZTCLbajVacBWJYyxROvi8C7D8%3D&reserved=0 or contact me at tara.ghafari at psych.ox.ac.uk. ======================= Tara Ghafari, MD-PhD Postdoctoral Research Associate Department of Psychiatry Department of Experimental Psychology University of Oxford tara.ghafari at psych.ox.ac.uk  -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PastedGraphic-1.tiff Type: image/tiff Size: 18104 bytes Desc: not available URL: From robert.oostenveld at donders.ru.nl Tue May 13 10:48:52 2025 From: robert.oostenveld at donders.ru.nl (Oostenveld, R. (Robert)) Date: Tue, 13 May 2025 08:48:52 +0000 Subject: [FieldTrip] MEG UKI 2025 conference invitation Message-ID: <9F36973E-C8C0-476F-BD68-81FF4DDB84B6@donders.ru.nl> On behalf of Yulia Bezsudnova : Dear colleague Happy to advertise MEGUKI 2025 in London at (https://www.marywardhouse.com/home) from 16th-18th July inclusive. Website now open for abstract submission and registration. https://meguk.ac.uk/meg-uki-2025/ We hope to see you all there! [Image.png] Kind regards, Gareth and Yulia -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Image.png Type: image/png Size: 59055 bytes Desc: Image.png URL: From robert.oostenveld at donders.ru.nl Thu May 15 14:26:18 2025 From: robert.oostenveld at donders.ru.nl (Oostenveld, R. (Robert)) Date: Thu, 15 May 2025 12:26:18 +0000 Subject: [FieldTrip] Neurophysics Master at Donders Institute, Radboud University Nijmegen Message-ID: Dear Fieldtrip users, On behalf of Francesco Battaglia I would like to point your attention to our renovated Master's program in Neurophysics at Radboud University Nijmegen. The program is hosted within the Donders Institute for Brain, Cognition and Behavior and is an ideal setting for students with a Physics, exact sciences background who wish to learn about the brain and pursue a career in brain research and neurotechnology. Please see below for more info and contacts, or download our brochure here https://www.dropbox.com/scl/fi/pl3g19qetscdf5t317evm/Neurophysics_master_flyer_v1.pdf?rlkey=2tm7n2hn8ekm9b0eealfcfrd6&dl=0 ============== Neurophysics master at Radboud University and the Donders Institute, Nijmegen, Netherlands * Study the brain and artificial neural networks through the lens of mathematical modeling and physics. * This 2-year masters—unique in Europe—provides a rigorous theoretical foundation in neural systems using methods from experimental physics, machine learning, and computational modelling. * Advances in network theory—illustrated by recent physics Nobel Prizes (Hinton, Hopfield, Parisi)— and brain imaging technologies are expanding research opportunities in this developing field. * Open to students from physics, science, or related backgrounds (computer science, mathematics, engineering), and awards a master degree in physics. All courses are taught in English. Curriculum * Courses in Computational Neuroscience, Machine Learning, Theory of Brain Machine Interfaces, Neurobiophysics, Theory of Complex Systems, Neural Data Analysis, and many more. * By choosing Data Science electives, the master can include an 18 EC Data Science Minor. * Many elective neuroscience courses across campus (incl. Cognitive Neuroscience / AI master). Studying at Radboud University and the Donders Institute * Radboud University is one of Europe’s leading universities in Neuroscience (#7 at research.com). * Courses are taught by faculty from the Donders institute for brain, cognition and behavior. * The Donders institute hosts more than 100 world-class neuroscience departments, offering rich internship choices for neurophysics students. * Access to cutting-edge technology: invasive neural recordings, state-of-the-art MRI, and large-scale neurotechnology initiatives like NeurotechEU and the Dutch Brain Interface Initiative. Career prospects * Trains students with a quantitative, multidisciplinary background and prepares for careers in: • Neuroscience, computational neuroscience, neuroAI, physics. • Neurotechnology, neuroprosthetics, biomedical technology. • Data science, machine learning, artificial intelligence. neuromorphic computing technologies. ============== Learn more: www.ru.nl/masters/neurophysics Rosa van Heesch +31 6 50 01 04 15 rosa.vanheesch at ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From janmathijs.schoffelen at donders.ru.nl Thu May 15 16:13:24 2025 From: janmathijs.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 15 May 2025 14:13:24 +0000 Subject: [FieldTrip] Help Running ft_postfreesurferscript.sh In-Reply-To: References: Message-ID: <6B18FA1A-7726-4671-B599-E64C54476795@donders.ru.nl> Hi Michael, The error suggests that an expected file is missing. Could it be that freesurfer produced incomplete output? (in other words: do you get an error only for this particular subject?) If you don’t need the sulc/curv/thickness information, you can also try and bypass this error by commenting out the respective lines of code in the bash-script (including the lines that rely on using the newly create .gii files of those metrics). Best wishes, Jan-Mathijs On 8 May 2025, at 15:37, Michael Houston via fieldtrip wrote: Hi, everyone! I am trying to create a cortical sheet source model from the standard colin27 brain with accompanying DKT atlas for EEG source reconstruction (single_subj.nii in Fieldtrip template directory). After doing recon-all in FreeSurfer, the resulting meshes are far too large ~160k vertices per hemisphere which is taking too long to run the source analysis on. I followed the instructions according to this tutorial (https://www.fieldtriptoolbox.org/tutorial/source/sourcemodel/) and set up the HCP-Workbench and copied the requested directory contents to a common folder to use ft_postfreesurferscript.sh to make the lower resolution cortical meshes. While I can get the script to run, I am facing the output and error copied below. If there is any other information I should provide please let me know. I am confused about this output because it looks like the error file is one that should be created by the script however it is not found. I would greatly appreciate any insight on how to fix this.: Command -------------- /mnt/c/Users/mjame/Documents/MATLAB/fieldtrip-20240504/bin/ft_postfreesurferscript.sh /usr/local/freesurfer/7.4.1/subjects single_subj /usr/local/freesurfer/7.4.1/subjects/workbench_freesurfer Output & Error -------------------- START: FS2CaretConvertRegisterNonlinear Saving /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.white.native.surf.gii as a surface in TKREGISTER space Saving /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.pial.native.surf.gii as a surface in TKREGISTER space Saving /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.sphere.reg.native.surf.gii as a surface in TKREGISTER space Saving /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.sphere.native.surf.gii as a surface in TKREGISTER space While running: wb_command -set-structure /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.sulc.native.shape.gii CORTEX_LEFT ERROR: NAME OF FILE: single_subj.L.sulc.native.shape.gii PATH TO FILE: /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench File does not exist. Thanks, Michael _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Tineke.Grent at glasgow.ac.uk Fri May 16 08:52:49 2025 From: Tineke.Grent at glasgow.ac.uk (Tineke Grent-'T-Jong) Date: Fri, 16 May 2025 06:52:49 +0000 Subject: [FieldTrip] New Post-Doc position in Berlin Message-ID: There is a new Post-Doc position available in the lab of Prof. Dr. P.J. Uhlhaas in Berlin, see below: Post-Doctoral Position in OPM-MEG Research at Charité-Universitätsmedizin, Berlin “Language Processing as a Window into Circuit Dysfunctions in Schizophrenia with Optically Pumped Magnetometers (OPMs)” is a joint project funded by the German Research Foundation (DFG) between the Laboratory for Biomarkers, Early Intervention and Digital Medicine, Charité – Universitätsmedizin Berlin (Prof. Peter Uhlhaas), the Institute for Biomagnetism and Biosignalanalysis, University of Münster (Prof. Joachim Gross), and the Dept. of Biosignals, Physikalisch-Technischen Bundesanstalt (PTB) (Prof. Peter Krüger). For this project, we are looking for a motivated post-doctoral researcher with extensive experience in electrophysiology (EEG/MEG) and data-analysis to support the team. The earliest start-date is the 1st of November 2025. The position is funded for three years (salary level: E/14). Specifically, the post-doctoral researcher shall assist in: * Execution of OPM-MEG measurements * Analysis of OPM-MEG data using source-reconstruction, time-frequency analysis and connectivity measures * Generation of manuscripts for publication * Supervision of pre-doctoral students Candidate(s) should have the following qualifications: * a masters degree in a relevant field * a completed/submitted doctoral thesis in a relevant area * extensive experience in quantitative analyses of EEG/MEG-data * strong computational and programming skills * experience in working in an interdisciplinary environment Inquiries should be directed to Prof. Peter J. Uhlhaas (peter.uhlhaas at charite.de). For applications, please submit a letter of interest, a CV plus two potential referees by the 1st of July 2025. Best wishes Tineke Grent-'t-Jong -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthias.duempelmann at uniklinik-freiburg.de Fri May 16 14:04:58 2025 From: matthias.duempelmann at uniklinik-freiburg.de (=?utf-8?B?UEQgRHIuIE1hdHRoaWFzIETDvG1wZWxtYW5u?=) Date: Fri, 16 May 2025 12:04:58 +0000 Subject: [FieldTrip] Seizure Prediction Challenge Based on Ultra Long-Term EEG Recordings Message-ID: <762d4886b8f84cbdba2c1ef70c73861c@uniklinik-freiburg.de> 5th International Congress on Mobile Health and Digital Technology in Epilepsy: Seizure Prediction Challenge Based on Ultra Long-Term EEG Recordings Epilepsy affects millions of people worldwide, and one of its most debilitating aspects is the unpredictability of seizures. Advances in machine learning and neurotechnology offer new opportunities to tackle this challenge. This competition invites researchers, data scientists, and clinicians to develop robust algorithms capable of predicting seizures using ultra long-term (months) EEG recordings with a subcutaneous EEG device. Objective Participants will create algorithms to predict seizure occurrences based on extended EEG covering several months of almost continuous subcutaneous EEG recordings in a real life setting. The focus is on detecting pre-ictal states—specific patterns or biomarkers indicating an impending seizure—while minimizing false positives to ensure practical utility. Dataset The competition dataset comprises: ● A dataset containing ultra long-term EEG recordings from three patients using a 24/7 EEG SubQ device (UNEEG medical A/S, Lynge, Denmark) is provided for the challenge. At least 25 lead seizures per patient are included in the training data. ● Annotations marking seizures. ● An independent test dataset is used to evaluate submitted algorithms Challenge Goals ● Sensitivity: High detection rate of true pre-ictal periods. ● Specificity: Minimizing false alarms to avoid undue burden on patients. ● Scalability: Algorithms must handle ultra long-term recordings efficiently. ● Generalizability: Solutions should perform well across diverse patients and seizure types. Evaluation Metrics Consider that your algorithm is developed to detect preictal periods that start 1h5min before seizures, and that a warning is useful if it is raised at least five minutes before seizures. This means that a seizure occurrence period (SOP) of 1h and an intervention time (IT) of 5 min are considered. Following metrics will be considered: ● Sensitivity(%): Defined as the ratio of predicted seizures. ● Time in warning (TiW) (%): Defined as the fraction of time spent in alarm. ● Improvement over chance (IoC) (%) ● Area Under the Receiver Operating Characteristic Curve (AUC-ROC). ● False Alarm Rate (FAR) to assess the algorithm’s reliability. Latency: Time difference between predicted pre-ictal periods and actual seizure onset. Algorithms will be ranked using AUC-ROC Competition Stages ● Development Phase: Access to training data and annotated seizures onset times for model development. Data will be supplied as EDF files. ● Submission of algorithms and models to the organizers. Submission details will be given by May 1st. Publication policy The competition organizers aim at a joint publication with the winning teams. We explicitly discourage use of the data for publications independent of this competition and this will not be covered by the download policies of the dataset. Incentive ● Presentation of the algorithms of the teams at first and second position at the 5th International Congress on Mobile Health and Digital Technology in Epilepsy ● Registration fee and hotel costs for the conference for one presenter of the two winning submissions. Who Should Participate? This challenge is open to: ● Data scientists with expertise in time-series analysis and Artificial Intelligence/Machine Learning. ● Neuroscientists and clinicians interested in translational research. ● Multidisciplinary teams combining domain knowledge and technical expertise. Impact The outcomes of this challenge have the potential to transform epilepsy management by enabling: ● Early warnings for patients, improving their quality of life. ● Development of closed-loop systems for seizure intervention. ● Insights into the neurophysiology of seizure generation. Timeline ● Publication of the training dataset and reference algorithm: May 1st; 2025 ● Submission deadline for algorithms: June 30th, 2025 ● Running the algorithms on test dataset and ranking of contributions: July, 20th, 2025 ● Presenting of winner algorithms in person or online: 4 - 6 September 2025, at International Congress on Mobile Health and Digital Technology in Epilepsy Join the Challenge Be part of this groundbreaking effort to make seizures predictable and manageable. Collaborate, innovate, and push the boundaries of neurotechnology. For more details on registration, dataset access, and timelines, visit https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fepilongcontest.cisuc.uc.pt%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C73b5cbe488014020509a08dd9471e453%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638829939081620492%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=yRtldS56VRTKhUF1eMaMt4Sms0T13VIpMvHVb3Jlahk%3D&reserved=0 or contact epilong at dei.uc.pt. On behalf the organizing team, PD Dr. Matthias Dümpelmann UNIVERSITÄTSKLINIKUM FREIBURG Abteilung Epileptologie Neurozentrum Breisacher Str. 64 · 79106 Freiburg Telefon: +49 761 270-52410 matthias.duempelmann at uniklinik-freiburg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From ayelet.landau at mail.huji.ac.il Sun May 18 18:59:53 2025 From: ayelet.landau at mail.huji.ac.il (Ayelet Landau) Date: Sun, 18 May 2025 18:59:53 +0200 Subject: [FieldTrip] M/EEG Postdoc Opportunity - Ayelet Landau's Lab - UCL Message-ID: Dear M/EEG and neurophysiology community! If you are interested in studying attention & exploration w/ cutting edge M/EEG - please get in touch. If you know any trainees who would like to join the bustling London Cognitive Neuroscience Community - send them this call!I would love to receive applications from resourceful, curious and creative cognitive neuroscientists who can join the newly forming London-based team! all details below: Research Fellow in M/EEG Research on Exploration and Attention About us We have an opening for a postdoctoral research fellow to join the Brain Attention and Time laboratory at the Department of Experimental Psychology, within the Division of Psychology and Language Sciences. The lab comprises a team of researchers and PhD students led by Prof Ayelet N. Landau . We research the psychological and neural mechanisms of attention, time perception with a specific interest in the role of rhythmic processes in cognition. The post is available for 12 months in the first instance with the possibility of further extension. About the role The postdoc researcher will work on a project investigating the neural mechanisms underlying the relationship of attention and oculomotor exploration in a naturalistic task using M/EEG. Specifically, the project involves rapid frequency tagging, the monitoring of eye movements and sophisticated assessment of behaviour and perception using psychophysics. A job description and person specification can be accessed below. Please click the ‘apply now’ button at the bottom of the page. Applications should include a covering letter and CV. For informal queries about the position, please contact: ayelet.landau at ucl.ac.uk For information about the application process, please contact: pals.hr at ucl.ac.uk About you The successful candidate will hold a PhD in cognitive neuroscience or related areas and have knowledge of a range of relevant research techniques and scientific literature. The candidate will also have experience of psychophysiological methods, preferably EEG or MEG, and strong quantitative and programming skills in time series analyses using Python/MATLAB (or equivalent). The successful applicant will have effective written and verbal communication skills, a proven ability to analyse and write up data, as well as previous experience of working in a research environment. Additional desirable skills include: knowledge of programming and analysing RIFT experiments and the resulting EEG/MEG data; expertise in the fields of the neurobiology of, and psychology of attention; ability to present complex information effectively to a range of audiences, and experience of contributing effective to the work of a team. *more info on how to apply here !* -- Ayelet N. Landau, PhD *Associate Professor * *Department of Experimental Psychology* *University College London, UK* *and* *Department of Psychology& Department of Cognitive SciencesThe Hebrew University of Jerusalem,IsraelWhatsApp +972543444039Tel +4917688493520* *https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.landaulab.com%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C3ae3a848688948ec994708dd962d71dd%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638831844114788249%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=L11D%2F%2BR1nyOp88tyHN5mpZ8TYCKfXhfEun7APIxfQj0%3D&reserved=0 * -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.jameshouston81 at gmail.com Mon May 19 01:23:54 2025 From: m.jameshouston81 at gmail.com (Michael Houston) Date: Sun, 18 May 2025 18:23:54 -0500 Subject: [FieldTrip] Help Running ft_postfreesurferscript.sh In-Reply-To: <6B18FA1A-7726-4671-B599-E64C54476795@donders.ru.nl> References: <6B18FA1A-7726-4671-B599-E64C54476795@donders.ru.nl> Message-ID: Hi Jan-Mathijs, thanks for checking this. I've looked into the script and realized that, for the issue presented above, the wb_command function was expecting the file called "single_subj.L.sulc.native.shape.gii" but it seems an earlier wb function saved the expected file as "lh.single_subj.L.sulc.native.shape.gii". After some trial and error I am able to extract and display the decimated cortical sheets and their corresponding atlases correctly with Fieldtrip visualization functions. Thanks for your help! Thanks, Michael On Thu, May 15, 2025 at 9:14 AM Schoffelen, J.M. (Jan Mathijs) via fieldtrip wrote: > Hi Michael, > > The error suggests that an expected file is missing. Could it be that > freesurfer produced incomplete output? (in other words: do you get an error > only for this particular subject?) > If you don’t need the sulc/curv/thickness information, you can also try > and bypass this error by commenting out the respective lines of code in the > bash-script (including the lines that rely on using the newly create .gii > files of those metrics). > > Best wishes, > Jan-Mathijs > > On 8 May 2025, at 15:37, Michael Houston via fieldtrip < > fieldtrip at science.ru.nl> wrote: > > Hi, everyone! I am trying to create a cortical sheet source model from the > standard colin27 brain with accompanying DKT atlas for EEG source > reconstruction (single_subj.nii in Fieldtrip template directory). After > doing recon-all in FreeSurfer, the resulting meshes are far too large ~160k > vertices per hemisphere which is taking too long to run the source analysis > on. I followed the instructions according to this tutorial ( > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fsource%2Fsourcemodel%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cc0562f63b6cb41d679fe08dd96631b53%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638832074728909298%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C60000%7C%7C%7C&sdata=BfctUY1cmdsAn9WNb7maz%2Fqd%2Bp7gMxkfpe4Phl%2F1nUU%3D&reserved=0 > ) > and set up the HCP-Workbench and copied the requested directory contents to > a common folder to use ft_postfreesurferscript.sh to make the lower > resolution cortical meshes. > > While I can get the script to run, I am facing the output and error copied > below. If there is any other information I should provide please let me > know. I am confused about this output because it looks like the error file > is one that should be created by the script however it is not found. I > would greatly appreciate any insight on how to fix this.: > > Command > -------------- > /mnt/c/Users/mjame/Documents/MATLAB/fieldtrip-20240504/bin/ft_postfreesurferscript.sh > /usr/local/freesurfer/7.4.1/subjects single_subj > /usr/local/freesurfer/7.4.1/subjects/workbench_freesurfer > > Output & Error > -------------------- > START: FS2CaretConvertRegisterNonlinear > Saving > /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.white.native.surf.gii > as a surface in TKREGISTER space > Saving > /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.pial.native.surf.gii > as a surface in TKREGISTER space > Saving > /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.sphere.reg.native.surf.gii > as a surface in TKREGISTER space > Saving > /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.sphere.native.surf.gii > as a surface in TKREGISTER space > > While running: > wb_command -set-structure > /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench/single_subj.L.sulc.native.shape.gii > CORTEX_LEFT > > ERROR: NAME OF FILE: single_subj.L.sulc.native.shape.gii > PATH TO FILE: /usr/local/freesurfer/7.4.1/subjects/single_subj/workbench > > File does not exist. > > Thanks, > Michael > _______________________________________________ > fieldtrip mailing list > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cc0562f63b6cb41d679fe08dd96631b53%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638832074728953135%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C60000%7C%7C%7C&sdata=dm4xNyMTT%2Fo%2FlPo%2BEYFbJMH15T%2B7%2FJK0NgdyIfvf0yo%3D&reserved=0 > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cc0562f63b6cb41d679fe08dd96631b53%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638832074728966331%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C60000%7C%7C%7C&sdata=leXIIqKTo3oxFLhbD5CopS%2FT4LhJaj94zUOLhG%2BMYrs%3D&reserved=0 > > > _______________________________________________ > fieldtrip mailing list > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cc0562f63b6cb41d679fe08dd96631b53%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638832074728980420%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C60000%7C%7C%7C&sdata=WDqn0dlOBwmul4tNEmWzfrEt%2BLNtarE7QKzc3i794uA%3D&reserved=0 > https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cc0562f63b6cb41d679fe08dd96631b53%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638832074728993147%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C60000%7C%7C%7C&sdata=ylEAD3cD4isBeQGTlTJ%2BMLi1LhIwhx5n0YKA2oOF35U%3D&reserved=0 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From aurelie.bidet-caulet at inserm.fr Wed May 21 15:37:57 2025 From: aurelie.bidet-caulet at inserm.fr (=?UTF-8?Q?Aur=C3=A9lie_Bidet-Caulet?=) Date: Wed, 21 May 2025 15:37:57 +0200 Subject: [FieldTrip] Announcement: OPM Workshop in Marseille - October 2-3 In-Reply-To: <20250324120802.A8D7F1F64D@ccsdcron.ccsd.cnrs.fr> References: <20250324120802.A8D7F1F64D@ccsdcron.ccsd.cnrs.fr> Message-ID: <0edfb6c8-2cc4-4f7c-879e-33e20713496a@inserm.fr> header_logo OPMs: The future of MEG Dear speakers and moderators, I’m pleased to share the official announcement for our upcoming workshop! Please take a moment to *register through the website*, including your *updated institutional affiliation* and any other relevant details. This will help us keep the program accurate and up-to-date. We would also greatly appreciate it if you could *help us disseminate the workshop information* through your networks and mailing lists. The success of the event relies greatly on your support and outreach. Thank you once again for being part of this event — we’re very much looking forward to your contributions! Warm regards, Organization Committee OPM 2025 Conference OPMs: The Future of Magnetoencephalography? Marseille, October 2-3, 2025 Join leading experts in the field of optically pumped magnetometers (OPMs) to explore the latest advances in this technology and its potential for the understanding of the human brain and for clinical applications. Confirmed Speakers Gareth BarnesUniversity College London, UK James BonaiutoUniversity Lyon, France Francesca BoniniAix-Marseille University, France Matthew BrookesThe University of Nottingham, UK Sarang DalalAarhus University, Denmark Xavier De TiègeUniversité libre de Bruxelles, Belgium Nathalie GeorgeSorbonne University, France Julien JungNeuroscience Research Center in Lyon, France Jan Mathijs SchoffelenRadboud University, The Netherlands Robert OostenveldRadboud University, The Netherlands Lauri ParkonnenAalto University, Finland Margot TaylorSickKids Research Institute, Canada Fabrice WalloisJules Verne University of Picardie, France Caroline WittonAston University, UK Okito YamashitaAdvanced Telecommunications Research Institute International, Japan Learn More & Register -------------- next part -------------- An HTML attachment was scrubbed... URL: From 3190101881 at zju.edu.cn Wed May 28 11:21:10 2025 From: 3190101881 at zju.edu.cn (Shikai Chen) Date: Wed, 28 May 2025 17:21:10 +0800 Subject: [FieldTrip] Can I define the trials with only header, data, and event Message-ID: Dear all members, May I ask if I can define the trials with only header, data, and event? I see cfg.dataset = “filename” and can I use the information of header, data, and event instead? These are generated by ft_read_header, ft_read_data and ft_read_event. My MEG data is recorded into two data sets accidentally. So I combine these two into one using ft_read_header, ft_read_data and ft_read_event and cat. But I didn’t find the “MEG "format in ft_write_data and other formats would lose some information and regard the data as EEG data. So how can I make some changes to the following code? hdr1 = ft_read_header(filename1); dat1 = ft_read_data(filename1); evt1 = ft_read_event(filename1); hdr2 = ft_read_header(filename2); dat2 = ft_read_data(filename2); evt2 = ft_read_event(filename2); hdr = hdr1; hdr.nSamples = hdr1.nSamples + hdr2.nSamples; dat = cat(2,dat1,dat2); nsamples1 = hdr1.nSamples; for i = 1:length(evt2) evt2(i).sample = evt2(i).sample + nsamples1; end evt = cat(1,evt1,evt2); cfg = []; cfg.dataset = [path, '\data.vhdr’]; cfg.trialfun = 'trialfun_conditionaltrigger’; cfg.trialdef.pre = 5; cfg.trialdef.post = 68; cfg = ft_definetrial(cfg); data = ft_preprocessing(cfg); Thank you so much for your help! Best, Shikai -------------- next part -------------- An HTML attachment was scrubbed... URL: From mklados at gmail.com Wed May 28 13:30:55 2025 From: mklados at gmail.com (Manousos Klados) Date: Wed, 28 May 2025 14:30:55 +0300 Subject: [FieldTrip] =?utf-8?q?Brain_Graphs_Workshop_=E2=80=93_50=25_Disc?= =?utf-8?q?ount_Vouchers_for_Students_=26_Researchers?= Message-ID: Dear Colleagues, I hope this message finds you well. I'm writing to share an exciting update about our upcoming workshop *“Brain Graphs: From Zero to Hero”* – a hands-on workshop on brain connectivity analysis scheduled for *June 7, 2025 (11:00–13:00 EEST)* as a live online session. After an overwhelming response, our early-bird registration has sold out. In line with our commitment to inclusivity and global reach, we are launching a new initiative to make the workshop more accessible to early-career researchers and colleagues facing financial barriers. As part of this effort, we are offering a limited number of *5**0% discount vouchers* for eligible participants. These vouchers are available upon request to *MSc and PhD students*, as well as *researchers from financially under-resourced or underrepresented regions*. We strongly believe that cost should not be a barrier for passionate learners, so we hope this initiative will enable more early-career scholars from around the world to participate. (With the 50% voucher, the standard $100 registration fee is reduced to $50.) Please note that the number of vouchers is limited (first-come, first-served) and each is subject to availability, so eligible participants are encouraged to request one soon. *Why attend “Brain Graphs: From Zero to Hero”?* This workshop offers a rich, hands-on introduction to brain connectivity and graph theory in neuroscience. By joining, you will: - *Gain practical skills:* Learn to preprocess and analyze neuroimaging data (fMRI, EEG, MEG, fNIRS) to construct and interpret functional connectivity matrices. - *Hands-on experience:* Engage in practical sessions to build and analyze brain network models (applying graph theory to real datasets). - *Graph theory insights:* Explore the fundamentals of functional connectivity and graph theory in neuroscience through interactive exercises with real data. - *Apply it to your research:* Develop the ability to interpret connectivity results and immediately apply these techniques in your own research projects. Whether you work with fMRI, EEG, MEG, or fNIRS, this is a fantastic opportunity to strengthen your analytical toolkit in neuroimaging. The skills and knowledge gained will be directly relevant to anyone dealing with brain data, from functional MRI connectivity analysis to EEG/MEG network modeling. *Registration Link: * https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mklados.com%2Fevent-details%2Fbrain-graphs-from-zero-to-hero-hands-on-workshop-on-connectivity&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Ca926a2fbaa2d4713cfd708dd9ddb25c0%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638840286734081911%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=UjT8mbWbfoh9gTpU7RC%2FeQWthMw2tZ%2BJHnep7MWDTIo%3D&reserved=0 To register for the workshop, please visit the link above. If you are eligible for a voucher and would like to request one, simply reply to this email or contact us to receive your personal discount code. We will be happy to provide the 50% off voucher to qualifying participants as long as vouchers remain available (on a first-come, first-served basis). We are committed to inclusivity and global participation – no matter where you are located, we want to support your learning and collaboration in this field. If you have any questions or need more information, feel free to reach out. We are happy to assist and want to ensure everyone interested can attend. Thank you for your attention and support in helping us make *“Brain Graphs: >From Zero to Hero”* a welcoming, enriching experience for all. We look forward to seeing you at the workshop and embarking on this journey from zero to hero in brain connectivity analysis together! Kind Regards Manousos Klados *Dr. Manousos Klados*, MSc, PhD. PGCert. FHEA, FIMA Associate Professor in Psychology Director of MSc/MA in Cognitive/Clinical Neuropsychology Editor in Chief of Brain Organoid and System Neuroscience Journal Scientific Consultant NIRx _______________________________________________ *Department of Psychology, **CITY College,** University of York Europe Campus* 24 Pr. 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URL: From janmathijs.schoffelen at donders.ru.nl Wed May 28 14:10:42 2025 From: janmathijs.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 28 May 2025 12:10:42 +0000 Subject: [FieldTrip] Can I define the trials with only header, data, and event In-Reply-To: References: Message-ID: <6D5D0380-7CAB-4E16-A415-6D8A4A0C4C32@donders.ru.nl> Hi Shikai, Please can you reformulate your question a bit more coherently (provided the below does not give you enough pointers to proceed with your endeavours)? You mention a lot of functions and a lot of things, but it is unclear what you really aim to achieve. It’s unclear why you think that you need to use ft_write_data to ’stitch’ two raw datafiles together in a ‘raw’ fileformat that is the same (or similar) as the vendor specific acquisition system. If you are facing the reality that the data recorded from a single subject ended up in 2 datafiles, and need to be processed together at some point, then import/epoch the data per file, and append the two resulting data structures in FieldTrip, using ft_appenddata. Good luck, Jan-Mathijs May I ask if I can define the trials with only header, data, and event? I see cfg.dataset = “filename” and can I use the information of header, data, and event instead? These are generated by ft_read_header, ft_read_data and ft_read_event. My MEG data is recorded into two data sets accidentally. So I combine these two into one using ft_read_header, ft_read_data and ft_read_event and cat. But I didn’t find the “MEG "format in ft_write_data and other formats would lose some information and regard the data as EEG data. So how can I make some changes to the following code? hdr1 = ft_read_header(filename1); dat1 = ft_read_data(filename1); evt1 = ft_read_event(filename1); hdr2 = ft_read_header(filename2); dat2 = ft_read_data(filename2); evt2 = ft_read_event(filename2); hdr = hdr1; hdr.nSamples = hdr1.nSamples + hdr2.nSamples; dat = cat(2,dat1,dat2); nsamples1 = hdr1.nSamples; for i = 1:length(evt2) evt2(i).sample = evt2(i).sample + nsamples1; end evt = cat(1,evt1,evt2); cfg = []; cfg.dataset = [path, '\data.vhdr’]; cfg.trialfun = 'trialfun_conditionaltrigger’; cfg.trialdef.pre = 5; cfg.trialdef.post = 68; cfg = ft_definetrial(cfg); data = ft_preprocessing(cfg); Thank you so much for your help! Best, Shikai _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From 3190101881 at zju.edu.cn Thu May 29 16:20:22 2025 From: 3190101881 at zju.edu.cn (Shikai Chen) Date: Thu, 29 May 2025 22:20:22 +0800 Subject: [FieldTrip] Can I define the trials with only header, data, and event (Schoffelen, J.M. (Jan Mathijs)) In-Reply-To: References: Message-ID: <69EC1135-8743-4671-BC16-DDB23DDFCEEF@zju.edu.cn> Hi Jan-Mathijs, Thank you so much for your reply! I want to define the trials, but I found in the tutorials, I have to use the name of the MEG data, like cfg.dataset = ‘filename”. And my two data files are continuous—the second starts in the middle of one trial from the first one. So I want to combine them into one, save the data as new file and then define the trials. I was wondering if I have to use cfg.dataset = ‘filename”. I also tried ft_appenddata. But I am confused what should I do after this to define the trials. When I had the defined trials in cfg, and tried this: data = ft_preprocessing(cfg,data), it shows warning: The field cfg.trl is forbidden, it will be removed from your configuration. So I can’t successfully define the trials through this. Thank you again for your help! Best, Shikai > 2025年5月29日 18:00,fieldtrip-request at science.ru.nl 写道: > > Hi Shikai, > > Please can you reformulate your question a bit more coherently (provided the below does not give you enough pointers to proceed with your endeavours)? You mention a lot of functions and a lot of things, but it is unclear what you really aim to achieve. It’s unclear why you think that you need to use ft_write_data to ’stitch’ two raw datafiles together in a ‘raw’ fileformat that is the same (or similar) as the vendor specific acquisition system. > > If you are facing the reality that the data recorded from a single subject ended up in 2 datafiles, and need to be processed together at some point, then import/epoch the data per file, and append the two resulting data structures in FieldTrip, using ft_appenddata. > > Good luck, > Jan-Mathijs > > May I ask if I can define the trials with only header, data, and event? I see cfg.dataset = “filename” and can I use the information of header, data, and event instead? These are generated by ft_read_header, ft_read_data and ft_read_event. > > My MEG data is recorded into two data sets accidentally. So I combine these two into one using ft_read_header, ft_read_data and ft_read_event and cat. But I didn’t find the “MEG "format in ft_write_data and other formats would lose some information and regard the data as EEG data. So how can I make some changes to the following code? > hdr1 = ft_read_header(filename1); > dat1 = ft_read_data(filename1); > evt1 = ft_read_event(filename1); > hdr2 = ft_read_header(filename2); > dat2 = ft_read_data(filename2); > evt2 = ft_read_event(filename2); > hdr = hdr1; > hdr.nSamples = hdr1.nSamples + hdr2.nSamples; > dat = cat(2,dat1,dat2); > nsamples1 = hdr1.nSamples; > for i = 1:length(evt2) > evt2(i).sample = evt2(i).sample + nsamples1; > end > evt = cat(1,evt1,evt2); > > cfg = []; > cfg.dataset = [path, '\data.vhdr’]; > cfg.trialfun = 'trialfun_conditionaltrigger’; > cfg.trialdef.pre = 5; > cfg.trialdef.post = 68; > cfg = ft_definetrial(cfg); > data = ft_preprocessing(cfg); > Thank you so much for your help! > > Best, > Shikai -------------- next part -------------- An HTML attachment was scrubbed... URL: From janmathijs.schoffelen at donders.ru.nl Thu May 29 19:09:05 2025 From: janmathijs.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Thu, 29 May 2025 17:09:05 +0000 Subject: [FieldTrip] Can I define the trials with only header, data, and event In-Reply-To: <69EC1135-8743-4671-BC16-DDB23DDFCEEF@zju.edu.cn> References: <69EC1135-8743-4671-BC16-DDB23DDFCEEF@zju.edu.cn> Message-ID: <61CBB4F2-3937-4415-A204-04AD40452E92@donders.ru.nl> Hi Shikai, If I understand correctly, you have a - what you call - ’trial’ for which a part is represented in datafile1, and another part is represented in datafile2. From what you describe, I can only conclude that there is a temporal discontinuity from the end of datafile1 to the beginning of datafile2. In other words, it does not make sense to salvage this trial by sticking the ends together, so consider this trial lost for further analysis. Good luck with your analysis endeavours, Jan-Mathijs On 29 May 2025, at 16:20, Shikai Chen via fieldtrip wrote: Hi Jan-Mathijs, Thank you so much for your reply! I want to define the trials, but I found in the tutorials, I have to use the name of the MEG data, like cfg.dataset = ‘filename”. And my two data files are continuous—the second starts in the middle of one trial from the first one. So I want to combine them into one, save the data as new file and then define the trials. I was wondering if I have to use cfg.dataset = ‘filename”. I also tried ft_appenddata. But I am confused what should I do after this to define the trials. When I had the defined trials in cfg, and tried this: data = ft_preprocessing(cfg,data), it shows warning: The field cfg.trl is forbidden, it will be removed from your configuration. So I can’t successfully define the trials through this. Thank you again for your help! Best, Shikai 2025年5月29日 18:00,fieldtrip-request at science.ru.nl 写道: Hi Shikai, Please can you reformulate your question a bit more coherently (provided the below does not give you enough pointers to proceed with your endeavours)? You mention a lot of functions and a lot of things, but it is unclear what you really aim to achieve. It’s unclear why you think that you need to use ft_write_data to ’stitch’ two raw datafiles together in a ‘raw’ fileformat that is the same (or similar) as the vendor specific acquisition system. If you are facing the reality that the data recorded from a single subject ended up in 2 datafiles, and need to be processed together at some point, then import/epoch the data per file, and append the two resulting data structures in FieldTrip, using ft_appenddata. Good luck, Jan-Mathijs May I ask if I can define the trials with only header, data, and event? I see cfg.dataset = “filename” and can I use the information of header, data, and event instead? These are generated by ft_read_header, ft_read_data and ft_read_event. My MEG data is recorded into two data sets accidentally. So I combine these two into one using ft_read_header, ft_read_data and ft_read_event and cat. But I didn’t find the “MEG "format in ft_write_data and other formats would lose some information and regard the data as EEG data. So how can I make some changes to the following code? hdr1 = ft_read_header(filename1); dat1 = ft_read_data(filename1); evt1 = ft_read_event(filename1); hdr2 = ft_read_header(filename2); dat2 = ft_read_data(filename2); evt2 = ft_read_event(filename2); hdr = hdr1; hdr.nSamples = hdr1.nSamples + hdr2.nSamples; dat = cat(2,dat1,dat2); nsamples1 = hdr1.nSamples; for i = 1:length(evt2) evt2(i).sample = evt2(i).sample + nsamples1; end evt = cat(1,evt1,evt2); cfg = []; cfg.dataset = [path, '\data.vhdr’]; cfg.trialfun = 'trialfun_conditionaltrigger’; cfg.trialdef.pre = 5; cfg.trialdef.post = 68; cfg = ft_definetrial(cfg); data = ft_preprocessing(cfg); Thank you so much for your help! Best, Shikai _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From 3190101881 at zju.edu.cn Fri May 30 03:19:11 2025 From: 3190101881 at zju.edu.cn (Shikai Chen) Date: Fri, 30 May 2025 09:19:11 +0800 Subject: [FieldTrip] Can I define the trials with only header, data, and event In-Reply-To: <61CBB4F2-3937-4415-A204-04AD40452E92@donders.ru.nl> References: <61CBB4F2-3937-4415-A204-04AD40452E92@donders.ru.nl> Message-ID: Hi Jan-Mathijs, OK! Thank you so much for your help! Best, Shikai > On 30 May 2025, at 01:09, Schoffelen, J.M. (Jan Mathijs) wrote: > >  Hi Shikai, > > If I understand correctly, you have a - what you call - ’trial’ for which a part is represented in datafile1, and another part is represented in datafile2. From what you describe, I can only conclude that there is a temporal discontinuity from the end of datafile1 to the beginning of datafile2. In other words, it does not make sense to salvage this trial by sticking the ends together, so consider this trial lost for further analysis. > > Good luck with your analysis endeavours, > Jan-Mathijs > > >>> On 29 May 2025, at 16:20, Shikai Chen via fieldtrip wrote: >>> >>> Hi Jan-Mathijs, >>> >>> Thank you so much for your reply! I want to define the trials, but I found in the tutorials, I have to use the name of the MEG data, like cfg.dataset = ‘filename”. And my two data files are continuous—the second starts in the middle of one trial from the first one. So I want to combine them into one, save the data as new file and then define the trials. I was wondering if I have to use cfg.dataset = ‘filename”. >>> >>> I also tried ft_appenddata. But I am confused what should I do after this to define the trials. When I had the defined trials in cfg, and tried this: data = ft_preprocessing(cfg,data), it shows warning: The field cfg.trl is forbidden, it will be removed from your configuration. So I can’t successfully define the trials through this. >>> >>> Thank you again for your help! >>> >>> Best, >>> Shikai >>> >>> 2025年5月29日 18:00,fieldtrip-request at science.ru.nl 写道: >>> >>> Hi Shikai, >>> >>> Please can you reformulate your question a bit more coherently (provided the below does not give you enough pointers to proceed with your endeavours)? You mention a lot of functions and a lot of things, but it is unclear what you really aim to achieve. It’s unclear why you think that you need to use ft_write_data to ’stitch’ two raw datafiles together in a ‘raw’ fileformat that is the same (or similar) as the vendor specific acquisition system. >>> >>> If you are facing the reality that the data recorded from a single subject ended up in 2 datafiles, and need to be processed together at some point, then import/epoch the data per file, and append the two resulting data structures in FieldTrip, using ft_appenddata. >>> >>> Good luck, >>> Jan-Mathijs >>> >>> May I ask if I can define the trials with only header, data, and event? I see cfg.dataset = “filename” and can I use the information of header, data, and event instead? These are generated by ft_read_header, ft_read_data and ft_read_event. >>> >>> My MEG data is recorded into two data sets accidentally. So I combine these two into one using ft_read_header, ft_read_data and ft_read_event and cat. But I didn’t find the “MEG "format in ft_write_data and other formats would lose some information and regard the data as EEG data. So how can I make some changes to the following code? >>> hdr1 = ft_read_header(filename1); >>> dat1 = ft_read_data(filename1); >>> evt1 = ft_read_event(filename1); >>> hdr2 = ft_read_header(filename2); >>> dat2 = ft_read_data(filename2); >>> evt2 = ft_read_event(filename2); >>> hdr = hdr1; >>> hdr.nSamples = hdr1.nSamples + hdr2.nSamples; >>> dat = cat(2,dat1,dat2); >>> nsamples1 = hdr1.nSamples; >>> for i = 1:length(evt2) >>> evt2(i).sample = evt2(i).sample + nsamples1; >>> end >>> evt = cat(1,evt1,evt2); >>> >>> cfg = []; >>> cfg.dataset = [path, '\data.vhdr’]; >>> cfg.trialfun = 'trialfun_conditionaltrigger’; >>> cfg.trialdef.pre = 5; >>> cfg.trialdef.post = 68; >>> cfg = ft_definetrial(cfg); >>> data = ft_preprocessing(cfg); >>> Thank you so much for your help! >>> >>> Best, >>> Shikai >> >> _______________________________________________ >> fieldtrip mailing list >> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C461c28055bdf43183d3d08dd9f180c10%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638841647827827902%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=n0weLyCEb82XeLFDdHoBTa%2BNYJRzf8qoxD58mF1aafk%3D&reserved=0 >> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C461c28055bdf43183d3d08dd9f180c10%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638841647827867614%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=pYR%2BuA%2FBbtxuutjJPnEqp3KY29dB%2BNKKIejflyQkB7E%3D&reserved=0 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From psc.dav at gmail.com Wed May 28 19:06:08 2025 From: psc.dav at gmail.com (David Pascucci) Date: Wed, 28 May 2025 19:06:08 +0200 Subject: [FieldTrip] PhD Position in visual perception and EEG Message-ID: *PhD Position in Visual Perception – Joint Opportunity in Iceland and Switzerland* The *Icelandic Vision Lab* (https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvisionlab.is%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C0d818a3173254b6ec7c108dd9e09fbfe%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638840487897860877%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=AsrpxAhpD1TXq%2BZk%2FjSgSB7fRjsTlCGLnPEXEeVVcTA%3D&reserved=0) at the University of Iceland and the *Psychophysics and Neural Dynamics Lab* (PND ) at the University of Lausanne and Lausanne University Hospital (CHUV) invite applications for a fully funded 3-year PhD position, supported by the University of Iceland Research Fund. *Supervisors:* - Prof. Árni Kristjánsson (University of Iceland) - Prof. David Pascucci (University of Lausanne & CHUV) - In collaboration with Prof. David Whitney (UC Berkeley) The successful candidate will be primarily based in Reykjavík, with research visits to Lausanne, engaging with two complementary research environments. ------------------------------ *Project Title* *Out of the Corner of the Eye and Back: Functional Interactions between Foveal and Peripheral Vision* *Project Summary* Peripheral vision is often perceived as blurred or disorganized compared to the sharp detail of central (foveal) vision. This has led to the view that these systems operate largely independently. This project challenges that assumption by investigating how foveal and peripheral vision interact in real time. The work will involve visual *psychophysics*, *EEG*, and *computational* *modeling*, conducted across both research sites. ------------------------------ *Candidate Profile* Applicants should hold a Master’s degree in Neuroscience, Psychology, Biology, Engineering, Computer Science, Mathematics, or a related field. Experience in visual perception is welcome but not required. *Preferred skills:* - Psychophysics software (e.g., PsychoPy, Psychtoolbox) - Programming (e.g., Python, MATLAB, C/C++) - EEG and/or computational modeling - Statistical analysis (e.g., in R) We seek dedicated, enthusiastic candidates with strong motivation to contribute to interdisciplinary research. ------------------------------ *Research Environment* The *Icelandic Vision Lab* is an internationally active group with state-of-the-art facilities for eye tracking, EEG, and high-precision psychophysics. The *PND Lab* in Lausanne brings strong expertise in visual cognition, EEG, and computational methods, embedded within the collaborative research ecosystem of UNIL and CHUV. ------------------------------ *Why Apply?* Iceland and Switzerland offer outstanding research environments and exceptional quality of life, regularly ranking high in global indices of happiness, safety, and equality. We welcome applications from candidates of all backgrounds and genders. ------------------------------ *Contact* For informal inquiries, feel free to contact the supervisors directly. ak at hi.is david.pascucci at chuv.ch We look forward to hearing from you! [image: Post_ppt.png] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Post_ppt.png Type: image/png Size: 94499 bytes Desc: not available URL: