From tine.kolenik at login5.org  Mon Oct  2 16:38:29 2023
From: tine.kolenik at login5.org (Tine Kolenik)
Date: Mon, 2 Oct 2023 16:38:29 +0200
Subject: [FieldTrip] EGI EEG systems for sale (10x128 caps, 3x256 caps,
 amps ...)
Message-ID: <CALEzWsx9qk5n_dQPKRamay00qUdwVJ10UOPQ7Ct-D5NQgyKtNg@mail.gmail.com>

Dear all,

A former EEG lab AST from Slovenia is selling its EGI EEG systems.

The systems have been professionally evaluated for possible technical
issues and a full report on them can be produced (some caps have some dead
electrodes).

There are two full GES 400 systems
<https://www.egi.com/research-division/eeg-systems/geodesic-eeg-systems>
available (together with GES power supplies and Black Box fiber optic
network boxes), together (and compatible) with 10x128-channel caps and
3x256-channel caps.

We can offer a very good price on the systems. If there is any interest,
please write to me at tine.kolenik at login5.org. I would also appreciate
sharing any contact that would possibly be interested in this equipment.

Thank you,
Tine Kolenik

-- 
Tine Kolenik

*Human Research & Data Analytics Lead*
End Consumer Product | LoginEKO | Login5 Foundation
tine.kolenik at login5.org | logineko.com <https://www.logineko.com/> |
<https://www.logineko.com/>login5.org <https://www.login5.org/>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231002/4397e5cc/attachment.htm>

From marios.philiastides at gmail.com  Sat Oct  7 10:43:58 2023
From: marios.philiastides at gmail.com (Marios Philiastides)
Date: Sat, 7 Oct 2023 09:43:58 +0100
Subject: [FieldTrip] Postdoctoral fellow positions in learning and decision
 neuroscience
Message-ID: <CANrv7RMULvNEhaRGuQebUnexEzpZ=k6eqjHuxQCqowQuBx1Yag@mail.gmail.com>

We have an opportunity for two postdoctoral research positions - funded by
the  ERC - to work in our lab at the Centre for Cognitive Neuroimaging
(CCNi), within the School of Psychology and Neuroscience at the University
of Glasgow. The School of Psychology and Neuroscience is a world-class
research and teaching unit and it has recently been rated 4th in the UK and
1st in Scotland on research outputs (REF2021).



The posts have a strong computational cognitive neuroimaging component,
requiring advances in *1) theoretical neuroscience* – to enable the
development of a unified computational framework for integrating perceptual
and reward learning and decision making – and *2) multimodal brain imaging* –
to offer a high spatiotemporal characterisation of the relevant cortical
and subcortical pathways. Main research themes include, but not limited to:
reinforcement learning and valuation, risk and uncertainty, confidence and
metacognition, evidence integration and decision making.


The post holders will have the opportunity to be involved in cutting-edge
bespoke neuroimaging technology [3T/7TfMRI-EEG fusion] and advanced data
analytics to uncover and predict patterns in large multimodal datasets
[e.g. behaviour, simultaneous EEG-fMRI and eye-tracking data]. Please see
below for representative lab publications.


Apply here:
https://www.jobs.ac.uk/job/DDD932/research-assistant-associate-postdoctoral-2-posts


This post is full time and has funding up to 31st May 2026 in the first
instance with the possibility for an extension beyond this date.


Related Publications:

[1] Elsa Fouragnan, Chris Retzler, Karen Mullinger and Marios G.
Philiastides (2015), *Two spatiotemporally distinct value systems shape
reward-based learning in the human brain*, Nature Communications, 6: 8107.

[2] Sabina Gherman and Marios G. Philiastides (2018), *Human VMPFC encodes
early signatures of confidence in perceptual decisions*, eLife, 7: e38293.

[3] Tarryn Balsdon, Stijn Verdonck, Tim Loossens, and Marios G.
Philiastides (2023), *Secondary motor integration as a final arbiter in
sensorimotor decision-making, *PLOS Biology 21(7): e3002200

[4] Tarryn Balsdon,
<http://orcid.org/0000-0001-6087-2597%22%20%5Ct%20%22_blank>M.
Andrea Pisauro,
<http://orcid.org/0000-0002-7683-3506%22%20%5Ct%20%22_blank> Marios
G. Philiastides (2023), Distinct basal ganglia contributions to learning
from implicit and explicit value signals in perceptual
decision-making, bioRxiv,
doi: https://doi.org/10.1101/2023.09.05.556317

-- 

Marios G. Philiastides, Ph.D.
Professor of Decision Neuroscience
School of Psychology and Neuroscience
Centre for Cognitive Neuroimaging
University of Glasgow
Glasgow, G12 8QB

Web: https://mphiliastides.org <http://mphiliastides.org>
Email: marios.philiastides at glasgow.ac.uk
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231007/93d53996/attachment.htm>

From KCross at mednet.ucla.edu  Tue Oct 10 00:40:05 2023
From: KCross at mednet.ucla.edu (Cross, Kathryn A.)
Date: Mon, 9 Oct 2023 22:40:05 +0000
Subject: [FieldTrip] Lab Manager/Research Assistant Position @ UCLA
Message-ID: <IA1PR12MB761603D8CFE08377CA09057293CEA@IA1PR12MB7616.namprd12.prod.outlook.com>

Dear colleagues, I would appreciate your help in forwarding the advertisement to relevant members of your team or department.


My lab in the Neurology Department at UCLA is seeking a full-time Laboratory Manager / Research Assistant to provide support for ongoing research investigating electrophysiological mechanisms of movement and gait in patients with Parkinson's disease and other Movement Disorders. We use a variety of techniques in controlled and naturalistic settings, including: EEG, intracranial recordings from deep brain stimulation devices, functional and structural MRI, virtual reality and motion capture.
Applicants seeking additional research experience in preparation for graduate school are encouraged to apply.

Responsibilities include patient recruitment, screening and scheduling; coordination of multiple projects and team members; regulatory submissions and compliance; administration of cognitive and neuropsychological tests; electrophysiology and imaging data collection and data entry; maintenance of study documents; electrophysiology or neuroimaging data analysis depending on interest and skills.

Qualifications & requirements:

  *   Minimum 2 year commitment with possibility of extension
  *   Bachelor's or higher in Psychology, Neuroscience, Data science or related field
  *   Superior communication skills
  *   Previous experience with human neuroscience research, functional imaging and/or electrophysiology is desirable

APPLY HERE:  https://uclahealth.avature.net/careers/JobDetail/9706
Please include a brief statement of research interests/experience in addition to the required documents.






Katy Cross, M.D., Ph.D.
Assistant Professor of Neurology
Movement Disorders Program
David Geffen School of Medicine at UCLA
710 Westwood Ave, Reed A153
Los Angeles, CA 90095
crosslab.dgsom.ucla.edu<http://crosslab.dgsom.ucla.edu/>


________________________________

UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231009/4d57aa12/attachment.htm>

From preted at mcmaster.ca  Thu Oct 12 21:56:05 2023
From: preted at mcmaster.ca (David Prete)
Date: Thu, 12 Oct 2023 19:56:05 +0000
Subject: [FieldTrip] Correction for multiple cluster permutation analysis?
Message-ID: <YTBPR01MB3837FD6BE83E9F12736A0AD0D6D3A@YTBPR01MB3837.CANPRD01.PROD.OUTLOOK.COM>

An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231012/1b630761/attachment.htm>

From ulrich.pomper at univie.ac.at  Fri Oct 13 20:26:49 2023
From: ulrich.pomper at univie.ac.at (Ulrich Pomper)
Date: Fri, 13 Oct 2023 20:26:49 +0200
Subject: [FieldTrip] PhD position in Visual Attention, Vienna, Austria
In-Reply-To: <636901e2b2dd7a7c5a9f53ec2cd95c94@univie.ac.at>
References: <636901e2b2dd7a7c5a9f53ec2cd95c94@univie.ac.at>
Message-ID: <3caadcd52a4d72bad59edbaad28ab4f7@univie.ac.at>

Dear colleagues,

In the group of Prof. Ulrich Ansorge, we have a PhD position (30 
hrs/week) in the area of visual attention research open at the 
University of Vienna. Planned start is November 15th, 2023, and the 
advertisement is open until October 22nd, 2023. Your major task is to 
conduct research in the topical focus area of the group (e.g., visual 
attention, eye-tracking, perception) to work toward your doctoral 
degree. This includes planning, programming, and running of experiments 
with human participants, as well as analyses and write up of the 
resulting data. The corresponding manuscripts should be published in ISI 
listed, peer-reviewed journals, so as to allow a cumulative dissertation 
based on at least three manuscripts, at least one of which needs to be 
accepted for publication at the time of the submission of your PhD 
thesis for independent and external review. Job ID is 1388. Further 
information can be found here: 
https://jobs.univie.ac.at/job/University-assistant-predoctoral/988791301/. 
Please apply via the job portal of the University of Vienna, 
https://career5.successfactors.eu/careers?company=univie.

Also, you can contact ulrich.ansorge at univie.ac.at for additional 
inquiries about the position.

Kind regards,

Ulrich Pomper

-- 
Dr. Ulrich Pomper

Senior Scientist
Department of Cognition, Emotion, and Methods in Psychology
  University of Vienna
  Liebiggasse 5
  1010 Vienna
  Austria

www.rhythmsincognition.org [1]
ulrich.pomper at univie.ac.at
+43-1-4277-47149 [2]



Links:
------
[1] http://www.rhythmsincognition.org
[2] tel:+431-4277-47149
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231013/2768c18c/attachment.htm>

From ronconi.luca at unisr.it  Mon Oct 16 15:56:52 2023
From: ronconi.luca at unisr.it (Ronconi Luca)
Date: Mon, 16 Oct 2023 13:56:52 +0000
Subject: [FieldTrip] 2 years post-doc position - EEG/tES - Milan, Italy
Message-ID: <AS8PR02MB8295C9CCF075749D5D191FA2F7D7A@AS8PR02MB8295.eurprd02.prod.outlook.com>

Dear colleagues,

One post-doctoral position (‘assegno di ricerca’) is available for 2 years in my laboratory (www.bdaclab.com<http://www.bdaclab.com>) at the School of Psychology of Vita-Salute San Raffaele University in Milan, to work on a recently funded project entitled: “Investigating the plasticity of human predictive coding through neuromodulation” (Italian Ministry of University and Research – MUR; PRIN PNRR 2022).

The project aims at studying the plasticity of neural networks underlying predictive processes in the context of human perception. It will make use of different and complementary non-invasive brain stimulation (NIBS) approaches that have the potential to modulate the precision of sensory sampling, as well as the learning and exploitation of statistical regularities (i.e. the ability to generate predictive models).

The project entails a close collaboration with the laboratory of Prof. Vincenzo Romei at the University of Bologna, and with the laboratory of Dr. Luca Battaglini and Prof. Marco Bertamini at University of Padova.

The ideal candidate has (or is about to obtain) a PhD in psychology, cognitive neuroscience, or a related field, and experience in using electroencephalography (EEG) and transcranial electrical stimulation (tES: e.g. tACS, tDCS, tRNS or other non-invasive brain stimulation techniques) in humans. Expertise in analyzing multidimensional data (EEG, behavioral, etc.) is also required.

Interested candidates should send their CV to the P.I., Prof. Luca Ronconi (ronconi.luca at unisr.it<mailto:ronconi.luca at unisr.it>) with a brief motivational statement and the contact of at least one academic reference.
They are welcome to contact the P.I. also for informal questions regarding the project and position.

Important information:

  *   Salary: ~ 1800 net/month
  *   Start date: beginning of 2024
  *   Application deadline: 17/11/2023

Kind regards,
Luca Ronconi

--
Prof. Luca Ronconi, Ph.D.
Associate Professor
School of Psychology
Vita-Salute San Raffaele University
via Olgettina 58, 20132, Milan, Italy
Phone (Office): +39 02 2643 4887
Phone (Lab.): +39 02 2643 6132
Website: www.bdaclab.com<http://www.bdaclab.com/>
Email: ronconi.luca at unisr.it<mailto:ronconi.luca at unisr.it>





Rispetta l’ambiente: non stampare questa mail se non è necessario.
Respect the environment: print this email only if necessary.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231016/cb97f296/attachment.htm>

From merlinkelly75 at gmail.com  Tue Oct 17 14:23:43 2023
From: merlinkelly75 at gmail.com (Merlin Kelly)
Date: Tue, 17 Oct 2023 13:23:43 +0100
Subject: [FieldTrip] error: Unexpected dimord. Unsure what is incorrect
Message-ID: <CAJj0QmmPCtv4CZvsZh6gqfjdoVGW3Lfxswr1zOU8YotTYyn4bA@mail.gmail.com>

Hello
I am attempting to process my data to create timelockanalysis data for
later analysis. However when I run ft_preprocessing(cfg, Data), I get the
error:
Warning: could not determine dimord of "trial" in:

      label: {7×1 cell}
        hdr: [1×1 struct]
    fsample: 500
      trial: [240×7 single]
       time: [1 1 1 1 1 1 1]
     dimord: 'chan_freq'


Error using fixsampleinfo
unexpected dimord

Error in ft_datatype_timelock (line 152)
      timelock = fixsampleinfo(timelock);

Error in ft_checkdata (line 281)
  data = ft_datatype_timelock(data, 'hassampleinfo', hassampleinfo);

Error in ft_preprocessing (line 274)
  data = ft_checkdata(data, 'datatype', {'raw+comp', 'raw'},
'hassampleinfo', 'yes');

Error in Mean_data_prep (line 33)
        Data=ft_preprocessing(cfg, Data);

My code is based on literature that provide their fieldtrip code: "EEG
alpha–theta dynamics during mind wandering in the context of breath focus
meditation: An experience sampling approach with novice meditation
practitioners"

My data are Matlab 3D arrays of size 36 x 120 x 7, which represent subjects
x trial x channels where the data is the mean theta frequency of each
5-second trial and electrode. The code I'm using to convert data is present
below:
function [DATA, layout]=Mean_data_prep(data, Participant_index, index, Name)
load('electrode19.mat')
load('chanlocs.mat')
DATA = cell(1, max(unique(Participant_index)));
%for each participant, load data in struct form and prepare for
%fieldtrip
for i=1:max(unique(Participant_index))
if i == 1 || i == 3 || i == 6 || i == 9 || i == 10 %|| i == 4 || i == 7 ||
i == 5 || i == 8 || i == 21
continue
end
clear Data
Data=struct();
Data.label=electrode19;
Data.hdr.nChans=numel(electrode19);
Data.hdr.label=electrode19';
Data.hdr.Fs=500;
Data.fsample=500;
data_sel = data(Participant_index(index) == i, :,:);
if size(data_sel, 1) ~= 1
data_sel = reshape(data_sel, [], size(data_sel, 3));
else
data_sel = squeeze(data_sel);
end
Data.trial = data_sel;
Data.time=ones(1,size(data_sel,2));
Data.hdr.nSamples=1;
Data.dimord = 'chan_freq';
cfg=[];
Data=ft_preprocessing(cfg, Data);
Data = ft_timelockanalysis(cfg, Data);
%Data = ft_datatype_timelock(Data);
% Data.trialinfo=labels;
cfg.layout = 'biosemi32.lay';
Data.layout = ft_prepare_layout(cfg);
layout = ft_prepare_layout(cfg);
%Data.layout=Data;
DATA{i} = Data;
DATA{i} = NaN;
% else
% x = x - 1;
% end
end
end
I have changed the dimord and other factors of this code, but I believe the
issue is the Data.time variable as I have functioning code that is suitable
for a 4D array with time in the last dimension. If anyone knows how to
correct this error code, it would be appreciated.
Best
Merlin
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231017/0595144e/attachment.htm>

From janmathijs.schoffelen at donders.ru.nl  Tue Oct 17 16:23:30 2023
From: janmathijs.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Tue, 17 Oct 2023 14:23:30 +0000
Subject: [FieldTrip] error: Unexpected dimord. Unsure what is incorrect
In-Reply-To: <CAJj0QmmPCtv4CZvsZh6gqfjdoVGW3Lfxswr1zOU8YotTYyn4bA@mail.gmail.com>
References: <CAJj0QmmPCtv4CZvsZh6gqfjdoVGW3Lfxswr1zOU8YotTYyn4bA@mail.gmail.com>
Message-ID: <69245B60-990B-4840-BD79-49DA5F7B681F@donders.ru.nl>

Hi Merlin,

I don’t care too much about code that has been provided by third parties :), so I will only comment on the screen output of your data structure:


      label: {7×1 cell}
        hdr: [1×1 struct]
    fsample: 500
      trial: [240×7 single]
       time: [1 1 1 1 1 1 1]
     dimord: 'chan_freq'

This is inconsistent and indeed prone to give troubles.

The label field suggests that there are 7 channels in your data, which is in line with the second dimension (i.e. the numbor of columns) in the trial field. Assuming that the 240 rows correspond to the number of observations in your data, the appropriate dimord of the data structure should read ‘rpt_chan_<somethingelse>’. Given your context you seem to be working with spectral estimates (but without a time dimension per trial), so I don’t understand why in the reported data structure, there’s a ’time’ mentioned. Moreover, if the data matrix indeed is <number-of-observations> x <number-of-channels> the implicit third dimension (either ‘freq’, or ’time’, in your case ‘freq') seems to be singleton.

This would translate to a <data>.time, or <data>.freq field consisting of just a single element, with the appropriate value for the frequency.

As a side note, since you are dealing with frequency domain data, there’s no need to call ft_timelockanalysis, nor to call ft_preprocessing or ft_datatype_timelock

I suggest that you search the documentation on the website for information about the definition of a ‘freq’ structure (ft_datatype_freq) which is what you seem to be importing directly.

Good luck

Jan-Mathijs







Error using fixsampleinfo
unexpected dimord

Error in ft_datatype_timelock (line 152)
      timelock = fixsampleinfo(timelock);

Error in ft_checkdata (line 281)
  data = ft_datatype_timelock(data, 'hassampleinfo', hassampleinfo);

Error in ft_preprocessing (line 274)
  data = ft_checkdata(data, 'datatype', {'raw+comp', 'raw'}, 'hassampleinfo', 'yes');

Error in Mean_data_prep (line 33)
        Data=ft_preprocessing(cfg, Data);

My code is based on literature that provide their fieldtrip code: "EEG alpha–theta dynamics during mind wandering in the context of breath focus meditation: An experience sampling approach with novice meditation practitioners"

My data are Matlab 3D arrays of size 36 x 120 x 7, which represent subjects x trial x channels where the data is the mean theta frequency of each 5-second trial and electrode. The code I'm using to convert data is present below:
function [DATA, layout]=Mean_data_prep(data, Participant_index, index, Name)
load('electrode19.mat')
load('chanlocs.mat')
DATA = cell(1, max(unique(Participant_index)));
%for each participant, load data in struct form and prepare for
%fieldtrip
for i=1:max(unique(Participant_index))
if i == 1 || i == 3 || i == 6 || i == 9 || i == 10 %|| i == 4 || i == 7 || i == 5 || i == 8 || i == 21
continue
end
clear Data
Data=struct();
Data.label=electrode19;
Data.hdr.nChans=numel(electrode19);
Data.hdr.label=electrode19';
Data.hdr.Fs=500;
Data.fsample=500;
data_sel = data(Participant_index(index) == i, :,:);
if size(data_sel, 1) ~= 1
data_sel = reshape(data_sel, [], size(data_sel, 3));
else
data_sel = squeeze(data_sel);
end
Data.trial = data_sel;
Data.time=ones(1,size(data_sel,2));
Data.hdr.nSamples=1;
Data.dimord = 'chan_freq';
cfg=[];
Data=ft_preprocessing(cfg, Data);
Data = ft_timelockanalysis(cfg, Data);
%Data = ft_datatype_timelock(Data);
% Data.trialinfo=labels;
cfg.layout = 'biosemi32.lay';
Data.layout = ft_prepare_layout(cfg);
layout = ft_prepare_layout(cfg);
%Data.layout=Data;
DATA{i} = Data;
DATA{i} = NaN;
% else
% x = x - 1;
% end
end
end
I have changed the dimord and other factors of this code, but I believe the issue is the Data.time variable as I have functioning code that is suitable for a 4D array with time in the last dimension. If anyone knows how to correct this error code, it would be appreciated.
Best
Merlin
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=05%7C01%7Cfieldtrip%40science.ru.nl%7C5e2be508ab3840b49dfc08dbcf1ca314%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638331494113455677%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=nBcHltwn40E11MmPIsreKqhzWwjt8g2fYmApIEFvQXs%3D&reserved=0>
https://doi.org/10.1371/journal.pcbi.1002202

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231017/662f8a40/attachment.htm>

From preted at mcmaster.ca  Tue Oct 17 19:47:54 2023
From: preted at mcmaster.ca (David Prete)
Date: Tue, 17 Oct 2023 17:47:54 +0000
Subject: [FieldTrip] Correcting for multiple cluster analyses?
Message-ID: <YTBPR01MB3837F8E4045D0798F0739D85D6D6A@YTBPR01MB3837.CANPRD01.PROD.OUTLOOK.COM>

Hello Everyone, 

I asked this question last week, but it didn't show up in my Fieldtrip
emails so I'm trying to send this again to see if it works this time.
Sorry if you're seeing this twice.

I have run multiple cluster-based permutation analyses and I am
wondering if I need to correct for multiple comparisons and how
exactly would I do that? I know there was a previous thread that
suggested using Bonferroni correction but not how to apply the
correction. If I run the cluster analysis 9 times in total based on
different time windows and comparing different conditions, would I
divide 0.05 by 9 to get a corrected p-value of  0.00556? Or do I need
to correct based on the total number of clusters found from the 9
times I ran the analysis? So, for example let's say each time I ran
the analysis I found a positive and negative cluster leading to 18
different p-values, would the correction be 0.05 divided by 18?

Thank you,
David Prete (he/him)
Ph.D. Candidate
McMaster University




From barchiesi.guido at gmail.com  Thu Oct 19 17:12:21 2023
From: barchiesi.guido at gmail.com (Guido Barchiesi)
Date: Thu, 19 Oct 2023 17:12:21 +0200
Subject: [FieldTrip] Post-Doc Position at the University of Milan in Motor
 Control and Action Observation
Message-ID: <CA+r-HtvOUvwpU+LhFwPn4ZdKQ53SQc1yiROYQKmK1vua8C0m1w@mail.gmail.com>

*A Postdoc position *is available at the *Cognition In Action Lab *(
*http://cialab.unimi.it/* <http://cialab.unimi.it/>*) *at the *University
of Milan*, *Faculty of Philosophy.*


The position is funded by an Italian PRIN 2022 grant awarded to Guido
Barchiesi


*Theoretical framework*

The research project aims at studying the mechanisms of interaction between
"Motor Resonance" and efficient Motor Control during active action
observation in humans.

Evidence in the literature suggests that the observation of an action
performed by another individual facilitates the motor representations
corresponding to the action observed in the observer's motor system, a
mechanism called Motor Resonance. If this is the case, why do we not
imitate all the time when observing others' actions and especially when we
need to quickly react to them?


*Lab*

The CIAlab features a TMS, a new 64-channels EEG amplifier, a behavioral
lab soon to be equipped with a virtual reality system...and nice people :-)


*Ideal candidate profile*

The ideal candidate for the Post-doc position should have a PhD in
biomedical engineering, neuroscience/neurophysiology, psychology, or
related field, a solid background in designing and conducting M/EEG
experiments, data analysis/signal processing, and some experience with the
TMS.


*Desirable qualifications*

*- *experience in M/EEG both in data collection and analyses (fieldtrip
/eeglab).

- medium/strong experience in *programming* (ideally Matlab/Python)


*Expected Starting date*

Jan-Feb ’24


*Duration*

18 months




*Income*

*~2300 euros net/month*





If you are interested, please send your CV, names and contacts of 2
references, along with possible questions about the positions to Guido
Barchiesi guido.barchiesi at unimi.it



-- 
Guido Barchiesi, PhD
Department of Philosophy
University of Milan
via Festa del Perdono 7, 20122 Milano (Italy)
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231019/ff0d55ee/attachment.htm>

From ali.mazah at gmail.com  Fri Oct 20 11:07:34 2023
From: ali.mazah at gmail.com (Ali Mazaheri)
Date: Fri, 20 Oct 2023 10:07:34 +0100
Subject: [FieldTrip] Postdoc position investigating post-surgical cognitive
 outcomes
Message-ID: <CAEghnpSb8-tJEDuvyAL=dzPF_TdqX_e42xvJpnM6fpHQsvFxOA@mail.gmail.com>

Dear Fieldtrippers,

I have a new position available in my lab (University of Birmingham, UK)
tracking the cognitive function of older adults undergoing cancer surgery-
this work is part of a large multidisciplinary initiative funded by the
Wellcome Leap.

Besides a solid background in electrophysiology and cognitive neuroscience,
we are also looking for candidates who have a keen interest in and
enthusiasm for research in the area of aging and frailty.

More details and information on how to apply can be found in the link
below.
Email me if you have any questions.

https://edzz.fa.em3.oraclecloud.com/hcmUI/CandidateExperience/en/sites/CX_6001/job/3384/?utm_medium=jobshare


Thanks !
Ali

-- 
-
Dr Ali Mazaheri,
Associate Professor
University of Birmingham
www.alimazaheri.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231020/8d1dc581/attachment.htm>

From yeganemodaressnia at gmail.com  Fri Oct 20 19:31:36 2023
From: yeganemodaressnia at gmail.com (Yegane Modaresnia)
Date: Fri, 20 Oct 2023 21:01:36 +0330
Subject: [FieldTrip] Query Regarding Granger Causality Calculation in
 FieldTrip Toolbox
Message-ID: <CAD_GVFTwcG9pj+8cnsWXwb=NSHkdcUpnXofgvLT6sdOCBnJ2PQ@mail.gmail.com>

Dear Fieldtrip team,

I hope this message finds you well. I am currently working on calculating
the effective connectivity between sources using Granger causality in the
FieldTrip toolbox. I have been using the following code:

cfg         = [];
cfg.method  ='granger';
% cfg.complex = 'absimag';
source_conn = ft_connectivityanalysis(cfg, source);
figure(9);imagesc(source_conn.cohspctrm);

However, I have encountered an error message:
"This function requires 'mvar', 'freqmvar' or 'freq' data as input, see
ft_datatype_mvar or ft_datatype_freq."

Upon inspecting the ft_connectivityanalysis function, I noticed that it
accepts either two inputs in the form of (cfg, source) or (cfg, freq). My
confusion lies in understanding how to define 'freq' before applying this
Granger causality code, and how this relates to the 'source' data.

Could you kindly provide some guidance or insights on how to properly
handle the frequency data in conjunction with the source data for this
granger connectivity analysis?

Thank you very much for your assistance.

Warm regards,
Yeganeh
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231020/91695b49/attachment.htm>

From janmathijs.schoffelen at donders.ru.nl  Mon Oct 23 08:54:28 2023
From: janmathijs.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Mon, 23 Oct 2023 06:54:28 +0000
Subject: [FieldTrip] Query Regarding Granger Causality Calculation in
 FieldTrip Toolbox
In-Reply-To: <CAD_GVFTwcG9pj+8cnsWXwb=NSHkdcUpnXofgvLT6sdOCBnJ2PQ@mail.gmail.com>
References: <CAD_GVFTwcG9pj+8cnsWXwb=NSHkdcUpnXofgvLT6sdOCBnJ2PQ@mail.gmail.com>
Message-ID: <2E2D7526-BCBF-458B-882D-F405630DE5EE@donders.ru.nl>

Hi Yeganeh,

Consulting the help section of ft_connectivityanalysis, line 29 states:

%     'granger',   granger causality, support for freq and freqmvar data

This means that there is currently no support for source-level data to compute granger causality using only fieldtrip function calls. This is in line with the error message you receive.

Best wishes,
Jan-Mathijs





> On 20 Oct 2023, at 19:31, Yegane Modaresnia via fieldtrip <fieldtrip at science.ru.nl> wrote:
>
> Dear Fieldtrip team,
>
> I hope this message finds you well. I am currently working on calculating the effective connectivity between sources using Granger causality in the FieldTrip toolbox. I have been using the following code:
>
> cfg         = [];
> cfg.method  ='granger';
> % cfg.complex = 'absimag';
> source_conn = ft_connectivityanalysis(cfg, source);
> figure(9);imagesc(source_conn.cohspctrm);
>
> However, I have encountered an error message:
> "This function requires 'mvar', 'freqmvar' or 'freq' data as input, see ft_datatype_mvar or ft_datatype_freq."
>
> Upon inspecting the ft_connectivityanalysis function, I noticed that it accepts either two inputs in the form of (cfg, source) or (cfg, freq). My confusion lies in understanding how to define 'freq' before applying this Granger causality code, and how this relates to the 'source' data.
>
> Could you kindly provide some guidance or insights on how to properly handle the frequency data in conjunction with the source data for this granger connectivity analysis?
>
> Thank you very much for your assistance.
>
> Warm regards,
> Yeganeh
> _______________________________________________
> fieldtrip mailing list
> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=05%7C01%7Cfieldtrip%40science.ru.nl%7C41e5b11f0dad40f7dad208dbd394e714%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638336408714788862%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=EoERiWT4jhHnfF4SnUcPz7hLIjvH3e6SvPumwFy6lno%3D&reserved=0
> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=05%7C01%7Cfieldtrip%40science.ru.nl%7C41e5b11f0dad40f7dad208dbd394e714%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638336408714788862%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ZspLIysE9HgS%2F47lnHLkD9cTS30Kavd%2BhUaUuM7fVSk%3D&reserved=0




From janmathijs.schoffelen at donders.ru.nl  Mon Oct 23 10:01:27 2023
From: janmathijs.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Mon, 23 Oct 2023 08:01:27 +0000
Subject: [FieldTrip] Correcting for multiple cluster analyses?
In-Reply-To: <YTBPR01MB3837F8E4045D0798F0739D85D6D6A@YTBPR01MB3837.CANPRD01.PROD.OUTLOOK.COM>
References: <YTBPR01MB3837F8E4045D0798F0739D85D6D6A@YTBPR01MB3837.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <A4FB9DF1-C400-4E78-942F-30D80DDF4381@donders.ru.nl>

Hi David,

If you want to be strict about the multiple tests you are performing, you need to Bonferroni correct for the number of tests, not for the number of clusters as such. The clusters are a ‘byproduct’ of the inferential procedure, and are a means to reduce the number of comparisons per test to 1. Actually, you are right that in 2-sided testing you are performing 2 tests, one for each side (i.e. testing the largest positive and negative cluster in the observed data against their respective randomization distributions. The interpretation of the p-values associated with the most extreme clusters (i.e. the ones that are associated with the actual inferential decision), depends on the settings of the cfg.correcttail option. See https://www.fieldtriptoolbox.org/faq/why_should_i_use_the_cfg.correcttail_option_when_using_statistics_montecarlo/<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Ffaq%2Fwhy_should_i_use_the_cfg.correcttail_option_when_using_statistics_montecarlo%2F&data=05%7C01%7Cfieldtrip%40science.ru.nl%7Cc44000c71e984799a1bc08dbd39e426b%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638336448940467345%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Tkk%2BWcEZeYNlJ2R3mx5262sL94GJ2CfPEmX2UN8YHG8%3D&reserved=0> for more information.

I hope this helps,
Jan-Mathijs



On 17 Oct 2023, at 19:47, David Prete via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Hello Everyone,

I asked this question last week, but it didn't show up in my Fieldtrip
emails so I'm trying to send this again to see if it works this time.
Sorry if you're seeing this twice.

I have run multiple cluster-based permutation analyses and I am
wondering if I need to correct for multiple comparisons and how
exactly would I do that? I know there was a previous thread that
suggested using Bonferroni correction but not how to apply the
correction. If I run the cluster analysis 9 times in total based on
different time windows and comparing different conditions, would I
divide 0.05 by 9 to get a corrected p-value of  0.00556? Or do I need
to correct based on the total number of clusters found from the 9
times I ran the analysis? So, for example let's say each time I ran
the analysis I found a positive and negative cluster leading to 18
different p-values, would the correction be 0.05 divided by 18?

Thank you,
David Prete (he/him)
Ph.D. Candidate
McMaster University


_______________________________________________
fieldtrip mailing list
https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=05%7C01%7Cjanmathijs.schoffelen%40donders.ru.nl%7Cc6ac3241c5e3439f7d7808dbcf3c5540%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638331630260706725%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=THIhFBgc6VtNF%2BxCVK5gPFo4dd1oG%2FF2UvjsFP6Zg1o%3D&reserved=0<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=05%7C01%7Cfieldtrip%40science.ru.nl%7Cc44000c71e984799a1bc08dbd39e426b%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638336448940467345%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=5qvQIDcHAiqOH7MiDksSfdJOnZc5yiTSQemrHWeP0z0%3D&reserved=0>
https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=05%7C01%7Cjanmathijs.schoffelen%40donders.ru.nl%7Cc6ac3241c5e3439f7d7808dbcf3c5540%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638331630260706725%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=cZJOHWv%2FQPqbZQoQV0sSlryklBJOZpjggCL24PpGjLs%3D&reserved=0

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231023/046947cc/attachment.htm>

From robert.oostenveld at donders.ru.nl  Mon Oct 23 11:34:44 2023
From: robert.oostenveld at donders.ru.nl (Oostenveld, R. (Robert))
Date: Mon, 23 Oct 2023 09:34:44 +0000
Subject: [FieldTrip] One Hundred Years of EEG: Looking Back and Forwards
Message-ID: <7C98271D-05FF-4EAC-9CC3-46846A24171A@donders.ru.nl>

Dear Colleagues

We are coming up to the 100-year anniversary of the discovery of human EEG.

In celebration of this seminal moment for human neuroscience, we are asking the EEG, and neuroscience community at large, to document the impact this discovery has had on our understanding of the brain and to share thoughts on the short, medium, and long-term future of human non-invasive scalp EEG through this online survey. Importantly, this survey will also help in defining our collective perspectives on future research priorities.

I hope you will be able to spare the 10-15 minutes it will take to complete the survey and make your views heard about the past and future of EEG.

http://tinyurl.com/EEG100<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftinyurl.com%2FEEG100&data=05%7C01%7Cfieldtrip%40science.ru.nl%7C199543dfed1e42cb696e08dbd3ab4a6b%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638336504854134141%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8Rpc7GHTgisCjh%2Br%2BfwJfaKCr%2B%2FJJOWzg%2B%2FJd8GF4Nk%3D&reserved=0>

Thank you for your time.

best regards
Robert Oostenveld

-----------------------------------------------------------
Associate Professor
Donders Institute for Brain, Cognition and Behaviour
Radboud University, Nijmegen, The Netherlands

Affiliated Professor
NatMEG - the Swedish National MEG facility
Karolinska Institute, Stockholm, Sweden

tel.: +31 6 31132599
e-mail: robert.oostenveld at donders.ru.nl
web: http://www.ru.nl/donders
-----------------------------------------------------------

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231023/416f5381/attachment.htm>

From a.mazaheri at bham.ac.uk  Mon Oct 23 12:44:22 2023
From: a.mazaheri at bham.ac.uk (Ali Mazaheri)
Date: Mon, 23 Oct 2023 10:44:22 +0000
Subject: [FieldTrip] Post-Doc Position at the University of Birmingham:
 cognitive outcome of elderly patients after major surgery
Message-ID: <LO4P265MB7353A87F2DD1648D42176B18AED8A@LO4P265MB7353.GBRP265.PROD.OUTLOOK.COM>

Dear Fieldtrippers,

I have a new position available in my lab (University of Birmingham, UK) tracking the cognitive function of older adults undergoing cancer surgery-  this work is part of a large multidisciplinary initiative funded by the Wellcome Leap.

Besides a solid background in electrophysiology and cognitive neuroscience, we are also looking for candidates who have a keen interest in and enthusiasm for research in the area of aging and frailty.

More details and information on how to apply can be found in the link below.
Email me if you have any questions.

https://www.jobs.ac.uk/job/DDN255/research-fellow

Thanks !
Ali


Dr Ali Mazaheri
Associate Professor
School of Psychology
Centre for Human Brain Health
University of Birmingham
www.alimazaheri.com


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231023/a7531d12/attachment.htm>

From michele.scaltritti at gmail.com  Tue Oct 24 16:18:16 2023
From: michele.scaltritti at gmail.com (Michele Scaltritti)
Date: Tue, 24 Oct 2023 16:18:16 +0200
Subject: [FieldTrip] Two postdoctoral research positions,
 University of Trento and University of Milano-Bicocca, Italy
Message-ID: <CABGEo=Rbi1FS45m1+QaGLAuYEHvjvepKCrV0Y1DLi4kFS=0J3A@mail.gmail.com>

Dear all (apologies for cross-posting),

We are inviting expressions of interest for two forthcoming postdoctoral
positions, one at the Department of Psychology - University of
Milano-Bicocca (supervisor: Simone Sulpizio), and one at the Department of
Psychology and Cognitive Science - University of Trento (supervisor:
Michele Scaltritti).



Both positions will be supported by a recently funded project entitled
“FundDeMYO - Functional characterization of decisional components in motor
responses for young and older adults”. The project focuses on the
investigation of the decisional components affecting motor-response
execution during binary decision making, in an effort to better understand
the boundaries between cognition and action.


The research will use linguistic stimuli and tasks (lexical decision), and
will mainly rely on behavioural and electromyographic (EMG) measures as
well as on comparisons across different populations (young vs older adults) .




The ideal candidates should have a PhD in cognitive/experimental psychology
or related disciplines, as well as substantial experience with psychology
experiments (design, data collection, analyses). Previous experience with
physiological data, psycholinguistic and aging research are a plus. To
facilitate communication with older adults, a working knowledge of Italian
would be an asset, and the ideal candidate should be at least willing to
acquire it over the first year.



We offer a competitive salary and we make it a priority to support a good
work-life balance as well as a friendly and inclusive research environment.



Expressions of interest should be submitted via email to
simone.sulpizio at unimib.it or michele.scaltritti at unitn.it and include:

•   a CV

•   names and contacts of one or two references

Informal inquiries are welcomed.



Please note that this is just an informal call for expressions of interest.
Positions will be subject to a formal hiring procedure, in compliance with
national and institutional requirements.



*Duration*: 24 months

*Tentative starting date*: January 2024





*The Department of Psychology at UniMiB is extremely young (it was
established in 1999) and yet presents a great tradition The Department
combines basic and applied research, building on effective interactions
between various disciplines, which all contribute to the knowledge of mind.
Today is one of Italy’s most prestigious and high-ranked departments of
psychology, as well as being the largest, with its current 79 faculty
members, dozens of doctoral students and postdoctoral fellows, and over 20
research laboratories. Contact: simone.sulpizio at unimib.it
<simone.sulpizio at unimib.it>*



*The Department of Psychology and Cognitive Science at UNITN offers a great
research environment, and has been recently ranked among the top Psychology
Department of Italy. It provides state-of-the-art facilities (multiple
labs, 2 EEG systems, eye-trackers, and multiple devices for acquiring
physiological data), a multidisciplinary perspective on the study of the
mind and cognition, as well as a warm and friendly working environment. The
Department is located in Rovereto, a smaller but well-connected town (15
mins from Trento by train) with a remarkable quality of life. Contact:
michele.scaltritti at unitn.it <michele.scaltritti at unitn.it>*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231024/63341e13/attachment.htm>

From josephccchen at gmail.com  Wed Oct 25 10:14:49 2023
From: josephccchen at gmail.com (Joseph Chen)
Date: Wed, 25 Oct 2023 21:14:49 +1300
Subject: [FieldTrip] 2023-2024 OHBM Mentoring and Fellowship Program
Message-ID: <CAN6Zn6VaB7AZ1yYVUV0HPkoVOjzfd-NQeCX2JokEjSrVOuMyNA@mail.gmail.com>

Dear fellow neuroimagers,

Registration is now open for the eighth round of the OHBM Online
International Mentoring Program, organized by the OHBM Student and Postdoc
Special Interest Group (SP SIG). The program pairs mentees with more
experienced mentors in the OHBM community for (online) mentoring during the
2023-2024 academic year.

The goal of the program is to establish mentoring relationships across the
world. Our mentors can provide mentees with insight and support in topics
including career development, navigating academia, grant writing, and
work-life balance.

If you are interested in being a mentor and/or mentee, please fill out
this short
intake form <https://forms.gle/hqcALjvRCM9FbHxS9> and you will be contacted
with further details. Applications close on Monday 16th October, 2023
(23:59 Pacific Time).

Feel free to distribute this email to your networks. Based on feedback from
previous rounds, we have a lot of interest for mentors in industry roles.
Hence, we encourage scientists working in industry to apply as mentors for
our program.

Continuation of the OHBM SP SIG Fellowship Program

We are also continuing our OHBM Fellowship Program for 2023-2024 after our
successful pilot in 2022 - 2023. The aim of this Fellowship program is to
provide tailored support to people coming from underrepresented communities
based on - but not limited to - age, culture, ethnicity, gender identity or
expression, language, national origin, political beliefs, profession, race,
religion, sexual orientation, and socioeconomic status in line with the OHBM
Code of Conduct
<https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3846>. It
will include all the benefits of our Mentoring Program, plus additional
peer-mentoring sessions, online platform to interact with other Fellows,
highlighting of your profile on media platforms and/or blogs, and more. For
this second year, the OHBM Fellowship Program will take a select number of
Ph.D students contingent on available resources, please use the final
question of the regular intake form <https://forms.gle/hqcALjvRCM9FbHxS9>
to apply.

To find out more about the Mentoring Program, please visit the OHBM Student
and Postdoc SIG website <https://www.ohbmtrainees.com/> and check out our
publication in the European Journal of Neuroscience
<https://onlinelibrary.wiley.com/doi/full/10.1111/ejn.14320>. If you have
any questions, please contact us at
ohbmtrainees.mentorship.program at gmail.com.

We would like to thank all the OHBM mentors and mentees who participated in
the previous seven rounds of the Mentoring Program. We hope to welcome you
in the upcoming round very soon!

Best regards,

OHBM Student and Postdoc Special Interest Group
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231025/3880dc30/attachment.htm>

From sauppe.s at gmail.com  Wed Oct 25 21:29:43 2023
From: sauppe.s at gmail.com (Sebastian Sauppe)
Date: Wed, 25 Oct 2023 21:29:43 +0200
Subject: [FieldTrip] Error using ft_compile_mex>compile_mex_list
Message-ID: <C19A6E77-437F-4224-ABD4-44F17505E1AD@gmail.com>

Dear Fieldtrip community,

I am trying to compile the MEX files using "ft_compile_mex(true)“ on my Mac as described here: https://www.fieldtriptoolbox.org/faq/compile/. I also already removed all MEX files from the quarantine (https://www.fieldtriptoolbox.org/faq/mexmaci64_cannot_be_opened_because_the_developer_cannot_be_verified/).

However, after the ft_compile_mex function ran for a while, I get these errors. Does anybody know what they mean?

Error using ft_compile_mex>compile_mex_list
Error using mex
PATH_TO_FIELDTRIP/src/mxSerialize_cpp.cpp:10:1: error: unknown type name
'EXTERN_C'
EXTERN_C mxArray* mxSerialize(mxArray const *);
^
PATH_TO_FIELDTRIP/src/mxSerialize_cpp.cpp:10:17: error: expected ';' after
top level declarator
EXTERN_C mxArray* mxSerialize(mxArray const *);
                ^
                ;
PATH_TO_FIELDTRIP/src/mxSerialize_cpp.cpp:11:1: error: unknown type name
'EXTERN_C'
EXTERN_C mxArray* mxDeserialize(const void *, size_t);
^
PATH_TO_FIELDTRIP/src/mxSerialize_cpp.cpp:11:17: error: expected ';' after
top level declarator
EXTERN_C mxArray* mxDeserialize(const void *, size_t);
                ^
                ;
PATH_TO_FIELDTRIP/src/mxSerialize_cpp.cpp:22:31: error: use of undeclared
identifier 'mxSerialize'
        plhs[0] = (mxArray *) mxSerialize(prhs[0]);
                              ^
5 errors generated.


Error in ft_compile_mex (line 114)
  compile_mex_list(L, ftpath, force);

Kind regards,
Sebastian
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231025/f90cace9/attachment.htm>

From janmathijs.schoffelen at donders.ru.nl  Thu Oct 26 08:13:19 2023
From: janmathijs.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Thu, 26 Oct 2023 06:13:19 +0000
Subject: [FieldTrip] Error using ft_compile_mex>compile_mex_list
In-Reply-To: <C19A6E77-437F-4224-ABD4-44F17505E1AD@gmail.com>
References: <C19A6E77-437F-4224-ABD4-44F17505E1AD@gmail.com>
Message-ID: <8E0BB45A-BB9E-45E5-8FF3-80EC72DF627A@donders.ru.nl>

Hi Sebastian,

The error is low level, and suggests that compilation fails on your system. Can you please provide some relevant information?

-Fieldtrip version used.
-Matlab version used
-Operating system used.
-Type of processor in your Mac.

Thanks,
Jan-Mathijs


On 25 Oct 2023, at 21:29, Sebastian Sauppe via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Dear Fieldtrip community,

I am trying to compile the MEX files using "ft_compile_mex(true)“ on my Mac as described here: https://www.fieldtriptoolbox.org/faq/compile/<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Ffaq%2Fcompile%2F&data=05%7C01%7Cfieldtrip%40science.ru.nl%7Ce4fc6682164f41049ec608dbd5eaa6c1%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638338976017550695%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=PKmWKNDw51sCCC4EUEZ78dhcVYRB7pYINRNf0%2BH%2BZw0%3D&reserved=0>. I also already removed all MEX files from the quarantine (https://www.fieldtriptoolbox.org/faq/mexmaci64_cannot_be_opened_because_the_developer_cannot_be_verified/<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Ffaq%2Fmexmaci64_cannot_be_opened_because_the_developer_cannot_be_verified%2F&data=05%7C01%7Cfieldtrip%40science.ru.nl%7Ce4fc6682164f41049ec608dbd5eaa6c1%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638338976017550695%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=PQAY0qrGlvJMbQRN2CW%2FIXcT6tKzHmZ7Wwc37x2PtJk%3D&reserved=0>).

However, after the ft_compile_mex function ran for a while, I get these errors. Does anybody know what they mean?

Error using ft_compile_mex>compile_mex_list
Error using mex
PATH_TO_FIELDTRIP/src/mxSerialize_cpp.cpp:10:1: error: unknown type name
'EXTERN_C'
EXTERN_C mxArray* mxSerialize(mxArray const *);
^
PATH_TO_FIELDTRIP/src/mxSerialize_cpp.cpp:10:17: error: expected ';' after
top level declarator
EXTERN_C mxArray* mxSerialize(mxArray const *);
                ^
                ;
PATH_TO_FIELDTRIP/src/mxSerialize_cpp.cpp:11:1: error: unknown type name
'EXTERN_C'
EXTERN_C mxArray* mxDeserialize(const void *, size_t);
^
PATH_TO_FIELDTRIP/src/mxSerialize_cpp.cpp:11:17: error: expected ';' after
top level declarator
EXTERN_C mxArray* mxDeserialize(const void *, size_t);
                ^
                ;
PATH_TO_FIELDTRIP/src/mxSerialize_cpp.cpp:22:31: error: use of undeclared
identifier 'mxSerialize'
        plhs[0] = (mxArray *) mxSerialize(prhs[0]);
                              ^
5 errors generated.


Error in ft_compile_mex (line 114)
  compile_mex_list(L, ftpath, force);

Kind regards,
Sebastian
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=05%7C01%7Cfieldtrip%40science.ru.nl%7Ce4fc6682164f41049ec608dbd5eaa6c1%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638338976017550695%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=czqimKc2ShwFbYqRB70TUjVyfbqrSm%2FPgCJWHCiZMMM%3D&reserved=0>
https://doi.org/10.1371/journal.pcbi.1002202

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231026/ccd829b4/attachment.htm>

From maria.denhartog at ru.nl  Thu Oct 26 11:31:21 2023
From: maria.denhartog at ru.nl (Hartog, M.M.J. den (Maria))
Date: Thu, 26 Oct 2023 09:31:21 +0000
Subject: [FieldTrip] Artifact rejection problem due to samples occurring
 twice in the data
Message-ID: <DB8PR10MB37380BC356D873907E6ACDCCE1DEA@DB8PR10MB3738.EURPRD10.PROD.OUTLOOK.COM>

Dear community,

My name is Maria den Hartog and I am a PhD candidate at the Centre for Language Studies (CLS) at Radboud University in Nijmegen. I am currently preprocessing data from an ERP reading experiment about the processing of pronouns of address (e.g. he, she, they) within a text.

I want to use automatic artifact rejection to remove full trials with signal exceeding +-100 µV as part of my preprocessing pipeline, but I get an error message indicating that 'some of the requested samples occur twice in the data and have conflicting values'. This is true, and it is a consequence of the naturalistic reading paradigm I used. My trials run from -200 ms prestimulus to 1000 ms poststimulus. The t = 0 of each trial is the onset of a pronoun within a text, and the pronouns can occur less than 1000 ms after each other (e.g., the stimuli are he and his in 'He looked at his cat.'). I have baselined my trials to the 200 ms window up to the stimulus, meaning the same sample can have different values in different trials.

The code I use for artifact rejection is:
    cfg = [];
    cfg.continuous = 'no';
    cfg.artfctdef.threshold.min = -100;
    cfg.artfctdef.threshold.max = 100;
    art = ft_artifact_threshold(cfg,data);

    cfg = [];
    cfg.artfctdef.xxx.artifact = art.artfctdef.threshold.artifact;
    data_forERP = ft_rejectartifact(cfg,data);
The error I get:

Error using ft_fetch_data
some of the requested samples occur twice in the data and have conflicting values

Error in ft_artifact_threshold (line 186)
    dat = ft_fetch_data(data,        'header', hdr, 'begsample', trl(trlop,1), 'endsample', trl(trlop,2), 'chanindx', chanindx, 'checkboundary', strcmp(cfg.continuous, 'no'));

Is there a way to adjust the cfg for ft_rejectartifact so that the function will accept that samples do indeed occur twice in the data and that the same sample can have different values in different trials (and data from the correct trial will be fetched)?

Here are a few solutions that I have tried based on other discussion list questions, that I have found to be unsatisfactory or ineffective:

  *   For ft_databrowser, it is possible to use cfg.allowoverlap = 'yes' to avoid errors due to conflicting sample values, but this setting is not available for ft_rejectartifact.
  *   I do not want to remove or adjust the sampleinfo from the data, because I want to be able to relate trials to the original samples if necessary.
  *   I have found that downsampling my signal will lead ft_rejectartifact to reconstruct the sampleinfo assuming that the trials are consecutive segments of a continuous recording, but I do not want to 'hack' my way around the problem in this way.

Hope you can help me out!

Best,
Maria


------------------------------------------------------------------------
Maria den Hartog, MSc | PhD Candidate | Radboud University
Centre for Language Studies | Grammar and Cognition
Working days: Tuesday - Friday | Erasmus Building, Room 8.01


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231026/877fd5c0/attachment.htm>

From ajesse at umass.edu  Thu Oct 26 22:17:57 2023
From: ajesse at umass.edu (Alexandra Jesse)
Date: Thu, 26 Oct 2023 16:17:57 -0400
Subject: [FieldTrip] Ph.D. position in Speech Perception (Department of
 Psychological and Brain Sciences), University of Massachusetts Amherst
Message-ID: <70B289DC-15E9-42E4-B694-8082572968C3@umass.edu>

The Language, Intersensory Perception, and Speech (LIPS) lab of Dr. Alexandra Jesse at the University of Massachusetts Amherst invites applications for Ph.D. positions in Cognition and Cognitive Neuroscience, starting in Fall 2024.

The goal of Dr. Jesse’s research is to understand how humans recognize speech sounds and spoken words. A particular focus is on speech recognition in face-to-face communication, when listeners use information obtained from hearing and seeing the talker to recognize speech. Using both behavioral (e.g., eye tracking) and neuropsychological methods (EEG/ERP), Dr. Jesse’s research also investigates the underlying mechanisms of how listeners cope with variability in speech and adjust to talkers. A third line of research examines whether and how perceptual (e.g., hearing) and cognitive factors (e.g., attention, working memory) play a role in speech recognition and can hence explain individual differences in aging.

For more information on the UMass Language, Intersensory Perception, & Speech (LIPS) lab, please see http://lips.psych.umass.edu <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flips.psych.umass.edu%2F&data=05%7C01%7Cajesse%40psych.umass.edu%7Ccff413a16cfb48df969008dbd65fa811%7C7bd08b0b33954dc194bbd0b2e56a497f%7C0%7C0%7C638339478563288166%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qB2gBHG4VvXwRRqUnnXZFYZjF%2FtvP%2Bqt6X3K2MXonV0%3D&reserved=0>.

Applicants should have a bachelor’s or master’s degree in Psychology or other related fields (e.g., Cognitive Science; Linguistics; Neuroscience; Speech, Language, and Hearing Sciences). The candidate should have a strong interest in the research topics of the lab and excellent communication skills. Experience with experimental research is preferred. Prior experience with EEG/ERP is of advantage.

Please submit applications through the University of Massachusetts' general application process. Application guidelines can be found at the UMass PBS Cognition and Cognitive Neuroscience website <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.umass.edu%2Fpsychological-brain-sciences%2Fgraduate%2Fcognition-and-cognitive-neuroscience&data=05%7C01%7Cajesse%40psych.umass.edu%7Ccff413a16cfb48df969008dbd65fa811%7C7bd08b0b33954dc194bbd0b2e56a497f%7C0%7C0%7C638339478563288166%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=QdvpaEsZ4rbkKBhTy60z0ORGBEwlKbyO3mPq4LtgCzo%3D&reserved=0> and at the UMass Graduate School website <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.umass.edu%2Fgraduate%2F&data=05%7C01%7Cajesse%40psych.umass.edu%7Ccff413a16cfb48df969008dbd65fa811%7C7bd08b0b33954dc194bbd0b2e56a497f%7C0%7C0%7C638339478563443846%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=fKpY%2BqcUrYhJGWEdaFwHO5bTuVuhxFj%2Ft359dEI0qZE%3D&reserved=0>. The application deadline for entry next Fall is December 1, 2023. 

For informal inquiries, please contact Alexandra Jesse (ajesse at umass.edu <mailto:ajesse at umass.edu>).

The University is committed to active recruitment of a diverse faculty and student body. The University of Massachusetts is an Affirmative Action/Equal Opportunity Employer of women, minorities, protected veterans, and individuals with disabilities and encourages applications from these and other protected group members. Because broad diversity is essential to an inclusive climate and critical to the University’s goals of achieving excellence in all areas, we will holistically assess the many qualifications of each applicant and favorably consider an individual’s record working with students and colleagues with broadly diverse perspectives, experiences, and backgrounds in educational, research or other work activities.  We will also favorably consider experience overcoming or helping others overcome barriers to an academic career and degree.

--------------------------------------------------------------------
Alexandra Jesse, Ph.D. (she/her)
Associate Professor
Director of the Language, Intersensory Perception, 
and Speech (LIPS) Lab
Psychological and Brain Sciences
University of Massachusetts Amherst
——————————————————-------------

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231026/526da8a8/attachment.htm>

From devikadu at gmail.com  Thu Oct 26 22:43:33 2023
From: devikadu at gmail.com (Devika Duggal)
Date: Thu, 26 Oct 2023 16:43:33 -0400
Subject: [FieldTrip] Problem with preprocessed data extraction
Message-ID: <CANExTKJYRQgo8oC9bLcuFKkVsVS9xsVQ6_OhrwgduxwfJ=eixg@mail.gmail.com>

Dear Community,

I am a clinical psychology student working on a study about rejection
sensitivity in a clinical population. We use a modified version of
Cyberball that parametrically modulates the rate of exclusion and are
collecting data using Brain Vision Recorder.

We are running into an issue relating to extracting waves from the
preprocessed data and I am hoping to get some help with this. We
preprocessed the data using FieldTrip but when we try to extract, only 16
of the recorded 131 channels are represented. All the channels were
recording during data collection (as seen on Recorder) so we are not sure
what happened. The channel names were also imported from Recorder for use
in Fieldtrip.


I am new to EEG analysis so my apologies if I sound ignorant. If it is
helpful to look at our FieldTrip code or some of our raw data, I am happy
to send it over.


Best,
Dev
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231026/8f6e960c/attachment.htm>

From janmathijs.schoffelen at donders.ru.nl  Fri Oct 27 09:50:26 2023
From: janmathijs.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Fri, 27 Oct 2023 07:50:26 +0000
Subject: [FieldTrip] Problem with preprocessed data extraction
In-Reply-To: <CANExTKJYRQgo8oC9bLcuFKkVsVS9xsVQ6_OhrwgduxwfJ=eixg@mail.gmail.com>
References: <CANExTKJYRQgo8oC9bLcuFKkVsVS9xsVQ6_OhrwgduxwfJ=eixg@mail.gmail.com>
Message-ID: <9BCAC552-0BB7-4DCF-96F2-91FC5E96B28D@donders.ru.nl>

Dear Dev,

In order to be able to troubleshoot this with you, it would indeed be helpful if we get a bit more detailed insight into what you have been trying to do exactly, and what code you used for that.

But first, I would start with inspecting the EEG data file’s header, by calling:

hdr = ft_read_header(<name-of-the-file>);

Among others, there should be a hdr.label field, which lists the names of the channels in a Nx1 cell-array, where N is the number of detected channels in the data file. N should be hopefully closer to 131 than to 16.

If you can confirm that N is sufficiently large, then I think that in principle the data is OK, and that you need to scrutinize the code you have been using, to try and understand the unexpected outcome.

Perhaps superfluously, but I assume that you also found the following piece of documentation online? https://www.fieldtriptoolbox.org/tutorial/continuous/<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fcontinuous%2F&data=05%7C01%7Cfieldtrip%40science.ru.nl%7C73dc2dd3880d4ea8743c08dbd6c16217%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638339898297341844%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=1R8f4l6KkEY0mqH5Pv0BZ61g9%2FhNlAK%2FPVMnuRTdASE%3D&reserved=0>, and https://www.fieldtriptoolbox.org/getting_started/brainvision/<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Fgetting_started%2Fbrainvision%2F&data=05%7C01%7Cfieldtrip%40science.ru.nl%7C73dc2dd3880d4ea8743c08dbd6c16217%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638339898297495168%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=hKulr8QvZSjx19N%2BuQ0DZldZvDR5JVoUf9JebI9HEeI%3D&reserved=0>

Best wishes,
Jan-Mathijs

On 26 Oct 2023, at 22:43, Devika Duggal via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Dear Community,

I am a clinical psychology student working on a study about rejection sensitivity in a clinical population. We use a modified version of Cyberball that parametrically modulates the rate of exclusion and are collecting data using Brain Vision Recorder.

We are running into an issue relating to extracting waves from the preprocessed data and I am hoping to get some help with this. We preprocessed the data using FieldTrip but when we try to extract, only 16 of the recorded 131 channels are represented. All the channels were recording during data collection (as seen on Recorder) so we are not sure what happened. The channel names were also imported from Recorder for use in Fieldtrip.

I am new to EEG analysis so my apologies if I sound ignorant. If it is helpful to look at our FieldTrip code or some of our raw data, I am happy to send it over.

Best,
Dev

_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=05%7C01%7Cfieldtrip%40science.ru.nl%7C73dc2dd3880d4ea8743c08dbd6c16217%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638339898297495168%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=yacIgh1fJ17unJvbBU5GZqUGwITYPCzYNusvKc%2BJbWg%3D&reserved=0>
https://doi.org/10.1371/journal.pcbi.1002202

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231027/44e6bbac/attachment.htm>

From janmathijs.schoffelen at donders.ru.nl  Fri Oct 27 10:04:42 2023
From: janmathijs.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Fri, 27 Oct 2023 08:04:42 +0000
Subject: [FieldTrip] Artifact rejection problem due to samples occurring
 twice in the data
In-Reply-To: <DB8PR10MB37380BC356D873907E6ACDCCE1DEA@DB8PR10MB3738.EURPRD10.PROD.OUTLOOK.COM>
References: <DB8PR10MB37380BC356D873907E6ACDCCE1DEA@DB8PR10MB3738.EURPRD10.PROD.OUTLOOK.COM>
Message-ID: <244FB7A1-D7BD-4DDE-9B5A-486E940B4259@donders.ru.nl>

Dear Maria,

Thanks for your clear message and diagnostics so far. Just for the clear picture: the error is thrown by ft_artifact_threshold, isn’t it? If I read through the code of this function, I get the impression that you might get yourself back into the game, if you specify cfg.continuous = ‘yes’ for the cfg into ft_artifact_threshold. Although, this feels a bit at odds with the representation of the data that you give as an input to the function, because the time-axes of the individual trials clearly is not continuous. However, the sampelinfo field of the data object is still consistent with a continuous data representation (on disk). It’s the sampleinfo field that ft_fetch_data uses under the hood to determine the overlapping samples. I think that the error will convert into a warning with cfg.continuous = ‘yes’; (unless you have already tried this and can disconfirm my hunch). So, long story short, I’d recommend cfg.continuous = ‘yes’.

Best wishes,
Jan-Mathijs




On 26 Oct 2023, at 11:31, Hartog, M.M.J. den (Maria) via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Dear community,

My name is Maria den Hartog and I am a PhD candidate at the Centre for Language Studies (CLS) at Radboud University in Nijmegen. I am currently preprocessing data from an ERP reading experiment about the processing of pronouns of address (e.g. he, she, they) within a text.

I want to use automatic artifact rejection to remove full trials with signal exceeding +-100 µV as part of my preprocessing pipeline, but I get an error message indicating that 'some of the requested samples occur twice in the data and have conflicting values'. This is true, and it is a consequence of the naturalistic reading paradigm I used. My trials run from -200 ms prestimulus to 1000 ms poststimulus. The t = 0 of each trial is the onset of a pronoun within a text, and the pronouns can occur less than 1000 ms after each other (e.g., the stimuli are he and his in 'He looked at his cat.'). I have baselined my trials to the 200 ms window up to the stimulus, meaning the same sample can have different values in different trials.

The code I use for artifact rejection is:
    cfg = [];
    cfg.continuous = 'no';
    cfg.artfctdef.threshold.min = -100;
    cfg.artfctdef.threshold.max = 100;
    art = ft_artifact_threshold(cfg,data);

    cfg = [];
    cfg.artfctdef.xxx.artifact = art.artfctdef.threshold.artifact;
    data_forERP = ft_rejectartifact(cfg,data);
The error I get:

Error using ft_fetch_data
some of the requested samples occur twice in the data and have conflicting values

Error in ft_artifact_threshold (line 186)
    dat = ft_fetch_data(data,        'header', hdr, 'begsample', trl(trlop,1), 'endsample', trl(trlop,2), 'chanindx', chanindx, 'checkboundary', strcmp(cfg.continuous, 'no'));

Is there a way to adjust the cfg for ft_rejectartifact so that the function will accept that samples do indeed occur twice in the data and that the same sample can have different values in different trials (and data from the correct trial will be fetched)?

Here are a few solutions that I have tried based on other discussion list questions, that I have found to be unsatisfactory or ineffective:

  *   For ft_databrowser, it is possible to use cfg.allowoverlap = 'yes' to avoid errors due to conflicting sample values, but this setting is not available for ft_rejectartifact.
  *   I do not want to remove or adjust the sampleinfo from the data, because I want to be able to relate trials to the original samples if necessary.
  *   I have found that downsampling my signal will lead ft_rejectartifact to reconstruct the sampleinfo assuming that the trials are consecutive segments of a continuous recording, but I do not want to 'hack' my way around the problem in this way.

Hope you can help me out!

Best,
Maria


------------------------------------------------------------------------
Maria den Hartog, MSc | PhD Candidate | Radboud University
Centre for Language Studies | Grammar and Cognition
Working days: Tuesday - Friday | Erasmus Building, Room 8.01



_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=05%7C01%7Cfieldtrip%40science.ru.nl%7C8684386668d54017f87308dbd6c36083%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638339906841784195%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=FEVLnDZ8VZlNHWE%2BhsH9BxytcIDm1mL9jj%2FZMtLiCQw%3D&reserved=0>
https://doi.org/10.1371/journal.pcbi.1002202<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=05%7C01%7Cfieldtrip%40science.ru.nl%7C8684386668d54017f87308dbd6c36083%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638339906841784195%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=of6nOs6lqZHmvWpT4nBZxA0%2BDFJlx%2Ba1P1%2FQz0tTvs0%3D&reserved=0>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231027/e4f0f7a5/attachment.htm>

From nazmiye at mail.uni-paderborn.de  Fri Oct 27 11:57:58 2023
From: nazmiye at mail.uni-paderborn.de (Nazmiye Kurdoglu Turhan)
Date: Fri, 27 Oct 2023 11:57:58 +0200
Subject: [FieldTrip] Marker in the EEG raw data
Message-ID: <b2df8d8ec891329f500a65703df9fbf6@mail.uni-paderborn.de>

Dear community,

I am a master's student at Paderborn University and doing my internship 
at Münster University. I have resting state EEG data, and normally there 
is a marker which shows the beginning of the fixation point in the raw 
data. However, it is not visible on FieldTrip even though I loaded the 
eeg, vhdr and vmrk files. I checked the vmrk file on Matlab and can see 
the marker information there. I also checked the data on eeglab to be 
sure there is a marker, and there is. How can I make the marker visible 
in FieldTrip?

Excuse my question if it is too easy; I am pretty new to FieldTrip. 
Thank you very much in advance.

Sincerly,
Nazmiye Kurdoglu Turhan


From e.eliftulay at gmail.com  Sat Oct 28 11:21:05 2023
From: e.eliftulay at gmail.com (=?UTF-8?Q?Elif_T=C3=BClay?=)
Date: Sat, 28 Oct 2023 12:21:05 +0300
Subject: [FieldTrip] Marker in the EEG raw data
In-Reply-To: <b2df8d8ec891329f500a65703df9fbf6@mail.uni-paderborn.de>
References: <b2df8d8ec891329f500a65703df9fbf6@mail.uni-paderborn.de>
Message-ID: <CALtq08UATPKXHJA3f1mER=LyOivXCyjEmKbcRCGcTNYqbF+fTg@mail.gmail.com>

Dear Nazmiye,

If we assume that you read the data correctly, I have one suggestion which
is not be a good and professional one but it solved my problem temporarily.

I also experienced this problem and used the older version (very old :)) of
fieldtrip toolbox just for ft_databrowser function that help to visualize
the data with markers. I guess that you could store the markers in
fieldtrip structure (you can check this info from ---> data. trialinfo for
your data) but there is something wrong in newest versions when you want to
vizualize them. I actually do not know what is the reason and I could not
have enough time to find it. Probably more technical solutions will come
from the developers but this can be a quick way to solve your problem.

However, please also check your code for reading the data. Did you define
the marker name by using cfg.trialdef.eventvalue? If you share at least
your data reading script with the community, more solutions could come up.

I hope one of them works for you.

Best

On Fri, Oct 27, 2023 at 1:10 PM Nazmiye Kurdoglu Turhan via fieldtrip <
fieldtrip at science.ru.nl> wrote:

> Dear community,
>
> I am a master's student at Paderborn University and doing my internship
> at Münster University. I have resting state EEG data, and normally there
> is a marker which shows the beginning of the fixation point in the raw
> data. However, it is not visible on FieldTrip even though I loaded the
> eeg, vhdr and vmrk files. I checked the vmrk file on Matlab and can see
> the marker information there. I also checked the data on eeglab to be
> sure there is a marker, and there is. How can I make the marker visible
> in FieldTrip?
>
> Excuse my question if it is too easy; I am pretty new to FieldTrip.
> Thank you very much in advance.
>
> Sincerly,
> Nazmiye Kurdoglu Turhan
> _______________________________________________
> 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: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231028/3403b51c/attachment.htm>

From q.huys at ucl.ac.uk  Mon Oct 30 00:29:26 2023
From: q.huys at ucl.ac.uk (Quentin Huys)
Date: Sun, 29 Oct 2023 23:29:26 +0000
Subject: [FieldTrip] postdoc positions in computational psychiatry at UCL
Message-ID: <tnup3pemsed7rofb6pg2t2b7xdsj34ebwk4buwfbrz2aazvzuf@5ylkiztw6l2p>

(Apologies for cross-posting)

We are delighted to announce postdoctoral positions available at the UCL Applied
Computational Psychiatry Lab (www.acplab.org, PI Quentin Huys).

The RELMED project is an exciting computational psychiatry study that will
combine cutting-edge computational methods with two large three-arm randomized
clinical trials to test whether different antidepressants treat depression via
different reinforcement learning mechanisms.

The main outcomes are behaviour and EEG. So we are seeking experts in EITHER
cognitive/RL task design and analysis, OR design and analysis of RL tasks for
EEG. This will be a team, open-science effort, extensively involving lived
experience experts and the wider research community.

Researchers will work with a broad array of expert PIs including including
Michael Browning (Oxford), Ray Dolan (UCL), David Kessler (Bristol), Neil Nixon
(Nottingham), Richard Morriss (Nottingham), Stuart Watson (Newcastle) and Nicola
Wiles (Bristol), and an extensive network of collaborators including Isabel
Berwian (Princeton), Roshan Cools (Donders), Peter Dayan (Max Planck Tuebingen),
Michael Frank (Brown), Nathaniel Daw (Princeton), Catherine Harmer (Oxford), Rob
Howard (UCL), Yael Niv (Princeton), Diego Pizzagalli (Harvard), Argyris
Stringaris (UCL) and others.

The positions should be excellent career opportunities, with outstanding
networking possibilities, the ability to gain experience across clinical,
lived-experience, computational, pharmacological, neuroimaging and open-science
domains, and to answer societally important questions

The Applied Computational Psychiatry lab is situated within the UCL Max Planck
Centre for Computational Psychiatry and Ageing Research and the Division of
Psychiatry at UCL.

Official job advertisement is here:
https://www.ucl.ac.uk/work-at-ucl/search-ucl-jobs/details?nPostingId=7266&nPostingTargetId=16639&id=Q1KFK026203F3VBQBLO8M8M07&LG=UK&languageSelect=UK&mask=ext



From nazmiye at mail.uni-paderborn.de  Mon Oct 30 14:41:33 2023
From: nazmiye at mail.uni-paderborn.de (Nazmiye Kurdoglu Turhan)
Date: Mon, 30 Oct 2023 14:41:33 +0100
Subject: [FieldTrip] Marker in the EEG raw data
In-Reply-To: <CALtq08UATPKXHJA3f1mER=LyOivXCyjEmKbcRCGcTNYqbF+fTg@mail.gmail.com>
References: <b2df8d8ec891329f500a65703df9fbf6@mail.uni-paderborn.de>
 <CALtq08UATPKXHJA3f1mER=LyOivXCyjEmKbcRCGcTNYqbF+fTg@mail.gmail.com>
Message-ID: <349bb292d1c0772a32b1e2eeaaf75cbc@mail.uni-paderborn.de>

Dear Ms.Tülay,

Thank you very much for your email; I appreciate your help. I tried to 
visualize my EEG data with the marker on other versions of Fieldtrip 
(fieldtrip-20230118, fieldtrip-20230202, fieldtrip-20230926, 
fieldtrip-20231025). However, I could not visualize the marker again. Is 
it possible for you to share which version of FieldTrip you used?

I used this code to read the marker file;

cfg = [];
cfg.dataset = 'VP01_3.vmrk';
event = ft_read_event(cfg);

Thank you in advance,
Sincerely,
Nazmiye


From e.eliftulay at gmail.com  Mon Oct 30 16:34:46 2023
From: e.eliftulay at gmail.com (=?UTF-8?Q?Elif_T=C3=BClay?=)
Date: Mon, 30 Oct 2023 18:34:46 +0300
Subject: [FieldTrip] Marker in the EEG raw data
In-Reply-To: <349bb292d1c0772a32b1e2eeaaf75cbc@mail.uni-paderborn.de>
References: <b2df8d8ec891329f500a65703df9fbf6@mail.uni-paderborn.de>
 <CALtq08UATPKXHJA3f1mER=LyOivXCyjEmKbcRCGcTNYqbF+fTg@mail.gmail.com>
 <349bb292d1c0772a32b1e2eeaaf75cbc@mail.uni-paderborn.de>
Message-ID: <CALtq08VAHMxfTtDzBNGjpa5x_eiRED_SYD64zLp5VaLtjs3-jA@mail.gmail.com>

Dear Nazmiye,

I guess there is something wrong in the reading script. I understood that
your data was recorded via Brain products software. Did you check these
tutorials? There are some points that you should pay attention.

     https://www.fieldtriptoolbox.org/getting_started/brainvision/
     https://www.fieldtriptoolbox.org/tutorial/continuous/

https://github.com/fieldtrip/fieldtrip/blob/master/trialfun/ft_trialfun_brainvision_segmented.m
--> if your data has already segmented, you can prefer to use cfg.trialfun
=     'ft_trialfun_brainvision_segmented' for ft_definetrial function

If your problem still exist, then I can share my old version of fieldtrip
with you since it is too old, you can not reach it from download part.

Best


On Mon, Oct 30, 2023 at 4:48 PM Nazmiye Kurdoglu Turhan via fieldtrip <
fieldtrip at science.ru.nl> wrote:

> Dear Ms.Tülay,
>
> Thank you very much for your email; I appreciate your help. I tried to
> visualize my EEG data with the marker on other versions of Fieldtrip
> (fieldtrip-20230118, fieldtrip-20230202, fieldtrip-20230926,
> fieldtrip-20231025). However, I could not visualize the marker again. Is
> it possible for you to share which version of FieldTrip you used?
>
> I used this code to read the marker file;
>
> cfg = [];
> cfg.dataset = 'VP01_3.vmrk';
> event = ft_read_event(cfg);
>
> Thank you in advance,
> Sincerely,
> Nazmiye
> _______________________________________________
> 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: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231030/68a524b8/attachment.htm>

From malte.woestmann at uni-luebeck.de  Mon Oct 30 19:52:31 2023
From: malte.woestmann at uni-luebeck.de (Malte Woestmann)
Date: Mon, 30 Oct 2023 18:52:31 +0000
Subject: [FieldTrip] Open PhD Position - Study Auditory Attention using EEG
Message-ID: <E9E055BB-0E86-4B1E-B13A-80DCE0DE02B3@uni-luebeck.de>

Dear colleagues,

The Department of Psychology at the University of Lübeck is looking to hire a Research Scientist (m/f/d).

The position is available for 3 years. The possibility of obtaining a PhD is given.

The position is situated in the established research group "Auditory Cognition" (Prof. Jonas Obleser) under the supervision of me, PD Dr. rer. nat. Malte Wöstmann. The position is part of a research project funded by the German Science Foundation (DFG). The project aims to explore auditory attention and its neural bases. To this end, we will record behavioral and electroencephalography (EEG) data in younger and older adults to investigate the neuro-cognitive mechanisms underlying capture of attention and suppression of distraction. The position does not come with any teaching obligations.

The complete job ad can be found here (English: https://tinyurl.com/yc8pbffv; German: https://tinyurl.com/33pm7j2n).

Please don’t hesitate to contact me in case you have any further questions.

Kind regards, Malte


Malte Wöstmann
Institut für Psychologie I
Universität zu Lübeck
Tel.: +49 451 3101 3621
Mail: malte.woestmann at uni-luebeck.de

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231030/162bf128/attachment.htm>

From maria.denhartog at ru.nl  Tue Oct 31 08:47:43 2023
From: maria.denhartog at ru.nl (Hartog, M.M.J. den (Maria))
Date: Tue, 31 Oct 2023 07:47:43 +0000
Subject: [FieldTrip] Artifact rejection problem due to samples occurring
 twice in the data
Message-ID: <DB8PR10MB3738EC571089CFFA019E3B38E1A1A@DB8PR10MB3738.EURPRD10.PROD.OUTLOOK.COM>

Dear Jan-Mathijs,

Thank you for your reply.

The error is indeed thrown by ft_artifact_threshold. Unfortunately, specifying cfg.continuous = 'yes' does not solve the problem. The error message after this change is the same as before:

Error using ft_fetch_data
some of the requested samples occur twice in the data and have conflicting values

Error in ft_artifact_threshold (line 186)
    dat = ft_fetch_data(data,        'header', hdr, 'begsample', trl(trlop,1), 'endsample', trl(trlop,2), 'chanindx', chanindx, 'checkboundary', strcmp(cfg.continuous, 'no'));

Is there anything else I can try?

Best,
Maria

------------------------------------------------------------------------

Date: Fri, 27 Oct 2023 08:04:42 +0000
From: "Schoffelen, J.M. (Jan Mathijs)"
        <janmathijs.schoffelen at donders.ru.nl>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] Artifact rejection problem due to samples
        occurring twice in the data
Message-ID: <244FB7A1-D7BD-4DDE-9B5A-486E940B4259 at donders.ru.nl>
Content-Type: text/plain; charset="utf-8"

Dear Maria,

Thanks for your clear message and diagnostics so far. Just for the clear picture: the error is thrown by ft_artifact_threshold, isn’t it? If I read through the code of this function, I get the impression that you might get yourself back into the game, if you specify cfg.continuous = ‘yes’ for the cfg into ft_artifact_threshold. Although, this feels a bit at odds with the representation of the data that you give as an input to the function, because the time-axes of the individual trials clearly is not continuous. However, the sampelinfo field of the data object is still consistent with a continuous data representation (on disk). It’s the sampleinfo field that ft_fetch_data uses under the hood to determine the overlapping samples. I think that the error will convert into a warning with cfg.continuous = ‘yes’; (unless you have already tried this and can disconfirm my hunch). So, long story short, I’d recommend cfg.continuous = ‘yes’.

Best wishes,
Jan-Mathijs

------------------------------------------------------------------------

On 26 Oct 2023, at 11:31, Hartog, M.M.J. den (Maria) via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Dear community,

My name is Maria den Hartog and I am a PhD candidate at the Centre for Language Studies (CLS) at Radboud University in Nijmegen. I am currently preprocessing data from an ERP reading experiment about the processing of pronouns of address (e.g. he, she, they) within a text.

I want to use automatic artifact rejection to remove full trials with signal exceeding +-100 µV as part of my preprocessing pipeline, but I get an error message indicating that 'some of the requested samples occur twice in the data and have conflicting values'. This is true, and it is a consequence of the naturalistic reading paradigm I used. My trials run from -200 ms prestimulus to 1000 ms poststimulus. The t = 0 of each trial is the onset of a pronoun within a text, and the pronouns can occur less than 1000 ms after each other (e.g., the stimuli are he and his in 'He looked at his cat.'). I have baselined my trials to the 200 ms window up to the stimulus, meaning the same sample can have different values in different trials.

The code I use for artifact rejection is:
    cfg = [];
    cfg.continuous = 'no';
    cfg.artfctdef.threshold.min = -100;
    cfg.artfctdef.threshold.max = 100;
    art = ft_artifact_threshold(cfg,data);

    cfg = [];
    cfg.artfctdef.xxx.artifact = art.artfctdef.threshold.artifact;
    data_forERP = ft_rejectartifact(cfg,data);

The error I get:

Error using ft_fetch_data
some of the requested samples occur twice in the data and have conflicting values

Error in ft_artifact_threshold (line 186)
    dat = ft_fetch_data(data,        'header', hdr, 'begsample', trl(trlop,1), 'endsample', trl(trlop,2), 'chanindx', chanindx, 'checkboundary', strcmp(cfg.continuous, 'no'));

Is there a way to adjust the cfg for ft_rejectartifact so that the function will accept that samples do indeed occur twice in the data and that the same sample can have different values in different trials (and data from the correct trial will be fetched)?

Here are a few solutions that I have tried based on other discussion list questions, that I have found to be unsatisfactory or ineffective:

  *   For ft_databrowser, it is possible to use cfg.allowoverlap = 'yes' to avoid errors due to conflicting sample values, but this setting is not available for ft_rejectartifact.
  *   I do not want to remove or adjust the sampleinfo from the data, because I want to be able to relate trials to the original samples if necessary.
  *   I have found that downsampling my signal will lead ft_rejectartifact to reconstruct the sampleinfo assuming that the trials are consecutive segments of a continuous recording, but I do not want to 'hack' my way around the problem in this way.

Hope you can help me out!

Best,
Maria

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231031/53597b5b/attachment.htm>

