From j.ostrowski at uke.de  Thu Jun  1 14:09:58 2023
From: j.ostrowski at uke.de (Jan Ostrowski)
Date: Thu, 1 Jun 2023 14:09:58 +0200
Subject: [FieldTrip] Implementation for wavelet-enhanced ICA
Message-ID: <13497560-7f88-e7d2-7bb7-cd4adf21b646@uke.de>

Dear FieldTrip community,

I have been wondering whether there is an implementation in FieldTrip 
that allows the use of wavelet-enhanced ICA, since I have not been able 
to find one yet.

My aim is to preprocess EEG data that should later be used for analysis 
of phase-based connectivity. However, conventional ICA is said to cause 
distortions in amplitude and phase, and therefore lead to confounds in 
the data when analyzing connectivity. In wavelet-enhanced ICA, on the 
other hand, one would use discrete wavelet transform on the 
artifact-related independent components to filter out the artifacts and 
keep the components, rather than rejecting the whole component and with 
it also valuable signal. That is my understanding at least, so far.

If there is no such implementation in FieldTrip, can you think of other 
toolboxes that might have it? Maybe somebody implemented this in the 
past and could give some pointers on the exact steps of computation.

Any advice is greatly appreciated!

Many thanks!
Jan Ostrowski

-- 
Jan Ostrowski, M.Sc.
Department of Systems Neuroscience
University Medical Center Hamburg-Eppendorf
Martinistr. 52
Building W34, Room 320b
D-20246 Hamburg, Germany

--

_____________________________________________________________________

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | https://urldefense.com/v3/__http://www.uke.de__;!!HJOPV4FYYWzcc1jazlU!-K4pClO9-BOMFGq3-K6m2_GUOoH6Fq7IOUPxyFoxPdxcc_QnJKHze1QrY8HjaoLy9g-36Z7BQ5lxv3Gft11v4ApkFg$ 
Vorstandsmitglieder: Prof. Dr. Christian Gerloff (Vorsitzender), Joachim Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel
_____________________________________________________________________

SAVE PAPER - THINK BEFORE PRINTING



From z65.juhasz at gmail.com  Thu Jun  1 14:51:56 2023
From: z65.juhasz at gmail.com (Zoltan Juhasz)
Date: Thu, 1 Jun 2023 14:51:56 +0200
Subject: [FieldTrip] Implementation for wavelet-enhanced ICA
In-Reply-To: <13497560-7f88-e7d2-7bb7-cd4adf21b646@uke.de>
References: <13497560-7f88-e7d2-7bb7-cd4adf21b646@uke.de>
Message-ID: <CANxafJm=rDkKVaehY1Zut13m_aok6mK2fZo96OVke5MMSdCrTA@mail.gmail.com>

Dear Jan,
We have implemented one version with my -then- PhD student, which may be
usable but probably needs some update and polishing. It was not intended
for public use but for artifact removal research. If you are interested,
please, drop me an email and we can discuss it further.

Zoltan Juhasz (juhasz at virt.uni-pannon.hu)
University of Pannonia, Veszprem, Hungary

On Thu, Jun 1, 2023 at 2:45 PM Jan Ostrowski via fieldtrip <
fieldtrip at science.ru.nl> wrote:

> Dear FieldTrip community,
>
> I have been wondering whether there is an implementation in FieldTrip
> that allows the use of wavelet-enhanced ICA, since I have not been able
> to find one yet.
>
> My aim is to preprocess EEG data that should later be used for analysis
> of phase-based connectivity. However, conventional ICA is said to cause
> distortions in amplitude and phase, and therefore lead to confounds in
> the data when analyzing connectivity. In wavelet-enhanced ICA, on the
> other hand, one would use discrete wavelet transform on the
> artifact-related independent components to filter out the artifacts and
> keep the components, rather than rejecting the whole component and with
> it also valuable signal. That is my understanding at least, so far.
>
> If there is no such implementation in FieldTrip, can you think of other
> toolboxes that might have it? Maybe somebody implemented this in the
> past and could give some pointers on the exact steps of computation.
>
> Any advice is greatly appreciated!
>
> Many thanks!
> Jan Ostrowski
>
> --
> Jan Ostrowski, M.Sc.
> Department of Systems Neuroscience
> University Medical Center Hamburg-Eppendorf
> Martinistr. 52
> Building W34, Room 320b
> D-20246 Hamburg, Germany
>
> --
>
> _____________________________________________________________________
>
> Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen
> Rechts; Gerichtsstand: Hamburg |
> https://urldefense.com/v3/__http://www.uke.de__;!!HJOPV4FYYWzcc1jazlU!-K4pClO9-BOMFGq3-K6m2_GUOoH6Fq7IOUPxyFoxPdxcc_QnJKHze1QrY8HjaoLy9g-36Z7BQ5lxv3Gft11v4ApkFg$
> Vorstandsmitglieder: Prof. Dr. Christian Gerloff (Vorsitzender), Joachim
> Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel
> _____________________________________________________________________
>
> SAVE PAPER - THINK BEFORE PRINTING
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!-0nU0uexAyV0Cv-BRxHWsMXp2LAocg0Sr2QCqK00NBO1R38XtzAxc75EooN2yeSHZ3xPto0uE5koln4v_ThzSst-$ 
>
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From h.park at bham.ac.uk  Thu Jun  1 15:01:07 2023
From: h.park at bham.ac.uk (Hyojin Park)
Date: Thu, 1 Jun 2023 13:01:07 +0000
Subject: [FieldTrip] Competition Funded PhD Project (open to UK home and
 International students)
In-Reply-To: <LNXP265MB17565E5CBD9479ABD89814ADAE779@LNXP265MB1756.GBRP265.PROD.OUTLOOK.COM>
References: <LNXP265MB17565E5CBD9479ABD89814ADAE779@LNXP265MB1756.GBRP265.PROD.OUTLOOK.COM>
Message-ID: <dbcd4ec692ce453eaa7fb6156574e47b@LNXP265MB1756.GBRP265.PROD.OUTLOOK.COM>

Dear all,

This is the last reminder for the PhD opportunity below! (Deadline: 5th June).
Please apply and share with your network!! Any questions are welcome!

Thank you.
Best,
Hyojin

From: fieldtrip <fieldtrip-bounces at science.ru.nl> On Behalf Of Hyojin Park via fieldtrip
Sent: 10 May 2023 16:48
To: fieldtrip at science.ru.nl
Cc: Hyojin Park (Psychology) <h.park at bham.ac.uk>
Subject: [FieldTrip] Competition Funded PhD Project (open to UK home and International students)

CAUTION: This email originated from outside the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe.

Project Title: Information processing from childhood into older age: A developmental lifespan perspective on neural plasticity in learning strategies

Institution: University of Birmingham, School of Psychology, Centre for Human Brain Health (CHBH), Centre for Developmental Science (CDS)

Supervisors: Dr. Hyojin Park and Dr. Katrien Segaert


We are inviting applications for a PhD studentship (start date September 18th 2023) in the School of Psychology and Centre for Human Brain Health (CHBH) at the University of Birmingham. This is a fully funded studentship which also covers UK home fees but is open to international students (details below). We are searching for a highly talented and dedicated PhD student with a 1st class or 2:1 degree in the field of psychology, cognitive neuroscience or similar disciplines (see criteria below).
We are keen to recruit PhD students from under-represented groups, for example, home students who identify as BAME or those who grew up or went to school in an area where young people are less likely to enter higher education.
The project will be about learning strategies for effective communication. Effective communication in social situations relies heavily on the brain's ability to integrate information from different sources. Despite the fact that this ability is crucial for communication abilities throughout one's life, we know very little about the development of these strategies in early childhood and changes in the context of cognitive decline in older adulthood. This PhD project will take a lifespan perspective to investigate how the brain utilises and integrates visual and auditory information to process information efficiently in children, young adults and the elderly. To do this, the project will combine analysis of an existing neuroimaging dataset (including children) with new neuroimaging data-collection of young and older adults (using MEG/OPM-MEG). Brain oscillations data will then be linked to behavior. To do this, we will be using natural language processing (NLP) algorithms based on large-language models (LLMs) to decode the brain activity.

Essential skills:

  *   At least 1st class or 2:1 degree classification in relevant areas (MSc degree is a plus but we will consider students with a BSc degree)

  *   Degree in psychology, neuroscience, medicine, physics, computer science, experimental linguistics or a related discipline relevant to cognitive neuroscience/neuroimaging
  *   Relevant academic or non-academic experience or expertise relevant to the research project
  *   Excellent English language skills
  *   Strong organisation and time-management skills
  *   Strong commitment, flexibility, independence
  *   A positive problem-solving attitude and strong teamwork skills


Desirable skills:

  *   Experience with cognitive neuroscience research (human electrophysiology using MEG/EEG/OPM-MEG or other)
  *   Programming skills (MATLAB, Python, R or similar)
  *   Knowledge of general statistics for data analysis
  *   Notes: These are skills that will be required to complete the PhD. However, we will also consider applicants who do not yet have these skills but are highly motivated to learn them during the project.
  *   Candidates from underrepresented groups in the PGR cohort


How to apply
Deadline for applications: Monday 5th June 2023 midnight
Please send the documents (pdf, max 5 MB) below to supervisors' emails:
Dr. Hyojin Park: h.park at bham.ac.uk<mailto:h.park at bham.ac.uk>, Dr. Katrien Segaert: k.segaert at bham.ac.uk<mailto:k.segaert at bham.ac.uk>

  *   Application form (download<https://urldefense.com/v3/__https:/drive.google.com/uc?export=download&id=1CSazI0eQgfXDcunFcj0L-eLUPgcRLZrH__;!!HJOPV4FYYWzcc1jazlU!9Jwpp1Tm4pRanUi5VOwVjUES_RvnHsA0P_H0W_KLAI5SKUU1hyP8iCT_A4u7RO2knm7hQeogFHndIvHfFikpq1o$>)
  *   CV
  *   Academic transcripts
  *   Names and contact details of two referees
Email subject line should be [PhD application] Your name (First, Last)

The interview process will consist of two stages. The first interview stage will be with the supervisors (provisionally scheduled to take place on Friday June 9th). Candidates who pass the first stage, will proceed to a second stage with a wider University interview panel (provisionally scheduled June 22/June 23).
If you have any questions, please contact supervisors.


Funding Notes
The studentship will cover UK tuition fees and monthly stipend at UKRI rate for 3.5 years.
For international students: Funding will only cover home tuition fees, therefore, international students would need to cover the gap between home and international tuition fee rates. If you are an international student, you will need to confirm that you are able to cover the fee difference.


FindAPhD Link
https://urldefense.com/v3/__https://www.findaphd.com/phds/project/information-processing-from-childhood-into-older-age-a-developmental-lifespan-perspective-on-neural-plasticity-in-learning-strategies/?p158217__;!!HJOPV4FYYWzcc1jazlU!4AlYs5YLzf3m2-Asy2EJEAzEAEkNUmO_vbOgH4dxPhTxACnCnvcAg_qGizp1K7dJnJN4LzlycCO_NLH9cpv79Jk$ <https://urldefense.com/v3/__https:/www.findaphd.com/phds/project/information-processing-from-childhood-into-older-age-a-developmental-lifespan-perspective-on-neural-plasticity-in-learning-strategies/?p158217__;!!HJOPV4FYYWzcc1jazlU!9Jwpp1Tm4pRanUi5VOwVjUES_RvnHsA0P_H0W_KLAI5SKUU1hyP8iCT_A4u7RO2knm7hQeogFHndIvHfVv4dQlM$>


Please take a look at the group webpages of the supervisors and our Centres & University.

  *   Dr. Hyojin Park: https://urldefense.com/v3/__https://www.neureca.org/__;!!HJOPV4FYYWzcc1jazlU!4AlYs5YLzf3m2-Asy2EJEAzEAEkNUmO_vbOgH4dxPhTxACnCnvcAg_qGizp1K7dJnJN4LzlycCO_NLH9mh9MGTc$ <https://urldefense.com/v3/__https:/www.neureca.org/__;!!HJOPV4FYYWzcc1jazlU!9Jwpp1Tm4pRanUi5VOwVjUES_RvnHsA0P_H0W_KLAI5SKUU1hyP8iCT_A4u7RO2knm7hQeogFHndIvHf_zyftMk$>
  *   Dr. Katrien Segaert: https://urldefense.com/v3/__https://www.katriensegaert.com/__;!!HJOPV4FYYWzcc1jazlU!4AlYs5YLzf3m2-Asy2EJEAzEAEkNUmO_vbOgH4dxPhTxACnCnvcAg_qGizp1K7dJnJN4LzlycCO_NLH9bXTDEfA$ <https://urldefense.com/v3/__https:/www.katriensegaert.com/__;!!HJOPV4FYYWzcc1jazlU!9Jwpp1Tm4pRanUi5VOwVjUES_RvnHsA0P_H0W_KLAI5SKUU1hyP8iCT_A4u7RO2knm7hQeogFHndIvHfox_6dEs$>
  *   School of Psychology: https://urldefense.com/v3/__https://www.birmingham.ac.uk/schools/psychology/index.aspx__;!!HJOPV4FYYWzcc1jazlU!4AlYs5YLzf3m2-Asy2EJEAzEAEkNUmO_vbOgH4dxPhTxACnCnvcAg_qGizp1K7dJnJN4LzlycCO_NLH9GNglFWo$ <https://urldefense.com/v3/__https:/www.birmingham.ac.uk/schools/psychology/index.aspx__;!!HJOPV4FYYWzcc1jazlU!9Jwpp1Tm4pRanUi5VOwVjUES_RvnHsA0P_H0W_KLAI5SKUU1hyP8iCT_A4u7RO2knm7hQeogFHndIvHf4LOVBHg$>
  *   CHBH: https://urldefense.com/v3/__https://www.birmingham.ac.uk/research/centre-for-human-brain-health/index.aspx__;!!HJOPV4FYYWzcc1jazlU!4AlYs5YLzf3m2-Asy2EJEAzEAEkNUmO_vbOgH4dxPhTxACnCnvcAg_qGizp1K7dJnJN4LzlycCO_NLH9Dp_fOdE$ <https://urldefense.com/v3/__https:/www.birmingham.ac.uk/research/centre-for-human-brain-health/index.aspx__;!!HJOPV4FYYWzcc1jazlU!9Jwpp1Tm4pRanUi5VOwVjUES_RvnHsA0P_H0W_KLAI5SKUU1hyP8iCT_A4u7RO2knm7hQeogFHndIvHfGRHgxvo$>
  *   CDS: https://urldefense.com/v3/__https://www.birmingham.ac.uk/research/centre-for-developmental-science/index.aspx__;!!HJOPV4FYYWzcc1jazlU!4AlYs5YLzf3m2-Asy2EJEAzEAEkNUmO_vbOgH4dxPhTxACnCnvcAg_qGizp1K7dJnJN4LzlycCO_NLH9rTyPDXc$ <https://urldefense.com/v3/__https:/www.birmingham.ac.uk/research/centre-for-developmental-science/index.aspx__;!!HJOPV4FYYWzcc1jazlU!9Jwpp1Tm4pRanUi5VOwVjUES_RvnHsA0P_H0W_KLAI5SKUU1hyP8iCT_A4u7RO2knm7hQeogFHndIvHfG0-a_gE$>
  *   University of Birmingham: https://urldefense.com/v3/__https://www.birmingham.ac.uk/index.aspx__;!!HJOPV4FYYWzcc1jazlU!4AlYs5YLzf3m2-Asy2EJEAzEAEkNUmO_vbOgH4dxPhTxACnCnvcAg_qGizp1K7dJnJN4LzlycCO_NLH9ICmxHgA$ <https://urldefense.com/v3/__https:/www.birmingham.ac.uk/index.aspx__;!!HJOPV4FYYWzcc1jazlU!9Jwpp1Tm4pRanUi5VOwVjUES_RvnHsA0P_H0W_KLAI5SKUU1hyP8iCT_A4u7RO2knm7hQeogFHndIvHf4iRpnNE$>


---------------------
Hyojin Park, PhD

Assistant Professor & Birmingham Fellow
Centre for Human Brain Health (CHBH), School of Psychology
University of Birmingham
https://urldefense.com/v3/__https://www.birmingham.ac.uk/staff/profiles/psychology/park-hyojin.aspx__;!!HJOPV4FYYWzcc1jazlU!4AlYs5YLzf3m2-Asy2EJEAzEAEkNUmO_vbOgH4dxPhTxACnCnvcAg_qGizp1K7dJnJN4LzlycCO_NLH9VqHP80w$ <https://urldefense.com/v3/__https:/www.birmingham.ac.uk/staff/profiles/psychology/park-hyojin.aspx__;!!HJOPV4FYYWzcc1jazlU!9Jwpp1Tm4pRanUi5VOwVjUES_RvnHsA0P_H0W_KLAI5SKUU1hyP8iCT_A4u7RO2knm7hQeogFHndIvHf5Oa_eMo$>
https://urldefense.com/v3/__https://www.neureca.org/__;!!HJOPV4FYYWzcc1jazlU!4AlYs5YLzf3m2-Asy2EJEAzEAEkNUmO_vbOgH4dxPhTxACnCnvcAg_qGizp1K7dJnJN4LzlycCO_NLH9mh9MGTc$ <https://urldefense.com/v3/__https:/www.neureca.org/__;!!HJOPV4FYYWzcc1jazlU!9Jwpp1Tm4pRanUi5VOwVjUES_RvnHsA0P_H0W_KLAI5SKUU1hyP8iCT_A4u7RO2knm7hQeogFHndIvHf_zyftMk$>
[image001.png]


---
Dr. Katrien Segaert
Associate Professor - School of Psychology and Centre for Human Brain Health, University of Birmingham
Editor in Chief for Cognition
katriensegaert.com / @katrien_segaert

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From shlomitbeker at gmail.com  Thu Jun  1 23:01:18 2023
From: shlomitbeker at gmail.com (Shlomit Beker)
Date: Thu, 1 Jun 2023 17:01:18 -0400
Subject: [FieldTrip] =?utf-8?q?Postdoctoral_research_position_=E2=80=93_H?=
	=?utf-8?q?uman_Electrophysiology_Studies_in_Autism_=28Prof=2E_Molh?=
	=?utf-8?q?olm=29?=
Message-ID: <CALOh7+Ofc02N+sv3eqO=J5gh8dx48s1K9daFUvGdMF5XrEtKCw@mail.gmail.com>

Dear FieldTrip community -


*A postdoctoral research position is available in the Department of
Neuroscience at the Albert Einstein College of Medicine in the Cognitive
Neuropsychology Laboratory (CNL) of Dr. Sophie Molholm, PhD*. We are a
well-funded and highly productive lab (>100 publications and counting).We
work closely with a vibrant network of investigators within Einstein (Dr.
Ruben Coen-Cagli, PhD, Department of Systems & Computational Biology; Dr.
Peter Kaskan, Department of Neurosurgery) as well as collaborators at the
University of Rochester Medical Center (Dr. John Foxe, Department of
Neuroscience) and the University of Bologna (Dr. Cristiano Cuppini,
Department of Electrical Engineering).



We use psychophysics, EEG, and clinical and cognitive assessments to study
attention, auditory and visual perception, multisensory processing, and
executive function, in typical and clinical populations. We also have
access to research MRI which we use as appropriate. In our work we strive
to advance understanding of sensory, perceptual and cognitive processing
with the use of cutting-edge methodologies and data analytic techniques. In
turn, we seek to apply this understanding to explore the processing
differences underlying clinical and developmental disorders such as autism
and schizophrenia.

Current projects on autism focus on neuro-oscillatory dysfunction,
predictive processing, CNS-ANS-Environment interactions, multisensory
speech perception, and the interplay of the sensory systems.  In addition,
we have ongoing projects on rare genetic conditions including Rett Syndrome
and Cystinosis, and in 22q11.2 Deletion Syndrome and schizophrenia.



Successful applicants should have strong interests and skills in analyzing
multichannel neurophysiological data in both the spectral and temporal
domains and statistical and writing skills.  An interest in using
computational modeling and machine learning is a plus. A fully funded
position at NIH stipend levels with an initial appointment of two years is
available with the potential for continuation. Interested individuals may
send a CV and statement of interest to sophie.molholm at einsteinmed.edu.
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From christoph.braun at uni-tuebingen.de  Sat Jun  3 10:02:08 2023
From: christoph.braun at uni-tuebingen.de (Christoph Braun)
Date: Sat, 3 Jun 2023 10:02:08 +0200
Subject: [FieldTrip] =?utf-8?q?T=C3=BCbingen_Systems_Neuroscience_Symposi?=
 =?utf-8?q?um_2023?=
Message-ID: <d32bbb40-c554-aeff-33e7-5631cd1f420b@uni-tuebingen.de>

The Centre for Integrative Neuroscience and the MEG Center of
the University of Tuebingen are pleased to announce the

       2023 Tuebingen Systems Neuroscience Symposium (SNS2023)

The symposium takes place on September 14 and 15, 2023 at the University
of Tuebingen. This annual international meeting brings together
leading researchers in the field of systems neuroscience featuring
plenary talks, poster sessions and social events. Join us in Tuebingen
to learn about the latest advances in systems neuroscience.

Confirmed speakers:

Ivan de Araujo
Tatiana Engel
Anne-Lise Giraud
Klaus-Peter Hoffmann
Tadashi Isa
Katja Kornysheva
Michael Long
Lucia Melloni
Andreas Nieder
Ueli Rutishauser
Eleonora Russo
Alexander Thiele


For more information and registration, please visit:
https://urldefense.com/v3/__http://meg.medizin.uni-tuebingen.de/2023/__;!!HJOPV4FYYWzcc1jazlU!9Ohb7UBeh34u4q901mEOv0LFCz2NHA7dnvkVaoZUu3n170aPlfwwZU1Be17j3YHtkiIggdiNFFVAxb9ouuvkMaua7tfJE-EKX2n_wIQ$ 

Please forward this information to any of your colleagues and

collaborators that may be interested in the symposium.

--

Center for Integrative Neuroscience (CIN) &
MEG-Center University of Tübingen
Otfried-Müller-Str. 47
72076 Tübingen
Tel: +49 7071 29 87705
Email: christoph.braun at uni-tuebingen.de
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From emma.holmes at ucl.ac.uk  Mon Jun  5 17:37:07 2023
From: emma.holmes at ucl.ac.uk (Holmes, Emma)
Date: Mon, 5 Jun 2023 15:37:07 +0000
Subject: [FieldTrip] PhD and Postdoc positions at UCL
Message-ID: <AS8PR01MB7224CFD43FBF2D552962B524A64DA@AS8PR01MB7224.eurprd01.prod.exchangelabs.com>

*** Please forward to any potential candidates in your networks who may be interested in these positions ***


I am currently advertising two positions to join my lab, the Cognitive Hearing Lab, at UCL (London, UK). My lab combines behavioural techniques (e.g., auditory psychophysics), cognitive neuroscience (e.g., EEG, MEG, and fMRI), and computational modelling. Both positions are part of a Wellcome-funded grant to examine how central cognitive pathways interact with hearing loss.


(1) Funded PhD opportunity (3-4 years) - CLOSING SOON (Application deadline: 8th June 2023)

The appointed candidate will lead work using behaviour and pupillometry, to examine how central cognitive pathways interact with hearing loss. UK students will receive a salary at Grade 6 and their PhD fees fully covered. International students will receive a salary at Grade 6 and their PhD fees partially covered. The preferred start date for the position is 25th September 2023. Full details and application portal: https://urldefense.com/v3/__https://www.ucl.ac.uk/work-at-ucl/search-ucl-jobs/details?jobId=10345&jobTitle=Research*20Assistant*20(with*20MPhil*2FPhD*20enrollment)__;JSUlJSU!!HJOPV4FYYWzcc1jazlU!4zW5uXViFP4IB-kmOxwXJfoDP9D_0jQ2ouCRbZcbVE70z_i6o_g6a-EyI40kWBgAo0CckBWJC4AuvCXuDTbcyaJRPXDg$ 

(2) Postdoc position (3+ years) - Application deadline: 23rd June 2023
The appointed candidate will examine how central cognitive pathways interact with hearing loss, leading work using 7-Tesla MRI, which will allow us to estimate laminar-specific cortical responses in humans. The preferred start date for the position is September 2023. Full details and application portal: https://urldefense.com/v3/__https://www.ucl.ac.uk/work-at-ucl/search-ucl-jobs/details?jobId=10852&jobTitle=Resarch*20Fellow__;JQ!!HJOPV4FYYWzcc1jazlU!4zW5uXViFP4IB-kmOxwXJfoDP9D_0jQ2ouCRbZcbVE70z_i6o_g6a-EyI40kWBgAo0CckBWJC4AuvCXuDTbcyaVEY9ds$ 

Feel free to get in touch with me (emma.holmes at ucl.ac.uk) for informal queries about either position


Best wishes,

Emma


Emma Holmes
Lecturer in Speech and Hearing Science, UCL
(she/her)

e-mail: emma.holmes at ucl.ac.uk<mailto:emma.holmes at ucl.ac.uk>
website: https://urldefense.com/v3/__https://emmaholmes.co.uk/__;!!HJOPV4FYYWzcc1jazlU!4zW5uXViFP4IB-kmOxwXJfoDP9D_0jQ2ouCRbZcbVE70z_i6o_g6a-EyI40kWBgAo0CckBWJC4AuvCXuDTbcyU_wD7H6$ 
twitter: @Emma_Holmes_90<https://urldefense.com/v3/__https://twitter.com/Emma_Holmes_90__;!!HJOPV4FYYWzcc1jazlU!4zW5uXViFP4IB-kmOxwXJfoDP9D_0jQ2ouCRbZcbVE70z_i6o_g6a-EyI40kWBgAo0CckBWJC4AuvCXuDTbcyYU34hld$ >

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.
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From andyk at usc.edu  Tue Jun  6 02:42:27 2023
From: andyk at usc.edu (Andy Kim)
Date: Mon, 5 Jun 2023 17:42:27 -0700
Subject: [FieldTrip] Unrecognized field name "dimord" during
 ft_timelockanalysis
Message-ID: <CD8270F4-768B-4714-BC2D-5D011C3B6FE6@usc.edu>

Dear community,

My name is Andy Kim and I am trying to complete cluster-based permutation tests on event-related fields using the FieldTrip toolbox tutorial (https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock/__;!!HJOPV4FYYWzcc1jazlU!-SFXKQT1GL1-POlF7Tj2IUUkZ78bg-KMPsdhinve9Bd3ncr1xtEi7f54D21l6k0asfuAhWSb9wanXJa7lQ$ ). The issue I believe is that I have completed pre-processing using EEGLAB and converted the already pre-processed data using eeglab2fieldtrip.

ft_data_tar = eeglab2fieldtrip(EEG2, 'timelock’);

However, when I run ft_timelockanalysis, I get the following error.

timelock_tar    = ft_timelockanalysis(cfg, ft_data_tar);

The input is timelock data with 63 channels and 750 timebins
Unrecognized field name "dimord”. 
Error in dimlength (line 74) elseif strcmp(data.(fld), 'rpt_pos’) 
Error in fixsampleinfo (line 56) ntrial = dimlength(data, 'rpt’);
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_timelockanalysis (line 83) data = ft_checkdata(data, 'datatype', {'raw+comp', 'raw'}, 'feedback', 'yes', 'hassampleinfo', 'yes');

Is this “dimord” field name an issue with the data conversion from EEGLAB to FieldTrip? I am not quite sure where to look and would appreciate any help in sending me in the right direction for debugging. Thank you.

Best,
Andy
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From E.Sohoglu at sussex.ac.uk  Wed Jun  7 12:34:15 2023
From: E.Sohoglu at sussex.ac.uk (Ediz Sohoglu)
Date: Wed, 7 Jun 2023 10:34:15 +0000
Subject: [FieldTrip] RA position at University of Sussex, UK
Message-ID: <LO6P302MB0254FC63C992384EC19FFEFED353A@LO6P302MB0254.GBRP302.PROD.OUTLOOK.COM>

Dear colleagues,

I would be grateful if you could circulate details about a 1-year Research Assistant position available at the University of Sussex, Brighton, UK. This position would suit a recent BSc or MSc graduate with experience of running EEG experiments.

Many thanks,

Ed


We are seeking a research assistant to join an exciting one-year research project examining how our brains use top-down mechanisms to predict upcoming words in speech (‘predictive coding’). The project will use electroencephalography (EEG) recordings of brain activity from healthy volunteers.

The project is funded by a BIAL Foundation grant awarded to Dr Ediz Sohoglu. The post-holder will join the Auditory Cognition Group, which conducts research into the psychology and neuroscience of how we listen, with a particular focus on speech perception.

The project will take place at the University of Sussex, using the on-campus EEG facilities within the School of Psychology. The post-holder will join the highly collaborative and interdisciplinary Sussex Neuroscience research community, which includes over 50 research groups, forming one of the highest densities of Neuroscience faculty in any UK University.

The post-holder will support Dr Sohoglu in the day-to-day running of the project, including participant recruitment, data collection and management, and analysis.

The post is likely to be of most interest to applicants with research interests in perception and language, studied using methods from cognitive neuroscience (e.g. EEG or other neuroimaging method). The post-holder should have experience in the acquisition of EEG data. Experience of EEG data analysis is desirable.
Please contact Dr Ediz Sohoglu (e.sohoglu at sussex.ac.uk<mailto:e.sohoglu at sussex.ac.uk>) for informal enquiries. Further details, including how to apply, can be found here: https://urldefense.com/v3/__https://www.sussex.ac.uk/about/jobs/research-assistant-ref-20854__;!!HJOPV4FYYWzcc1jazlU!56xbggTEgY8UgWnxjtg6wkMaOMltdjq1wAgi8nYevU3PAOEqEXwx8z2ewqZt8x0hNXehnxkZRfrL5DvS7hLojRJKWfdK$ 


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From e.fraats at kpnmail.nl  Fri Jun  9 15:03:49 2023
From: e.fraats at kpnmail.nl (Evelyne Fraats)
Date: Fri, 9 Jun 2023 15:03:49 +0200
Subject: [FieldTrip] trial error
Message-ID: <001001d99ad2$d5bfd970$813f8c50$@kpnmail.nl>

Dear all,

 

My name is Evelyne and I am just started to explore fieldtrip.

I use fieldtrip to define trials in physiological recordings to estimate
physiological regressors for MRI preprocessing. 

However, when using the physio toolbox, no trials are detected within my
data.

When I run the separate ft_definetrial function, I get trials, but I seem to
fail to include this in my matlabbatch.

This is my output with error message:

 

evaluating trial function 'ft_trialfun_general'

reading the header from
'/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'

reading the events from
'/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'

found 169 events

created 20 trials

the call to "ft_definetrial" took 0 seconds and required the additional
allocation of an estimated 0 MB

Item model: No field(s) named

event

 

 

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

09-Jun-2023 15:02:40 - Running job #41

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

09-Jun-2023 15:02:40 - Running 'TAPAS PhysIO Toolbox'

Warning: cfg.trialdef.eventtype='?' is deprecated, please specify
cfg.trialfun='ft_trialfun_show' 

evaluating trial function 'ft_trialfun_show'

reading the events from
'/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'

the following events were found in the data

event type: 'New Segment' 

with event values: 

 

event type: 'Response' 

with event values: 'R  1' 

 

event type: 'Stimulus' 

with event values: 'S  1' 'S 97' 

 

no trials have been defined yet, see FT_DEFINETRIAL for further help

found 169 events

the call to "ft_definetrial" took 0 seconds and required the additional
allocation of an estimated 0 MB

evaluating trial function 'ft_trialfun_general'

reading the header from
'/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'

reading the events from
'/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'

09-Jun-2023 15:02:41 - Failed  'TAPAS PhysIO Toolbox'

Error using ft_definetrial

no trials were defined, see FT_DEFINETRIAL for help

 

The following modules did not run:

Failed: TAPAS PhysIO Toolbox

 

Error using MATLABbatch system

Job execution failed. The full log of this run can be found in MATLAB
command window, starting with the lines (look for the line showing the

exact #job as displayed in this error message)

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

Running job #41

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

 

 

This is my code:

 

if physio_regressor == 1

        %cd /home/affneu/evefra/Spinalcord/data/Physio/ 

        %define log input

        data_path_physio = fullfile(data_path, 'Physio');

        data_path_physio_sub = dir(fullfile(data_path_physio,
sprintf('subx%d*threat*.eeg', sub))) ; %CHANE FORMAT       

        filenames = {data_path_physio_sub.name};

        filenames = filenames';  

        filefolder = {data_path_physio_sub.folder};

        filefolder = filefolder';

        filename_folder = cellfun(@(folder, name) fullfile(folder, name),
filefolder, filenames, 'UniformOutput', false);

 

        %define vhdr

        data_path_physio_sub = dir(fullfile(data_path_physio,
sprintf('subx%d*threat*.vhdr', sub))) ; %CHANE FORMAT       

        filenames = {data_path_physio_sub.name};

        filenames = filenames';  

        filefolder = {data_path_physio_sub.folder};

        filefolder = filefolder';

        filename_folder_vhdr = cellfun(@(folder, name) fullfile(folder,
name), filefolder, filenames, 'UniformOutput', false);

 

        %define vmkr

        data_path_physio_sub = dir(fullfile(data_path_physio,
sprintf('subx%d*threat*.vmrk', sub))) ; %CHANE FORMAT       

        filenames = {data_path_physio_sub.name};

        filenames = filenames';  

        filefolder = {data_path_physio_sub.folder};

        filefolder = filefolder';

        filename_folder_vmrk = cellfun(@(folder, name) fullfile(folder,
name), filefolder, filenames, 'UniformOutput', false);

 

        %define trials

        cfg = [];

        cfg.headerfile = char(filename_folder_vhdr);

        cfg.eventfile = char(filename_folder_vmrk);

        cfg.trialdef.eventtype = 'Stimulus';  

        cfg.trialdef.eventvalue = 'S  1';   

        cfg.trialdef.prestim = 0;             

        cfg.trialdef.poststim = 0; 

        %cfg.trialfun = 'ft_trialfun_show';

        trials = ft_definetrial(cfg);

        

 

      

        %run regressor estimation

               

        clear matlabbatch

        matlabbatch{1}.spm.tools.physio.save_dir =
{fullfile(data_path_tos_brain,'physio_regressors')};

        matlabbatch{1}.spm.tools.physio.log_files.vendor = 'BrainProducts';

        matlabbatch{1}.spm.tools.physio.log_files.cardiac = filename_folder;

        matlabbatch{1}.spm.tools.physio.log_files.respiration =
filename_folder;

        matlabbatch{1}.spm.tools.physio.log_files.scan_timing = {''};

        matlabbatch{1}.spm.tools.physio.log_files.sampling_interval = [];

        matlabbatch{1}.spm.tools.physio.log_files.relative_start_acquisition
= 0;

        matlabbatch{1}.spm.tools.physio.log_files.align_scan = 'last';

        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nslices = 44;

        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.NslicesPerBeat =
[];

        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.TR = 3.39;

        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Ndummies = 0;

        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nscans = 147;

        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.onset_slice = 1;

 
matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.time_slice_to_slice = [];

        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nprep = [];

        matlabbatch{1}.spm.tools.physio.scan_timing.sync.nominal =
struct([]);

        matlabbatch{1}.spm.tools.physio.preproc.cardiac.modality = 'ECG';

        matlabbatch{1}.spm.tools.physio.preproc.cardiac.filter.no =
struct([]);

 
matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_m
atched.min = 0.4;

 
matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_m
atched.file = 'initial_cpulse_kRpeakfile.mat';

 
matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_m
atched.max_heart_rate_bpm = 90;

 
matlabbatch{1}.spm.tools.physio.preproc.cardiac.posthoc_cpulse_select.off =
struct([]);

        matlabbatch{1}.spm.tools.physio.preproc.respiratory.filter.passband
= [0.01 2];

        matlabbatch{1}.spm.tools.physio.preproc.respiratory.despike = false;

        matlabbatch{1}.spm.tools.physio.model.output_multiple_regressors =
'multiple_regressors.txt';

        matlabbatch{1}.spm.tools.physio.model.output_physio = 'physio.mat';

        matlabbatch{1}.spm.tools.physio.model.orthogonalise = 'none';

 
matlabbatch{1}.spm.tools.physio.model.censor_unreliable_recording_intervals
= false;

        matlabbatch{1}.spm.tools.physio.model.retroicor.yes.order.c = 3;

        matlabbatch{1}.spm.tools.physio.model.retroicor.yes.order.r = 4;

        matlabbatch{1}.spm.tools.physio.model.retroicor.yes.order.cr = 1;

        matlabbatch{1}.spm.tools.physio.model.rvt.no = struct([]);

        matlabbatch{1}.spm.tools.physio.model.hrv.no = struct([]);

        matlabbatch{1}.spm.tools.physio.model.noise_rois.no = struct([]);

        matlabbatch{1}.spm.tools.physio.model.movement.no = struct([]);

        matlabbatch{1}.spm.tools.physio.model.other.no = struct([]);

        matlabbatch{1}.spm.tools.physio.verbose.level = 2;

        matlabbatch{1}.spm.tools.physio.verbose.fig_output_file = '';

        matlabbatch{1}.spm.tools.physio.verbose.use_tabs = false;

        matlabbatch{1}.spm.tools.physio.model.event.trials =
trials.trl(:,1);

 

        spm_jobman('run', matlabbatch)

    end

 

 

If anybody has some tips, it would be greatly appreciated.

Best,
Evelyne

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From erfan1994vi at gmail.com  Fri Jun  9 17:56:44 2023
From: erfan1994vi at gmail.com (Erfan Vi)
Date: Fri, 9 Jun 2023 19:26:44 +0330
Subject: [FieldTrip] Removing artifacts by ICA
Message-ID: <CAOY-aAuXyrshMEgUg__WuqQ=e9YvDNdMHDQMn4n3htQw8Sxt5w@mail.gmail.com>

Dear FieldTrip users,
FieldTrip toolbox uses EEGLAB toolbox functions to implement ICA
decomposition to remove artifacts but it doesn't show spectrum power to
identify artifacts easily. On the other side, EEGLAB has automatic artifact
labeling to recognize artifacts with more precision. What can we do to
choose the correct artifact components to remove? Any document to train?
Thank you,
Erfan-Vajdi
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From rmontefusco at med.uchile.cl  Fri Jun  9 19:14:08 2023
From: rmontefusco at med.uchile.cl (Rodrigo Montefusco)
Date: Fri, 9 Jun 2023 13:14:08 -0400
Subject: [FieldTrip] Removing artifacts by ICA
In-Reply-To: <CAOY-aAuXyrshMEgUg__WuqQ=e9YvDNdMHDQMn4n3htQw8Sxt5w@mail.gmail.com>
References: <CAOY-aAuXyrshMEgUg__WuqQ=e9YvDNdMHDQMn4n3htQw8Sxt5w@mail.gmail.com>
Message-ID: <CAA1jCPLOdd-f897ywm5h8CcBM9=_bx=E=8bie1ddEXg280Laxw@mail.gmail.com>

Dear Erfan-Vajdi
In my brief experience, there are a couple of things you should do, in my
humble opinion:
1.- Study the bases of the ICA, what you can do, what you can't... what is
it good for and what is "not good" for.
2.- Explore a lot before applying it to your pipeline. Even knowing what it
does, you should never trust completely a tool without testing it first to
exhaustion.
3.- Train your eyes to detect the artifacts you are interested in removing.
(pretty much reinforcing what I said in point 2).
4.- Develop a strategy to confront independent components rejection. If you
are interested in removing an eyeblink component for example...do that, and
do not remove components associated with muscle activity, for example. If
you want to do both, it's ok... just stay consistent with your strategy.
5.- You can always perform a ft_timelockanalysis or a ft_freqanalysis on
your component if you need extra information.

That's for starters :)

Good luck!

RMS

On Fri, Jun 9, 2023 at 11:56 AM Erfan Vi via fieldtrip <
fieldtrip at science.ru.nl> wrote:

> Dear FieldTrip users,
> FieldTrip toolbox uses EEGLAB toolbox functions to implement ICA
> decomposition to remove artifacts but it doesn't show spectrum power to
> identify artifacts easily. On the other side, EEGLAB has automatic artifact
> labeling to recognize artifacts with more precision. What can we do to
> choose the correct artifact components to remove? Any document to train?
> Thank you,
> Erfan-Vajdi
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!4Rl0rbEeWBSWygP1FQYVU9lUF6iWA43hZOKUVLcIjoCDZFtB1IBg0ntLv41RAQztMURV1giH0XYqKNEQfK5GLx1a5RvZXac$ 
>
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From SMargerison at som.umaryland.edu  Fri Jun  9 20:38:40 2023
From: SMargerison at som.umaryland.edu (Margerison, Sarah)
Date: Fri, 9 Jun 2023 18:38:40 +0000
Subject: [FieldTrip] Runica: Output argument "sphere" (and maybe others) not
 assigned during call to "runica"
Message-ID: <SJ0PR03MB68749A8392571B72F0254CECEC51A@SJ0PR03MB6874.namprd03.prod.outlook.com>

Hello,

I am getting the following error message attempting to use runica:  Output argument "sphere" (and maybe others) not assigned during call to "runica"

This is occurring in a script which was working a few weeks ago when I ran it last.  We are running fieldtrip version 20211008 on Matlab 2019b.  As far as I know, nothing has been updated since I last used the script.

Currently, these are the fields in the cfg variable:
length = 4
overlap = 0
method = 'runica'
runica = 1x1 struct (cfg.runica.pca =15)

I've also used length = 1.75 and pad = 4 and had the same issue.

I ran which runica and got the following: /usr/local/EEGLAB2022/eeglab2022.1/functions/sigprocfunc/runica.m

I understand that this is an externally called function, but I am still hoping to get some clarity on what might be wrong.  Is there a specific field I should be adding that I am not? And what is the possible reason for the script to no longer want to run?

Thanks very much for your help!

Sarah Margerison, DPT

Graduate Student
University of Maryland School of Medicine

Dept. of Physical Therapy & Rehabilitation Science
University of Maryland, School of Dentistry
Dept. of Neural and Pain Sciences

650 W. Baltimore Street, Room 8404

Baltimore, MD  21201

smargerison at som.umaryland.edu

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From erfan1994vi at gmail.com  Sat Jun 10 09:45:32 2023
From: erfan1994vi at gmail.com (Erfan Vi)
Date: Sat, 10 Jun 2023 11:15:32 +0330
Subject: [FieldTrip] Removing artifacts by ICA
In-Reply-To: <CAA1jCPLOdd-f897ywm5h8CcBM9=_bx=E=8bie1ddEXg280Laxw@mail.gmail.com>
References: <CAOY-aAuXyrshMEgUg__WuqQ=e9YvDNdMHDQMn4n3htQw8Sxt5w@mail.gmail.com>
 <CAA1jCPLOdd-f897ywm5h8CcBM9=_bx=E=8bie1ddEXg280Laxw@mail.gmail.com>
Message-ID: <CAOY-aAuV+_cmGtTx=GnxO9qUfoNqHkhCNdj_Pgv-qhiQMGN=oA@mail.gmail.com>

Thank you for your complete response. Do you have example data to train
me with artifacts?

On Fri, Jun 9, 2023 at 8:45 PM Rodrigo Montefusco via fieldtrip <
fieldtrip at science.ru.nl> wrote:

> Dear Erfan-Vajdi
> In my brief experience, there are a couple of things you should do, in my
> humble opinion:
> 1.- Study the bases of the ICA, what you can do, what you can't... what is
> it good for and what is "not good" for.
> 2.- Explore a lot before applying it to your pipeline. Even knowing what
> it does, you should never trust completely a tool without testing it first
> to exhaustion.
> 3.- Train your eyes to detect the artifacts you are interested in
> removing. (pretty much reinforcing what I said in point 2).
> 4.- Develop a strategy to confront independent components rejection. If
> you are interested in removing an eyeblink component for example...do that,
> and do not remove components associated with muscle activity, for example.
> If you want to do both, it's ok... just stay consistent with your strategy.
> 5.- You can always perform a ft_timelockanalysis or a ft_freqanalysis on
> your component if you need extra information.
>
> That's for starters :)
>
> Good luck!
>
> RMS
>
> On Fri, Jun 9, 2023 at 11:56 AM Erfan Vi via fieldtrip <
> fieldtrip at science.ru.nl> wrote:
>
>> Dear FieldTrip users,
>> FieldTrip toolbox uses EEGLAB toolbox functions to implement ICA
>> decomposition to remove artifacts but it doesn't show spectrum power to
>> identify artifacts easily. On the other side, EEGLAB has automatic artifact
>> labeling to recognize artifacts with more precision. What can we do to
>> choose the correct artifact components to remove? Any document to train?
>> Thank you,
>> Erfan-Vajdi
>> _______________________________________________
>> fieldtrip mailing list
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!6zfXGPkw5X2fJBiCwTACtault0nOD8-Gs4igS7rJlwXwSH92OYXYB3JznyYMaXn6Oj9jqQP1-0WWHm-UqHXIdVz19A$ 
>> <https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!4Rl0rbEeWBSWygP1FQYVU9lUF6iWA43hZOKUVLcIjoCDZFtB1IBg0ntLv41RAQztMURV1giH0XYqKNEQfK5GLx1a5RvZXac$>
>>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!6zfXGPkw5X2fJBiCwTACtault0nOD8-Gs4igS7rJlwXwSH92OYXYB3JznyYMaXn6Oj9jqQP1-0WWHm-UqHXIdVz19A$ 
>
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From janmathijs.schoffelen at donders.ru.nl  Sat Jun 10 11:31:10 2023
From: janmathijs.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Sat, 10 Jun 2023 09:31:10 +0000
Subject: [FieldTrip] trial error
In-Reply-To: <001001d99ad2$d5bfd970$813f8c50$@kpnmail.nl>
References: <001001d99ad2$d5bfd970$813f8c50$@kpnmail.nl>
Message-ID: <B2AB9349-E2D5-4D37-B5A8-F4D80C607816@donders.ru.nl>

Dear Evelyne,

Hmmm, I think that your question is a bit out of scope for the fieldtrip discussion list, because your problem seems constrained to the a problem with the  PhysIO toolbox (which uses SPM, which uses Fieldtrip). It’s great that you already have identified that calling ft_definetrial directly works fine, which makes it unlikely that there’s a bug in the fieldtrip codebase.

I have never worked with this PhysIO toolbox myself, and the combination with the matlabbatch functionality of SPM does not make the detective work straightforward.

My first hunch would be that the (possibly hardcoded) definition of the eventtype/eventvalue is incorrect for your data. I checked the TAPAS code on github, and found the following function: https://urldefense.com/v3/__https://github.com/translationalneuromodeling/tapas/blob/master/PhysIO/code/readin/tapas_physio_read_physlogfiles_brainproducts.m__;!!HJOPV4FYYWzcc1jazlU!5H90oiOLBBCjs7OHHJjplyfnTinW865-Zaby40nl4EbZ9Bda9wsf7NqLgE9m8mYrIAP9JANXm36nW5J0LyH6YNuL50-nLh9h6Ob8-w$  , which looks as if this is the one where things might go wrong. Specifically, starting from line 54 in said function, the eventvalue that defines the ’trials’ within PhysIO is defined hardcoded as ‘R128’, which does not seem to be present in your data.

Could this be what is causing your issue? Given that the eventvalue is hardcoded (i.e. non configurable as an option in your matlabbatch) you can not get it to run without making a change to your version of the code. I would assume that - if this is indeed the cause of the problem - the change of ‘R128’ into ‘R  1’ would be sufficient, and that this will work for all of your recorded subjects. A more principled solution would be to liaise with the PhysIO developers (or to submit a Pull Request) to discuss the possibility of making the eventvalue for the brainproducts data configurable.

If things are unclear, or on the off chance that my suggestions don’t address the problem, please feel free to drop by at the office (01.158) with some data, code and versnaperingen, so that we can have a look at it together.

Best wishes,
Jan-Mathijs




On 9 Jun 2023, at 15:03, Evelyne Fraats via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Dear all,

My name is Evelyne and I am just started to explore fieldtrip.
I use fieldtrip to define trials in physiological recordings to estimate physiological regressors for MRI preprocessing.
However, when using the physio toolbox, no trials are detected within my data.
When I run the separate ft_definetrial function, I get trials, but I seem to fail to include this in my matlabbatch.
This is my output with error message:

evaluating trial function 'ft_trialfun_general'
reading the header from '/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'
reading the events from '/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'
found 169 events
created 20 trials
the call to "ft_definetrial" took 0 seconds and required the additional allocation of an estimated 0 MB
Item model: No field(s) named
event


------------------------------------------------------------------------
09-Jun-2023 15:02:40 - Running job #41
------------------------------------------------------------------------
09-Jun-2023 15:02:40 - Running 'TAPAS PhysIO Toolbox'
Warning: cfg.trialdef.eventtype='?' is deprecated, please specify cfg.trialfun='ft_trialfun_show'
evaluating trial function 'ft_trialfun_show'
reading the events from '/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'
the following events were found in the data
event type: 'New Segment'
with event values:

event type: 'Response'
with event values: 'R  1'

event type: 'Stimulus'
with event values: 'S  1' 'S 97'

no trials have been defined yet, see FT_DEFINETRIAL for further help
found 169 events
the call to "ft_definetrial" took 0 seconds and required the additional allocation of an estimated 0 MB
evaluating trial function 'ft_trialfun_general'
reading the header from '/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'
reading the events from '/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'
09-Jun-2023 15:02:41 - Failed  'TAPAS PhysIO Toolbox'
Error using ft_definetrial
no trials were defined, see FT_DEFINETRIAL for help

The following modules did not run:
Failed: TAPAS PhysIO Toolbox

Error using MATLABbatch system
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the
exact #job as displayed in this error message)
------------------
Running job #41
------------------


This is my code:

if physio_regressor == 1
        %cd /home/affneu/evefra/Spinalcord/data/Physio/
        %define log input
        data_path_physio = fullfile(data_path, 'Physio');
        data_path_physio_sub = dir(fullfile(data_path_physio, sprintf('subx%d*threat*.eeg', sub))) ; %CHANE FORMAT
        filenames = {data_path_physio_sub.name};
        filenames = filenames';
        filefolder = {data_path_physio_sub.folder};
        filefolder = filefolder';
        filename_folder = cellfun(@(folder, name) fullfile(folder, name), filefolder, filenames, 'UniformOutput', false);

        %define vhdr
        data_path_physio_sub = dir(fullfile(data_path_physio, sprintf('subx%d*threat*.vhdr', sub))) ; %CHANE FORMAT
        filenames = {data_path_physio_sub.name};
        filenames = filenames';
        filefolder = {data_path_physio_sub.folder};
        filefolder = filefolder';
        filename_folder_vhdr = cellfun(@(folder, name) fullfile(folder, name), filefolder, filenames, 'UniformOutput', false);

        %define vmkr
        data_path_physio_sub = dir(fullfile(data_path_physio, sprintf('subx%d*threat*.vmrk', sub))) ; %CHANE FORMAT
        filenames = {data_path_physio_sub.name};
        filenames = filenames';
        filefolder = {data_path_physio_sub.folder};
        filefolder = filefolder';
        filename_folder_vmrk = cellfun(@(folder, name) fullfile(folder, name), filefolder, filenames, 'UniformOutput', false);

        %define trials
        cfg = [];
        cfg.headerfile = char(filename_folder_vhdr);
        cfg.eventfile = char(filename_folder_vmrk);
        cfg.trialdef.eventtype = 'Stimulus';
        cfg.trialdef.eventvalue = 'S  1';
        cfg.trialdef.prestim = 0;
        cfg.trialdef.poststim = 0;
        %cfg.trialfun = 'ft_trialfun_show';
        trials = ft_definetrial(cfg);



        %run regressor estimation

        clear matlabbatch
        matlabbatch{1}.spm.tools.physio.save_dir = {fullfile(data_path_tos_brain,'physio_regressors')};
        matlabbatch{1}.spm.tools.physio.log_files.vendor = 'BrainProducts';
        matlabbatch{1}.spm.tools.physio.log_files.cardiac = filename_folder;
        matlabbatch{1}.spm.tools.physio.log_files.respiration = filename_folder;
        matlabbatch{1}.spm.tools.physio.log_files.scan_timing = {''};
        matlabbatch{1}.spm.tools.physio.log_files.sampling_interval = [];
        matlabbatch{1}.spm.tools.physio.log_files.relative_start_acquisition = 0;
        matlabbatch{1}.spm.tools.physio.log_files.align_scan = 'last';
        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nslices = 44;
        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.NslicesPerBeat = [];
        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.TR = 3.39;
        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Ndummies = 0;
        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nscans = 147;
        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.onset_slice = 1;
        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.time_slice_to_slice = [];
        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nprep = [];
        matlabbatch{1}.spm.tools.physio.scan_timing.sync.nominal = struct([]);
        matlabbatch{1}.spm.tools.physio.preproc.cardiac.modality = 'ECG';
        matlabbatch{1}.spm.tools.physio.preproc.cardiac.filter.no = struct([]);
        matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_matched.min = 0.4;
        matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_matched.file = 'initial_cpulse_kRpeakfile.mat';
        matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_matched.max_heart_rate_bpm = 90;
        matlabbatch{1}.spm.tools.physio.preproc.cardiac.posthoc_cpulse_select.off = struct([]);
        matlabbatch{1}.spm.tools.physio.preproc.respiratory.filter.passband = [0.01 2];
        matlabbatch{1}.spm.tools.physio.preproc.respiratory.despike = false;
        matlabbatch{1}.spm.tools.physio.model.output_multiple_regressors = 'multiple_regressors.txt';
        matlabbatch{1}.spm.tools.physio.model.output_physio = 'physio.mat';
        matlabbatch{1}.spm.tools.physio.model.orthogonalise = 'none';
        matlabbatch{1}.spm.tools.physio.model.censor_unreliable_recording_intervals = false;
        matlabbatch{1}.spm.tools.physio.model.retroicor.yes.order.c = 3;
        matlabbatch{1}.spm.tools.physio.model.retroicor.yes.order.r = 4;
        matlabbatch{1}.spm.tools.physio.model.retroicor.yes.order.cr = 1;
        matlabbatch{1}.spm.tools.physio.model.rvt.no = struct([]);
        matlabbatch{1}.spm.tools.physio.model.hrv.no = struct([]);
        matlabbatch{1}.spm.tools.physio.model.noise_rois.no = struct([]);
        matlabbatch{1}.spm.tools.physio.model.movement.no = struct([]);
        matlabbatch{1}.spm.tools.physio.model.other.no = struct([]);
        matlabbatch{1}.spm.tools.physio.verbose.level = 2;
        matlabbatch{1}.spm.tools.physio.verbose.fig_output_file = '';
        matlabbatch{1}.spm.tools.physio.verbose.use_tabs = false;
        matlabbatch{1}.spm.tools.physio.model.event.trials = trials.trl(:,1);

        spm_jobman('run', matlabbatch)
    end


If anybody has some tips, it would be greatly appreciated.
Best,
Evelyne
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From janmathijs.schoffelen at donders.ru.nl  Sat Jun 10 11:44:49 2023
From: janmathijs.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Sat, 10 Jun 2023 09:44:49 +0000
Subject: [FieldTrip] Runica: Output argument "sphere" (and maybe others)
 not assigned during call to "runica"
In-Reply-To: <SJ0PR03MB68749A8392571B72F0254CECEC51A@SJ0PR03MB6874.namprd03.prod.outlook.com>
References: <SJ0PR03MB68749A8392571B72F0254CECEC51A@SJ0PR03MB6874.namprd03.prod.outlook.com>
Message-ID: <23C16E46-BEF7-4AFB-BC03-0DBA42626400@donders.ru.nl>

Dear Sarah,

I am a bit confused by the cfg that you report: there are the options length/overlap, and the options method/runica. Typically, the options length/overlap - if defined - are used for a call to ft_redefinetrial. The options method/runica pertain to a function call to ft_componentanalysis. It is generally good practice to try and keep the cfg as clean as possible, i.e. create a new or empty cfg each time you call a new fieldtrip function.

Now, as to the error message: I don’t have a clue what’s going on, but what I noticed is that Matlab uses a version of runica which is on your /usr/local/EEGLAB2022/<etc>. This might in itself not be the cause of the problem, but I would want to rule out the possibility that there is an inconsistency caused by using a ‘wrong’ version of the runica code. FieldTrip has a version of runica in fieldtrip/external/eeglab.

Perhaps you could first try to clean the matlab path with the restoredefaultpath command, and then only add the path to the fieldtrip folder, followed by ft_defaults. This is explained on https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/faq/should_i_add_fieldtrip_with_all_subdirectories_to_my_matlab_path/__;!!HJOPV4FYYWzcc1jazlU!5DC4BJ4FTZPvSY3QH4ghaT60a0nxPj8jbmx2X3pMCk-n0-Uli10MwOCm6A7kE5paC3WlWq4ij2u7Xp_mdkRLJaNUVYiTMI4B55DM0g$ 

If you then run ft_componentanalysis, matlab should use the one that is shipped with fieldtrip. If the problem then persists, I recommend you to put a breakpoint in the code (of runica), and then go through the code step-by-step to try and understand why the variable ’sphere’ is not created during the function’s execution.

Good luck,

Jan-Mathijs




On 9 Jun 2023, at 20:38, Margerison, Sarah via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Hello,

I am getting the following error message attempting to use runica:  Output argument "sphere" (and maybe others) not assigned during call to "runica"

This is occurring in a script which was working a few weeks ago when I ran it last.  We are running fieldtrip version 20211008 on Matlab 2019b.  As far as I know, nothing has been updated since I last used the script.

Currently, these are the fields in the cfg variable:
length = 4
overlap = 0
method = 'runica'
runica = 1x1 struct (cfg.runica.pca =15)

I've also used length = 1.75 and pad = 4 and had the same issue.

I ran which runica and got the following: /usr/local/EEGLAB2022/eeglab2022.1/functions/sigprocfunc/runica.m

I understand that this is an externally called function, but I am still hoping to get some clarity on what might be wrong.  Is there a specific field I should be adding that I am not? And what is the possible reason for the script to no longer want to run?

Thanks very much for your help!

Sarah Margerison, DPT
Graduate Student
University of Maryland School of Medicine
Dept. of Physical Therapy & Rehabilitation Science
University of Maryland, School of Dentistry
Dept. of Neural and Pain Sciences
650 W. Baltimore Street, Room 8404
Baltimore, MD  21201
smargerison at som.umaryland.edu<mailto:smargerison at som.umaryland.edu>

_______________________________________________
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From giovanna.aiello at hest.ethz.ch  Mon Jun 12 20:26:23 2023
From: giovanna.aiello at hest.ethz.ch (Aiello  Giovanna)
Date: Mon, 12 Jun 2023 18:26:23 +0000
Subject: [FieldTrip] Partial Directed Coherence computation
Message-ID: <94ECC55C-260B-4F75-83B3-A2D7725D0911@ethz.ch>


Good morning,
I am interested in understanding the directed connectivity between the thalamus, where I am recording a Local Field Potential (in 1 channel) and the cortex, where I am recording EEGs (in 16 channels).

My signal is epoched in 4-seconds windows, and I am not interested in understanding the evolution of the directed connectivity in time but rather just which structure is leading which.


I have computed Partial Directed Connectivity (pdc) with the fieldtrip function ft_connectivityanalysis, feeding into the code the transformed, Fourier spectrum (complex double) of my signal (rpttap x channels x frequencies, where rpttap is repetitions (i.e., number of epochs) x tapers).

My final matrix of pdc is 17 x 17 x frequencies (where frequencies are my frequencies of interest). The first 16 channels represent the EEG channels, the 17th channel is the LFP channel in the thalamus. Let’s call this matrix A.
I have two questions:

1) Did I understand correctly that the element A( i, j, f ) for a given frequency f indicates the directed connectivity from element i to element j? (And not the other way around)

2) In my case, A( 1:16 , j  , f ) is a column vector containing the same number!
It looks like, independently on what EEG channel I am considering (unless I am considering the channel in the thalamus), the contribution of directed connectivity to a certain channel j is always the same. This also stays for the thalamus, so if I take A( 1:16, 17, f ), it seems like all the eeg channels have the same directed connectivity to the thalamus. Is that possible? I think it does not really make sense. Please notice that the numbers are not exactly the same, but differ in the 4th decimal digit.



Thank you in advance for your help
Giovanna



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From janmathijs.schoffelen at donders.ru.nl  Tue Jun 13 08:54:19 2023
From: janmathijs.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Tue, 13 Jun 2023 06:54:19 +0000
Subject: [FieldTrip] Partial Directed Coherence computation
In-Reply-To: <94ECC55C-260B-4F75-83B3-A2D7725D0911@ethz.ch>
References: <94ECC55C-260B-4F75-83B3-A2D7725D0911@ethz.ch>
Message-ID: <7DF25A25-0134-43EF-94C0-BF7ED9E2056F@donders.ru.nl>

Hi Giovanna,

Your questions have been addressed by my e-mail to the discussion list on May 6. See below.
Good luck,
Jan-Mathijs


Hi Giovanna,

w.r.t. 1: yes, the convention is that i goes to j.

w.r.t. 2: it seems that you performed the spectral factorisation on the 17 multivariate time series simultaneously. If there is a strong linear/instantaneous dependence between the individual time series (i.e. the EEG channels between themselves), it could be that the factorisation does not converge to a desired result, or it could be that the computation of the PDC breaks down (it requires a matrix inversion of the NxN transfer matrices, which are expected to be numerically well-conditioned). However, in either case I would expect some warnings thrown by matlab, but I am not entirely sure about that.

I would assume that you are primarily interested in the interaction between the EEG on the one hand, and the thalamus LFP signal on the other hand. Interpretation of the between EEG electrodes connectivity does not make much sense to begin with. To get a better idea of what’s going on, I would suggest 1): to use Granger causality as connectivity metric, and/because 2) it can be computed in a pairwise fashion (i.e. using a pairwise factorisation). The latter can be achieved by specifying cfg.granger.sfmethod = ‘bivariate’, and with an additional cfg.channelcmb you can define the pairs of channels between which you wish to compute the connectivity.

Good luck,
Jan-Mathijs

On 12 Jun 2023, at 20:26, Aiello Giovanna via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:


Good morning,
I am interested in understanding the directed connectivity between the thalamus, where I am recording a Local Field Potential (in 1 channel) and the cortex, where I am recording EEGs (in 16 channels).

My signal is epoched in 4-seconds windows, and I am not interested in understanding the evolution of the directed connectivity in time but rather just which structure is leading which.


I have computed Partial Directed Connectivity (pdc) with the fieldtrip function ft_connectivityanalysis, feeding into the code the transformed, Fourier spectrum (complex double) of my signal (rpttap x channels x frequencies, where rpttap is repetitions (i.e., number of epochs) x tapers).

My final matrix of pdc is 17 x 17 x frequencies (where frequencies are my frequencies of interest). The first 16 channels represent the EEG channels, the 17th channel is the LFP channel in the thalamus. Let’s call this matrix A.
I have two questions:

1) Did I understand correctly that the element A( i, j, f ) for a given frequency f indicates the directed connectivity from element i to element j? (And not the other way around)

2) In my case, A( 1:16 , j  , f ) is a column vector containing the same number!
It looks like, independently on what EEG channel I am considering (unless I am considering the channel in the thalamus), the contribution of directed connectivity to a certain channel j is always the same. This also stays for the thalamus, so if I take A( 1:16, 17, f ), it seems like all the eeg channels have the same directed connectivity to the thalamus. Is that possible? I think it does not really make sense. Please notice that the numbers are not exactly the same, but differ in the 4th decimal digit.



Thank you in advance for your help
Giovanna



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From neuroimaging.meg at uni-oldenburg.de  Tue Jun 13 15:26:26 2023
From: neuroimaging.meg at uni-oldenburg.de (Neuroimaging MEG)
Date: Tue, 13 Jun 2023 13:26:26 +0000
Subject: [FieldTrip] 1st Oldenburg MEG Symposium
Message-ID: <6217256692644ded855883596d19ce67@uni-oldenburg.de>

Dear all,


we would like to announce the first Oldenburg MEG Symposium taking place on September 21st and 22nd, 2023 at our Neuroimaging Unit in Oldenburg, Germany, hosting a 306 channel Elekta Triux MEG and a 3T Siemens Prisma. We would like to bring together scientists to exchange latest developments in MEG research. We plan for an interactive symposium with discussions and hands-on sessions. Therefore, and due to space restrictions in our Neuroimaging Unit attendance is limited to 50 participants.


We are happy to announce the following keynote lectures:

- Prof. Dr. Joachim Groß (Münster):

  Brain oscillations and brain/body states

- Prof. Dr.-Ing. habil. Jens Haueisen (Ilmenau):

  Dry EEG combined with MEG

- Dr. Burkhard Maess (Leipzig):

  Optically pumped magnetometers

- Dr. rer. nat. Guido Nolte (Hamburg):

  Methods to estimate brain coupling from non-invasive electrophysiological recordings


Abstracts can be submitted until July 31st, 2023 directly on the website.


Please visit our website for more information on location and further details:

https://urldefense.com/v3/__https://uol.de/neuroimaging/meg__;!!HJOPV4FYYWzcc1jazlU!9ZB-4dRUCP1DpbJpPTVJ54aqU4aQkPy8WwnuMgGJAfn_8z9kC2r-OohSK741EGWXd5uLiOR8BFAQHlqE6J2dcwoedBm1jtUJirOcU1Fg$ 


We hope you like the idea and take the effort to join,

 Christoph Herrmann & Andreas Spiegler
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From stefan.debener at uni-oldenburg.de  Thu Jun 15 09:59:17 2023
From: stefan.debener at uni-oldenburg.de (Stefan Debener)
Date: Thu, 15 Jun 2023 09:59:17 +0200
Subject: [FieldTrip] postdoc position - University of Oldenburg
Message-ID: <f6077129-6724-9b43-6e88-37a7804fe1d6@uni-oldenburg.de>

Postgraduate position in fNIRS and neurofeedback

We are looking for a postgraduate associate with an interest in the use 
of functional near infrared spectroscopy (fNIRS) for neurofeedback. The 
primary project will focus on fundamental methodological limitations 
that so far significantly limit the reach of fNIRS real-time 
applications such as neurofeedback. Of particular concern is evaluating 
the performance of real-time fNIRS data cleaning procedures and 
conclusions for reliable, standardized real-time processing. The project 
is funded for two years.

The ideal candidate will have completed a master’s degree and will have 
three or more years of postgraduate working experience in a related 
research field. For more details on the position see here: 
https://urldefense.com/v3/__https://uol.de/stellen?stelle=69625__;!!HJOPV4FYYWzcc1jazlU!-vsUaLx0MZTp5yQPdvZ9N31rzVGSvDBJheIzgWIKnnSf585aPrWyg7pCnkDpMDQ4TJYdnJCFAWC1O2L9ZO7eZpYeM_2Pr9_ryBOmQQ$  <https://urldefense.com/v3/__https://uol.de/stellen?stelle=69625__;!!HJOPV4FYYWzcc1jazlU!-vsUaLx0MZTp5yQPdvZ9N31rzVGSvDBJheIzgWIKnnSf585aPrWyg7pCnkDpMDQ4TJYdnJCFAWC1O2L9ZO7eZpYeM_2Pr9_ryBOmQQ$ >



-- 
Prof. Dr. Stefan Debener
Department of Psychology
Neuropsychology	Lab
University of Oldenburg
D-26111 Oldenburg
Germany

Office: A7 0-038
Phone: +49-441-798-4271
Fax:   +49-441-798-5522
Email:stefan.debener at uni-oldenburg.de
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From: Puluto Go via fieldtrip <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] Atlas used for 15684 vertices sourcemodel
Date: Sat, 13 May 2023 15:24:52 +0200
Size: 12680
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20230615/940b3ca5/attachment.eml>

From AFARNELL at tcd.ie  Thu Jun 15 14:07:52 2023
From: AFARNELL at tcd.ie (Adelais Farnell Sharp)
Date: Thu, 15 Jun 2023 12:07:52 +0000
Subject: [FieldTrip] Research Assistant position - Trinity College Dublin
Message-ID: <AM0PR0202MB3490823AB971FF9DB7DD5F03B45BA@AM0PR0202MB3490.eurprd02.prod.outlook.com>

Hi all!

We have a new job opening for a Research Assistant in the EEG lab at Trinity College Dublin. Please see the attached job description here:

bit.ly/3JxMRLp<https://urldefense.com/v3/__https://drive.google.com/file/d/1E1P4d9d4ICIfkCcf996SpEjH_WdWH0Kq/view?usp=sharing__;!!HJOPV4FYYWzcc1jazlU!7doXnZrZOeZ6LlIqaW4_xRozinmtpktY4jGP3lfvaj1novjcG5F9e2Vqb7nwNm-rLz7svRaBC3RReDtEeCpoAQ$ >

Please get in touch if you have any queries or would like to apply. Excited to hear from you!

Best

Adelais
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From shreya.sreekantham19 at gmail.com  Thu Jun 15 21:49:56 2023
From: shreya.sreekantham19 at gmail.com (Shreya Sreekantham)
Date: Thu, 15 Jun 2023 15:49:56 -0400
Subject: [FieldTrip] Question about CSV to Compatible Format Conversion
Message-ID: <CANY812=1R9=DTx6_=rjir82es9--gVA_O8HO_3_nP3b_foQ+Ug@mail.gmail.com>

Hi,

Quick question. If I have a csv for EEG data and I would like to run ICA on
the data, what file format conversions should I use? I'm getting a lot of
errors like unsupported type whenever I try to make it a '.ds' file or a
field-trip compatible structure.

Following this tutorial:
https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/ica_artifact_cleaning/__;!!HJOPV4FYYWzcc1jazlU!5TCj2dBgymY6-ANFsfVWD-jMO2dYTG2rfHk0WBYM6jrzBmRIClWZyofYlyUrNZd1ecjLMNY1i0dulMJ_jYLY5g24mIbO-4U$ 

Thank you!

P.S> the data is 16 x 3086 (channels x samples)
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From a.stolk8 at gmail.com  Fri Jun 16 02:35:50 2023
From: a.stolk8 at gmail.com (Arjen Stolk)
Date: Thu, 15 Jun 2023 20:35:50 -0400
Subject: [FieldTrip] Postdoc opportunity in human iEEG at Dartmouth
Message-ID: <CAAiwptTKw82xgLxbn83_rV+A3912vx4HwChyC1sYTq1yCa7NPQ@mail.gmail.com>

Dear community,

We are excited to announce an upcoming opportunity for a postdoctoral
researcher in the Department of Psychological and Brain Sciences at
Dartmouth College (NH, USA). The selected candidate will play a crucial
role in acquiring and analyzing intracranial EEG data from neurosurgical
patients while they engage in real-time social interactions. This research
opportunity offers a unique chance to delve into the intricate dynamics of
brain activity during interpersonal communication. The position is
initially for one year, with the potential for extension. If you are
interested, please contact me for further details.

Arjen Stolk

Assistant Professor, Dartmouth College

Director, Mutual Understanding Lab

https://urldefense.com/v3/__http://www.MutualUnderstanding.nl__;!!HJOPV4FYYWzcc1jazlU!4RVBzjCOtk_6EjpOoGgxZOVMag2QvZI3Fh5Lf6Mh4_GFe06KenST6gN_x_vE5c4oaOOknVMgvfUiyquaJKGuZA$ 

Arjen.Stolk at Dartmouth.edu
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From janmathijs.schoffelen at donders.ru.nl  Fri Jun 16 08:44:08 2023
From: janmathijs.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Fri, 16 Jun 2023 06:44:08 +0000
Subject: [FieldTrip] Question about CSV to Compatible Format Conversion
In-Reply-To: <CANY812=1R9=DTx6_=rjir82es9--gVA_O8HO_3_nP3b_foQ+Ug@mail.gmail.com>
References: <CANY812=1R9=DTx6_=rjir82es9--gVA_O8HO_3_nP3b_foQ+Ug@mail.gmail.com>
Message-ID: <63C37876-F909-4445-B9E7-B08311E27353@donders.ru.nl>

Hi Shreya,

Why do you think you need to create a *.ds file first?

I think a good point to get started is the below link.

https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/faq/how_can_i_import_my_own_dataformat/*circumvent-the-fieldtrip-reading-functions__;Iw!!HJOPV4FYYWzcc1jazlU!8qq654S1soboH44dxn1c-QhUiaSzqS_AfCBK2nHZIiPGR0SS8Shyod04w6ytozRpp2euUObSBS3MSWY_Y_oGVkaMCQ1dsyRwqXCVZg$ 


good luck,
Jan-Mathijs

On 15 Jun 2023, at 21:49, Shreya Sreekantham via fieldtrip <fieldtrip at science.ru.nl> wrote:

Hi,

Quick question. If I have a csv for EEG data and I would like to run ICA on the data, what file format conversions should I use? I'm getting a lot of errors like unsupported type whenever I try to make it a '.ds' file or a field-trip compatible structure.

Following this tutorial: https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/ica_artifact_cleaning/__;!!HJOPV4FYYWzcc1jazlU!8qq654S1soboH44dxn1c-QhUiaSzqS_AfCBK2nHZIiPGR0SS8Shyod04w6ytozRpp2euUObSBS3MSWY_Y_oGVkaMCQ1dsyRUK8cihw$ <https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/ica_artifact_cleaning/__;!!HJOPV4FYYWzcc1jazlU!5TCj2dBgymY6-ANFsfVWD-jMO2dYTG2rfHk0WBYM6jrzBmRIClWZyofYlyUrNZd1ecjLMNY1i0dulMJ_jYLY5g24mIbO-4U$>

Thank you!

P.S> the data is 16 x 3086 (channels x samples)
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!-vMtMEuA2EEx9mUc0DCw6UjGP6XxOae60BhK_lJwyoO-qTlZGs8lZ8eQVtPCssmJljXAi19IxsTt1BuHBuV516GoJO6BmvgHTInQLw$

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From agathalenartowicz at gmail.com  Tue Jun 20 00:39:39 2023
From: agathalenartowicz at gmail.com (Agatha Lenartowicz)
Date: Mon, 19 Jun 2023 15:39:39 -0700
Subject: [FieldTrip] Post-Doc in Analysis of EEG Signals of Attention
 Fluctuations - Los Angeles, CA
Message-ID: <BA97C375-DF65-48FC-A795-A897AE8C6C45@gmail.com>


Post-Doc in Analysis of EEG Signals of Attention Fluctuations - Los Angeles, CA
We are seeking an enthusiastic post-doctoral researcher to fill a newly opened position with focus on (a) EEG signals of brain state fluctuations that account for intra-individual variability in response times during sustained attention, and, (b) dynamic functional connectivity correlates that track such signals, a project funded by the NIH (see here for details <https://urldefense.com/v3/__https://reporter.nih.gov/search/mxFJWgPNikO1ZK3qZGGefA/project-details/10660737__;!!HJOPV4FYYWzcc1jazlU!8uGUc67pPWAZPEy7oyY6dovapikQCjPF3fpEM4B19bDm0hBTWi3YI3ny_daoHAOjXQ9flgK0TcwaElMY2aZ0qcqeOZj6A7o$ >). 

Duties & Responsibilities 

Conduct analyses of EEG signatures of attention control in task-related and continuous data, within and between subject
Independently develop data processing pipelines, implement existing pipelines and integrate multiple data streams (EEG, fMRI, behavior, peripheral signals)
Conduct statistical analyses and derive group-level inferences 
Develop manuscripts and presentations for the dissemination of research

Qualifications 

Ph.D. in psychology, cognitive neuroscience, biomedical/electrical engineering or a related field
Strong analytical skillset and proficiency with one or more major EEG software tools (EEGLAB, Fieltrip)
Experience with signal processing in EEG research and the extraction of one or more: oscillatory features, graph-theoretic measures, signal complexity measures, and source localization
Interest or background in fMRI (dFC) or multimodal EEG-fMRI analysis is a significant asset given the focus of the lab
Comfort with Matlab, R, Python or other programming languages, familiarity with Unix/Linux and high-performance computing  environments
Excellent communication skills, initiative, problem solving, and attention to detail are imperative
The position is primarily an analysis-focused opportunity. However, it is part of a broader research program on attention control that includes concurrent EEG-fMRI studies of mechanisms of alpha oscillations <https://urldefense.com/v3/__https://reporter.nih.gov/search/ZIMqZxDWXEG-yS8bdfHWKw/project-details/10528685__;!!HJOPV4FYYWzcc1jazlU!8uGUc67pPWAZPEy7oyY6dovapikQCjPF3fpEM4B19bDm0hBTWi3YI3ny_daoHAOjXQ9flgK0TcwaElMY2aZ0qcqen6uDv9A$ > and associated working memory deficits in ADHD <https://urldefense.com/v3/__https://projectreporter.nih.gov/project_info_description.cfm?aid=9819782&icde=51820520&ddparam=&ddvalue=&ddsub=&cr=2&csb=default&cs=ASC&pball=__;!!HJOPV4FYYWzcc1jazlU!8uGUc67pPWAZPEy7oyY6dovapikQCjPF3fpEM4B19bDm0hBTWi3YI3ny_daoHAOjXQ9flgK0TcwaElMY2aZ0qcqee2ou_fU$ > , as well as real-life mobile EEG studies <https://urldefense.com/v3/__https://reporter.nih.gov/search/mxFJWgPNikO1ZK3qZGGefA/project-details/9904763__;!!HJOPV4FYYWzcc1jazlU!8uGUc67pPWAZPEy7oyY6dovapikQCjPF3fpEM4B19bDm0hBTWi3YI3ny_daoHAOjXQ9flgK0TcwaElMY2aZ0qcqeusQeaA8$ > to examine the intersection between real-life context and attention. See lab website <https://urldefense.com/v3/__https://agathalenartowicz.com/__;!!HJOPV4FYYWzcc1jazlU!8uGUc67pPWAZPEy7oyY6dovapikQCjPF3fpEM4B19bDm0hBTWi3YI3ny_daoHAOjXQ9flgK0TcwaElMY2aZ0qcqefBzBqdc$ > for more info. 

Position start date is flexible but expected to occur by Spring 2024. 

For inquiries please contact Agatha Lenartowicz (alenarto at g dot ucla dot edu). 



A world-class university, UCLA consistently ranks in the top in terms of academics, research and medical services (https://urldefense.com/v3/__http://www.ucla.edu/about/rankings__;!!HJOPV4FYYWzcc1jazlU!8uGUc67pPWAZPEy7oyY6dovapikQCjPF3fpEM4B19bDm0hBTWi3YI3ny_daoHAOjXQ9flgK0TcwaElMY2aZ0qcqetTyohyQ$  <https://urldefense.com/v3/__http://www.ucla.edu/about/rankings__;!!HJOPV4FYYWzcc1jazlU!8uGUc67pPWAZPEy7oyY6dovapikQCjPF3fpEM4B19bDm0hBTWi3YI3ny_daoHAOjXQ9flgK0TcwaElMY2aZ0qcqetTyohyQ$ >). The Jane and Terry Semel Institute for Neuroscience and Human Behavior <https://urldefense.com/v3/__https://www.semel.ucla.edu/__;!!HJOPV4FYYWzcc1jazlU!8uGUc67pPWAZPEy7oyY6dovapikQCjPF3fpEM4B19bDm0hBTWi3YI3ny_daoHAOjXQ9flgK0TcwaElMY2aZ0qcqeM1CRmbE$ > is an interdisciplinary research and education institute devoted to the understanding of complex human behavior, including the genetic, biological, behavioral and sociocultural underpinnings of normal behavior, and the causes and consequences of neuropsychiatric disorders. It includes the Translational Research Center for Neuropsychiatry, purpose-built for phenotypic and application of quantitative methodologies (diagnostic assessment, EEG, sleep, medical procedures) as well as the Staglin One Mind Center for Cognitive Neuroscience <https://urldefense.com/v3/__https://www.staglincenterforcogneuro.semel.ucla.edu/__;!!HJOPV4FYYWzcc1jazlU!8uGUc67pPWAZPEy7oyY6dovapikQCjPF3fpEM4B19bDm0hBTWi3YI3ny_daoHAOjXQ9flgK0TcwaElMY2aZ0qcqesYLLm9E$ >, which houses a 3T Prisma Fit scanner, as well as 128 and 256 channel high density MR-compatible EEG systems. The Hoffman2 is UCLA’s high-performance computing cluster and includes 1200+ 64-bit computing nodes and >20,000 computing cores, with an aggregate of >50TB memory.




~~~~~~~~~~~~~~~~~~~~~
https://urldefense.com/v3/__http://www.agathalenartowicz.com__;!!HJOPV4FYYWzcc1jazlU!8uGUc67pPWAZPEy7oyY6dovapikQCjPF3fpEM4B19bDm0hBTWi3YI3ny_daoHAOjXQ9flgK0TcwaElMY2aZ0qcqejnKuy90$ 
LinkedIn <https://urldefense.com/v3/__https://www.linkedin.com/in/agatha-lenartowicz-ph-d-62554937/__;!!HJOPV4FYYWzcc1jazlU!8uGUc67pPWAZPEy7oyY6dovapikQCjPF3fpEM4B19bDm0hBTWi3YI3ny_daoHAOjXQ9flgK0TcwaElMY2aZ0qcqeRCLoTfE$ >



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From janmathijs.schoffelen at donders.ru.nl  Thu Jun 22 09:05:08 2023
From: janmathijs.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Thu, 22 Jun 2023 07:05:08 +0000
Subject: [FieldTrip] Unrecognized field name "dimord" during
 ft_timelockanalysis
In-Reply-To: <CD8270F4-768B-4714-BC2D-5D011C3B6FE6@usc.edu>
References: <CD8270F4-768B-4714-BC2D-5D011C3B6FE6@usc.edu>
Message-ID: <A249F39C-A4E9-4625-A5BE-BC84909849E2@donders.ru.nl>

Hi Andy,

Could you provide a little bit more information with respect to what the ‘ft_data_tar’ variable looks like ?

Best wishes,
Jan-Mathijs


On 6 Jun 2023, at 02:42, Andy Kim via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Dear community,

My name is Andy Kim and I am trying to complete cluster-based permutation tests on event-related fields using the FieldTrip toolbox tutorial (https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock/__;!!HJOPV4FYYWzcc1jazlU!8RTBCeXQO37SC3pH3min8AQCew1ah97-TZLv_h1tzJ0QT8ce5F60z4NeJchJtxELFqbZyy9Q1YrYFckZ-sycOnpayE9SIAZrQ75N1w$ <https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock/__;!!HJOPV4FYYWzcc1jazlU!-SFXKQT1GL1-POlF7Tj2IUUkZ78bg-KMPsdhinve9Bd3ncr1xtEi7f54D21l6k0asfuAhWSb9wanXJa7lQ$>). The issue I believe is that I have completed pre-processing using EEGLAB and converted the already pre-processed data using eeglab2fieldtrip.

ft_data_tar = eeglab2fieldtrip(EEG2, 'timelock’);

However, when I run ft_timelockanalysis, I get the following error.

timelock_tar = ft_timelockanalysis(cfg, ft_data_tar);

The input is timelock data with 63 channels and 750 timebins
Unrecognized field name "dimord”.
Error in dimlength (line 74) elseif strcmp(data.(fld), 'rpt_pos’)
Error in fixsampleinfo (line 56) ntrial = dimlength(data, 'rpt’);
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_timelockanalysis (line 83) data = ft_checkdata(data, 'datatype', {'raw+comp', 'raw'}, 'feedback', 'yes', 'hassampleinfo', 'yes');

Is this “dimord” field name an issue with the data conversion from EEGLAB to FieldTrip? I am not quite sure where to look and would appreciate any help in sending me in the right direction for debugging. Thank you.

Best,
Andy
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!-j07uKtFi15zpEQzEs3GMwyJ5_ZhGtpDTKUO-mrQXHD3KhS0_LS3ZrHtXb4tukxKNXFih92dgIm9-2_GfZ6LmAYuKVEod4afICOgzA$

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From alain.de.cheveigne at ens.psl.eu  Thu Jun 22 23:32:55 2023
From: alain.de.cheveigne at ens.psl.eu (Alain de Cheveigne)
Date: Thu, 22 Jun 2023 22:32:55 +0100
Subject: [FieldTrip] High pass filtering before epoching
In-Reply-To: <CAEWorwAo_QBKL-j3ZnGzWv6iNXO=K8esQThsbnki3vJV6fYPWA@mail.gmail.com>
References: <CAEWorwAo_QBKL-j3ZnGzWv6iNXO=K8esQThsbnki3vJV6fYPWA@mail.gmail.com>
Message-ID: <D6AA0142-D315-4DBE-9D6F-06EA9F8F5449@ens.psl.eu>

I also didn't agree with their conclusions, so I wrote up a commentary for Scientific Reports. It was rejected without review so I put it on bioRxiv: https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2023.06.19.545602v1__;!!HJOPV4FYYWzcc1jazlU!4wikriMIK6eAqGLhSfwIO-To6fCuRwxt5XCTp_CBJrtTdwFfA7Zc44WjnX8WBD1RjYH9S9RLO2NO__OYhfmcStONak-mk_W3kOM$ .
Alain


> On 15 Feb 2023, at 10:33, Frans Nord via fieldtrip <fieldtrip at science.ru.nl> wrote:
> 
> Hello mailing-list,
> 
> I have a question regarding the comment about Fieldtrip in the recently published paper "EEG is better left alone" [1]. While I don't agree with the conclusions of the paper there is a specific comment regarding Fieldtrip that I would like some comments about:
> 
> "We realized that the FieldTrip preprocessing function extracts data epochs before filtering the data when provided with both filter settings and epoch information. After consulting with FieldTrip developers, for all analyses using FieldTrip, we used an alternate multi-step implementation allowing us to extract epochs after the raw data had been filtered."
> 
> Looking through the code of ft_preprocessing and how the preproc function is used in my own preprocessing pipeline i realized that I seem to do the filtering on raw data epochs with this code:
> 
> cfg = [];
> cfg.continuous           ='yes';
> cfg.trialfun                = 'ft_trialfun_general';
> cfg.trialdef.eventtype       = 'STATUS';
> cfg.trialdef.eventvalue      = {1,2,3,4}; % Trigger values
> cfg.trialdef.prestim         =.5; % -500 ms before the stimulation
> cfg.trialdef.poststim        = 2; % +2000ms after the stimulation
> cfg.dataset            = path_to_dataset;             % set the name of the dataset
> cfg            = ft_definetrial(cfg);   % read the list of the specific stimuluscfg.hpfilter       = 'yes';
> cfg.hpfreq         = 1;[data]                     =ft_preprocessing(cfg);
> 
> I did however think that the code above would apply the high pass filter on the continuous data and not on the epochs but it seems that I was wrong. Or am I? So I'm now consulting the E-mail list to get some clarity about this and a potential recommendation on what to do instead. Basically, how to implement the "multi-step implementation" within Fieldtrip.
> 
> Thank you for providing the Fieldtrip toolbox
> Best
> Frans
> 
> [1] Delorme, A. EEG is better left alone. Sci Rep 13, 2372 (2023). https://urldefense.com/v3/__https://doi.org/10.1038/s41598-023-27528-0__;!!HJOPV4FYYWzcc1jazlU!4wikriMIK6eAqGLhSfwIO-To6fCuRwxt5XCTp_CBJrtTdwFfA7Zc44WjnX8WBD1RjYH9S9RLO2NO__OYhfmcStONak-mmQWUCUQ$ 
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!4wikriMIK6eAqGLhSfwIO-To6fCuRwxt5XCTp_CBJrtTdwFfA7Zc44WjnX8WBD1RjYH9S9RLO2NO__OYhfmcStONak-mfMZ1DDI$ 




From janmathijs.schoffelen at donders.ru.nl  Fri Jun 23 08:54:49 2023
From: janmathijs.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Fri, 23 Jun 2023 06:54:49 +0000
Subject: [FieldTrip] High pass filtering before epoching
In-Reply-To: <CAEWorwAo_QBKL-j3ZnGzWv6iNXO=K8esQThsbnki3vJV6fYPWA@mail.gmail.com>
References: <CAEWorwAo_QBKL-j3ZnGzWv6iNXO=K8esQThsbnki3vJV6fYPWA@mail.gmail.com>
Message-ID: <328D7710-EB1C-40D2-9E70-63518FF85B14@donders.ru.nl>

Hi Frans,

Historically, due to RAM constraints etc. a tradition FieldTrip pipeline started with epoching, then filtering. However, currently there is no reason to load in the continuous data first, then do the filtering, and then do the epoching. Although I didn’t read Julian’s reply in detail, I suspect that his code is doing exactly that.

There is just still a lot of documentation online which reverses this optimal order.

Note, in addition, that if one uses a filter with a finite impulse response, the filtered signal will not depend on the overall length of the data segment that you supply to the filter, once you get sufficiently far away from the edges. In other words, for instance, the center piece a one minute data segment that has been filtered will look exactly the same as a filtered version of the exact same center piece obtained from the 1-hour continuous recording.

Fieldtrip allows for cfg.padding in ft_preprocessing, which will allow you to obtain epoched and filtered data in a single call to ft_preprocessing, without suffering from the edge effects of the filter. Once the value for cfg.padding exceeds the maximum epoch length + the filter order (and provided you use a finite impulse response filter) then you should be good.

Best wishes,
Jan-Mathijs


On 15 Feb 2023, at 11:33, Frans Nord via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Hello mailing-list,

I have a question regarding the comment about Fieldtrip in the recently published paper "EEG is better left alone" [1]. While I don't agree with the conclusions of the paper there is a specific comment regarding Fieldtrip that I would like some comments about:

"We realized that the FieldTrip preprocessing function extracts data epochs before filtering the data when provided with both filter settings and epoch information. After consulting with FieldTrip developers, for all analyses using FieldTrip, we used an alternate multi-step implementation allowing us to extract epochs after the raw data had been filtered."

Looking through the code of ft_preprocessing and how the preproc function is used in my own preprocessing pipeline i realized that I seem to do the filtering on raw data epochs with this code:

cfg = [];
cfg.continuous ='yes';
cfg.trialfun = 'ft_trialfun_general';
cfg.trialdef.eventtype = 'STATUS';
cfg.trialdef.eventvalue = {1,2,3,4}; % Trigger values
cfg.trialdef.prestim =.5; % -500 ms before the stimulation
cfg.trialdef.poststim = 2; % +2000ms after the stimulation
cfg.dataset = path_to_dataset; % set the name of the dataset
cfg = ft_definetrial(cfg); % read the list of the specific stimuluscfg.hpfilter = 'yes';
cfg.hpfreq = 1;[data] =ft_preprocessing(cfg);

I did however think that the code above would apply the high pass filter on the continuous data and not on the epochs but it seems that I was wrong. Or am I? So I'm now consulting the E-mail list to get some clarity about this and a potential recommendation on what to do instead. Basically, how to implement the "multi-step implementation" within Fieldtrip.

Thank you for providing the Fieldtrip toolbox
Best
Frans

[1] Delorme, A. EEG is better left alone. Sci Rep 13, 2372 (2023). https://urldefense.com/v3/__https://doi.org/10.1038/s41598-023-27528-0__;!!HJOPV4FYYWzcc1jazlU!6kEZP86f4bgt2ARcX7863-yoptmy-dkOs3laiNe30BiJKGGueB0Mz8rLMIPNpn3t_8nhurJluaLVRRMdZLJYVmsPDhI_ssl-pt5LhA$ <https://urldefense.com/v3/__https://doi.org/10.1038/s41598-023-27528-0__;!!HJOPV4FYYWzcc1jazlU!4hjKg111dQ7s9-L3G_ddKy01SDzvgiEvo8gLx_R-WDx6Qxj6JJS0HuEwuUx1atexqoHmVc8kvd5ouM4p4smQ$>
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From alain.de.cheveigne at ens.psl.eu  Fri Jun 23 15:06:36 2023
From: alain.de.cheveigne at ens.psl.eu (Alain de Cheveigne)
Date: Fri, 23 Jun 2023 14:06:36 +0100
Subject: [FieldTrip] High pass filtering before epoching
In-Reply-To: <328D7710-EB1C-40D2-9E70-63518FF85B14@donders.ru.nl>
References: <CAEWorwAo_QBKL-j3ZnGzWv6iNXO=K8esQThsbnki3vJV6fYPWA@mail.gmail.com>
 <328D7710-EB1C-40D2-9E70-63518FF85B14@donders.ru.nl>
Message-ID: <D83E571C-0489-428D-87BD-2C3E917C0EFA@ens.psl.eu>

Hi Jan-Mathijs, all,

You are right that with proper precautions one can epoch then filter with no ill effects. 

However filtering before epoching remains attractive because simple and relatively safe (less likely to get things wrong). No need to worry about whether the FIR is a good enough approximation to the IIR one had in mind, padding is sufficient, etc.

For example, one might want to high-pass with a low cutoff frequency (e.g. 0.1 Hz) to minimize distortion of the ERP. This requires an impulse response duration on the order of tens of seconds. An investigator might find this out of proportion and prefer some other strategy prone to edge effects.

Note that an alternative to filtering is detrending, which can be applied before and/or after epoching.  Applied before epoching, it reduces the implicit steps at the onset and/or offset of each trial (the origin of the edge effects). Applied after epoching, it removes the trend local to each trial with minimal impact on the ERP. A typical strategy is to epoch with padding on both sides, fit and remove the trend (possibly with zero weight on the interval of interest), then clip off the padding.  

Filtering and detrending are both vulnerable to high-amplitude glitches outside the interval of interest but within the span of the filter or fit. For example, a subject might tend to blink before or after each trial. This can be addressed with robust detrending for which there is no filtering equivalent (I think).

Alain

> On 23 Jun 2023, at 07:54, Schoffelen, J.M. (Jan Mathijs) via fieldtrip <fieldtrip at science.ru.nl> wrote:
> 
> Hi Frans,
> 
> Historically, due to RAM constraints etc. a tradition FieldTrip pipeline started with epoching, then filtering. However, currently there is no reason to load in the continuous data first, then do the filtering, and then do the epoching. Although I didn’t read Julian’s reply in detail, I suspect that his code is doing exactly that.
> 
> There is just still a lot of documentation online which reverses this optimal order.
> 
> Note, in addition, that if one uses a filter with a finite impulse response, the filtered signal will not depend on the overall length of the data segment that you supply to the filter, once you get sufficiently far away from the edges. In other words, for instance, the center piece a one minute data segment that has been filtered will look exactly the same as a filtered version of the exact same center piece obtained from the 1-hour continuous recording. 
> 
> Fieldtrip allows for cfg.padding in ft_preprocessing, which will allow you to obtain epoched and filtered data in a single call to ft_preprocessing, without suffering from the edge effects of the filter. Once the value for cfg.padding exceeds the maximum epoch length + the filter order (and provided you use a finite impulse response filter) then you should be good.
> 
> Best wishes,
> Jan-Mathijs
> 
> 
>> On 15 Feb 2023, at 11:33, Frans Nord via fieldtrip <fieldtrip at science.ru.nl> wrote:
>> 
>> Hello mailing-list,
>> 
>> I have a question regarding the comment about Fieldtrip in the recently published paper "EEG is better left alone" [1]. While I don't agree with the conclusions of the paper there is a specific comment regarding Fieldtrip that I would like some comments about:
>> 
>> "We realized that the FieldTrip preprocessing function extracts data epochs before filtering the data when provided with both filter settings and epoch information. After consulting with FieldTrip developers, for all analyses using FieldTrip, we used an alternate multi-step implementation allowing us to extract epochs after the raw data had been filtered."
>> 
>> Looking through the code of ft_preprocessing and how the preproc function is used in my own preprocessing pipeline i realized that I seem to do the filtering on raw data epochs with this code:
>> 
>> cfg = [];
>> cfg.continuous ='yes';
>> cfg.trialfun = 
>> 
>> 'ft_trialfun_general'
>> ;
>> cfg.trialdef.eventtype = 
>> 
>> 'STATUS'
>> ;
>> cfg.trialdef.eventvalue = {1,2,3,4}; 
>> 
>> % Trigger values
>> 
>> cfg.trialdef.prestim =.5; 
>> 
>> % -500 ms before the stimulation
>> 
>> cfg.trialdef.poststim = 2; 
>> 
>> % +2000ms after the stimulation
>> 
>> cfg.dataset = path_to_dataset; 
>> 
>> % set the name of the dataset
>> 
>> cfg = ft_definetrial(cfg); 
>> 
>> % read the list of the specific stimulus
>> cfg.hpfilter
>>  =
>> 
>> 'yes';
>> cfg.hpfreq = 1;[data] =ft_preprocessing(cfg);
>> 
>> 
>> I did however think that the code above would apply the high pass filter on the continuous data and not on the epochs but it seems that I was wrong. Or am I? So I'm now consulting the E-mail list to get some clarity about this and a potential recommendation on what to do instead. Basically, how to implement the "multi-step implementation" within Fieldtrip.
>> 
>> Thank you for providing the Fieldtrip toolbox
>> Best
>> Frans
>> 
>> [1] Delorme, A. EEG is better left alone. Sci Rep 13, 2372 (2023). https://urldefense.com/v3/__https://doi.org/10.1038/s41598-023-27528-0__;!!HJOPV4FYYWzcc1jazlU!49ARQZhij07QcXbznLgyQvIp4PNcdVSoZ2EsDDB043TbF0wd09QCDkgHP7DO1BXEz9jwCWU0q6yBAjm91FJ0WtPuFdr4qia6CZo$ 
>> _______________________________________________
>> fieldtrip mailing list
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!-_6L05NY4jlsfrP8C3I8I2jFQwOMSiDKS1tqSQ21aLsqyTB_rndzUnLg-8WiMQbKsVsuFCrx5lJzqbdD1tXsy2Tu8f4-RQxPapetqA$ 
> 
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> fieldtrip mailing list
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From janmathijs.schoffelen at donders.ru.nl  Fri Jun 23 15:41:51 2023
From: janmathijs.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Fri, 23 Jun 2023 13:41:51 +0000
Subject: [FieldTrip] High pass filtering before epoching
In-Reply-To: <D83E571C-0489-428D-87BD-2C3E917C0EFA@ens.psl.eu>
References: <CAEWorwAo_QBKL-j3ZnGzWv6iNXO=K8esQThsbnki3vJV6fYPWA@mail.gmail.com>
 <328D7710-EB1C-40D2-9E70-63518FF85B14@donders.ru.nl>
 <D83E571C-0489-428D-87BD-2C3E917C0EFA@ens.psl.eu>
Message-ID: <AD2CABFD-08AD-4E80-A9A6-AE4BC66285B5@donders.ru.nl>

Hi Alain, I totally agree with your points.

I noticed a typo in my earlier e-mail, which should have stated:

"However, currently there is no reason NOT to load in the continuous data first, then do the filtering, and then do the epoching."

Have a good weekend,
JM



On 23 Jun 2023, at 15:06, Alain de Cheveigne via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Hi Jan-Mathijs, all,

You are right that with proper precautions one can epoch then filter with no ill effects.

However filtering before epoching remains attractive because simple and relatively safe (less likely to get things wrong). No need to worry about whether the FIR is a good enough approximation to the IIR one had in mind, padding is sufficient, etc.

For example, one might want to high-pass with a low cutoff frequency (e.g. 0.1 Hz) to minimize distortion of the ERP. This requires an impulse response duration on the order of tens of seconds. An investigator might find this out of proportion and prefer some other strategy prone to edge effects.

Note that an alternative to filtering is detrending, which can be applied before and/or after epoching. Applied before epoching, it reduces the implicit steps at the onset and/or offset of each trial (the origin of the edge effects). Applied after epoching, it removes the trend local to each trial with minimal impact on the ERP. A typical strategy is to epoch with padding on both sides, fit and remove the trend (possibly with zero weight on the interval of interest), then clip off the padding.

Filtering and detrending are both vulnerable to high-amplitude glitches outside the interval of interest but within the span of the filter or fit. For example, a subject might tend to blink before or after each trial. This can be addressed with robust detrending for which there is no filtering equivalent (I think).

Alain

On 23 Jun 2023, at 07:54, Schoffelen, J.M. (Jan Mathijs) via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Hi Frans,

Historically, due to RAM constraints etc. a tradition FieldTrip pipeline started with epoching, then filtering. However, currently there is no reason to load in the continuous data first, then do the filtering, and then do the epoching. Although I didn’t read Julian’s reply in detail, I suspect that his code is doing exactly that.

There is just still a lot of documentation online which reverses this optimal order.

Note, in addition, that if one uses a filter with a finite impulse response, the filtered signal will not depend on the overall length of the data segment that you supply to the filter, once you get sufficiently far away from the edges. In other words, for instance, the center piece a one minute data segment that has been filtered will look exactly the same as a filtered version of the exact same center piece obtained from the 1-hour continuous recording.

Fieldtrip allows for cfg.padding in ft_preprocessing, which will allow you to obtain epoched and filtered data in a single call to ft_preprocessing, without suffering from the edge effects of the filter. Once the value for cfg.padding exceeds the maximum epoch length + the filter order (and provided you use a finite impulse response filter) then you should be good.

Best wishes,
Jan-Mathijs


On 15 Feb 2023, at 11:33, Frans Nord via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Hello mailing-list,

I have a question regarding the comment about Fieldtrip in the recently published paper "EEG is better left alone" [1]. While I don't agree with the conclusions of the paper there is a specific comment regarding Fieldtrip that I would like some comments about:

"We realized that the FieldTrip preprocessing function extracts data epochs before filtering the data when provided with both filter settings and epoch information. After consulting with FieldTrip developers, for all analyses using FieldTrip, we used an alternate multi-step implementation allowing us to extract epochs after the raw data had been filtered."

Looking through the code of ft_preprocessing and how the preproc function is used in my own preprocessing pipeline i realized that I seem to do the filtering on raw data epochs with this code:

cfg = [];
cfg.continuous ='yes';
cfg.trialfun =

'ft_trialfun_general'
;
cfg.trialdef.eventtype =

'STATUS'
;
cfg.trialdef.eventvalue = {1,2,3,4};

% Trigger values

cfg.trialdef.prestim =.5;

% -500 ms before the stimulation

cfg.trialdef.poststim = 2;

% +2000ms after the stimulation

cfg.dataset = path_to_dataset;

% set the name of the dataset

cfg = ft_definetrial(cfg);

% read the list of the specific stimulus
cfg.hpfilter
=

'yes';
cfg.hpfreq = 1;[data] =ft_preprocessing(cfg);


I did however think that the code above would apply the high pass filter on the continuous data and not on the epochs but it seems that I was wrong. Or am I? So I'm now consulting the E-mail list to get some clarity about this and a potential recommendation on what to do instead. Basically, how to implement the "multi-step implementation" within Fieldtrip.

Thank you for providing the Fieldtrip toolbox
Best
Frans

[1] Delorme, A. EEG is better left alone. Sci Rep 13, 2372 (2023). https://urldefense.com/v3/__https://doi.org/10.1038/s41598-023-27528-0__;!!HJOPV4FYYWzcc1jazlU!49ARQZhij07QcXbznLgyQvIp4PNcdVSoZ2EsDDB043TbF0wd09QCDkgHP7DO1BXEz9jwCWU0q6yBAjm91FJ0WtPuFdr4qia6CZo$
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https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From a.wollbrink at wwu.de  Fri Jun 23 15:52:14 2023
From: a.wollbrink at wwu.de (Andreas Wollbrink)
Date: Fri, 23 Jun 2023 15:52:14 +0200
Subject: [FieldTrip] malfunction if ft_icabrowser
Message-ID: <8acbe7242728b7728bf3f56a16b91b00f43f033f.camel@uni-muenster.de>

Dear All,
I recently encountered a malfunction of ft_icabrowser:
(at least) under Linux the TopoPlots of the components do not open in
the intended locations but in their own figures.
This means that the entire layout and the otherwise excellent
functionality of the ICA browser is then lost. 
The behaviour is due to the fact that ft_topoplotIC opens a new figure
for each plot by default. 

I therefore suggest adding the entry 'cfgtopo.figure =
subcomp{3}{row};' to the ft_icabrowser function in lines 218.

Then everything works as intended.

Best, Andreas

-- 


Dipl.-Ing., Biomedical Engineer

MEG / EEG Lab Manager

Institute for Biomagnetism and Biosignalanalysis
University Hospital, University of Muenster

Malmedyweg 15, 48149 Muenster, Germany

office:    +49-251-83-52546
email: a.wollbrink at uni-muenster.de

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Wir erfüllen unsere Informationspflichten zum Datenschutz gem. Art. 13-
14 DS-GVO durch Veröffentlichung auf unserer Internetseite
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From e.fraats at kpnmail.nl  Fri Jun 23 17:09:39 2023
From: e.fraats at kpnmail.nl (Evelyne Fraats)
Date: Fri, 23 Jun 2023 17:09:39 +0200
Subject: [FieldTrip] trial error
In-Reply-To: <B2AB9349-E2D5-4D37-B5A8-F4D80C607816@donders.ru.nl>
References: <001001d99ad2$d5bfd970$813f8c50$@kpnmail.nl>
 <B2AB9349-E2D5-4D37-B5A8-F4D80C607816@donders.ru.nl>
Message-ID: <000f01d9a5e4$bb848110$328d8330$@kpnmail.nl>

Dear all,

 

This was indeed the case!

Within the tapas_physio_read_physlogfiles_brainproducts.m function, I could indeed define the event value.

 

Goodluck to you all.

 

Best,

Evelyne

 

Van: fieldtrip <fieldtrip-bounces at science.ru.nl> Namens Schoffelen, J.M. (Jan Mathijs) via fieldtrip
Verzonden: zaterdag 10 juni 2023 11:31
Aan: FieldTrip discussion list <fieldtrip at science.ru.nl>
CC: Schoffelen, J.M. (Jan Mathijs) <janmathijs.schoffelen at donders.ru.nl>
Onderwerp: Re: [FieldTrip] trial error

 

Dear Evelyne, 

 

Hmmm, I think that your question is a bit out of scope for the fieldtrip discussion list, because your problem seems constrained to the a problem with the  PhysIO toolbox (which uses SPM, which uses Fieldtrip). It’s great that you already have identified that calling ft_definetrial directly works fine, which makes it unlikely that there’s a bug in the fieldtrip codebase.

 

I have never worked with this PhysIO toolbox myself, and the combination with the matlabbatch functionality of SPM does not make the detective work straightforward. 

 

My first hunch would be that the (possibly hardcoded) definition of the eventtype/eventvalue is incorrect for your data. I checked the TAPAS code on github, and found the following function: https://urldefense.com/v3/__https://github.com/translationalneuromodeling/tapas/blob/master/PhysIO/code/readin/tapas_physio_read_physlogfiles_brainproducts.m__;!!HJOPV4FYYWzcc1jazlU!65cMoGmD91tFeJcdTZy2Itp4CXx1PaExrrhVzOP3df3NwkoRpyakwdsrZ_pN1YNlisx_YHltsb1Pan3447jnr5jG$  <https://urldefense.com/v3/__https:/github.com/translationalneuromodeling/tapas/blob/master/PhysIO/code/readin/tapas_physio_read_physlogfiles_brainproducts.m__;!!HJOPV4FYYWzcc1jazlU!5H90oiOLBBCjs7OHHJjplyfnTinW865-Zaby40nl4EbZ9Bda9wsf7NqLgE9m8mYrIAP9JANXm36nW5J0LyH6YNuL50-nLh9h6Ob8-w$>  , which looks as if this is the one where things might go wrong. Specifically, starting from line 54 in said function, the eventvalue that defines the ’trials’ within PhysIO is defined hardcoded as ‘R128’, which does not seem to be present in your data.

 

Could this be what is causing your issue? Given that the eventvalue is hardcoded (i.e. non configurable as an option in your matlabbatch) you can not get it to run without making a change to your version of the code. I would assume that - if this is indeed the cause of the problem - the change of ‘R128’ into ‘R  1’ would be sufficient, and that this will work for all of your recorded subjects. A more principled solution would be to liaise with the PhysIO developers (or to submit a Pull Request) to discuss the possibility of making the eventvalue for the brainproducts data configurable.

 

If things are unclear, or on the off chance that my suggestions don’t address the problem, please feel free to drop by at the office (01.158) with some data, code and versnaperingen, so that we can have a look at it together.

 

Best wishes,

Jan-Mathijs

 

 

 





On 9 Jun 2023, at 15:03, Evelyne Fraats via fieldtrip <fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl> > wrote:

 

Dear all,

 

My name is Evelyne and I am just started to explore fieldtrip.

I use fieldtrip to define trials in physiological recordings to estimate physiological regressors for MRI preprocessing. 

However, when using the physio toolbox, no trials are detected within my data.

When I run the separate ft_definetrial function, I get trials, but I seem to fail to include this in my matlabbatch.

This is my output with error message:

 

evaluating trial function 'ft_trialfun_general'

reading the header from '/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'

reading the events from '/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'

found 169 events

created 20 trials

the call to "ft_definetrial" took 0 seconds and required the additional allocation of an estimated 0 MB

Item model: No field(s) named

event

 

 

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

09-Jun-2023 15:02:40 - Running job #41

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

09-Jun-2023 15:02:40 - Running 'TAPAS PhysIO Toolbox'

Warning: cfg.trialdef.eventtype='?' is deprecated, please specify cfg.trialfun='ft_trialfun_show' 

evaluating trial function 'ft_trialfun_show'

reading the events from '/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'

the following events were found in the data

event type: 'New Segment' 

with event values: 

 

event type: 'Response' 

with event values: 'R  1' 

 

event type: 'Stimulus' 

with event values: 'S  1' 'S 97' 

 

no trials have been defined yet, see FT_DEFINETRIAL for further help

found 169 events

the call to "ft_definetrial" took 0 seconds and required the additional allocation of an estimated 0 MB

evaluating trial function 'ft_trialfun_general'

reading the header from '/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'

reading the events from '/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'

09-Jun-2023 15:02:41 - Failed  'TAPAS PhysIO Toolbox'

Error using ft_definetrial

no trials were defined, see FT_DEFINETRIAL for help

 

The following modules did not run:

Failed: TAPAS PhysIO Toolbox

 

Error using MATLABbatch system

Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the

exact #job as displayed in this error message)

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

Running job #41

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

 

 

This is my code:

 

if physio_regressor == 1

        %cd /home/affneu/evefra/Spinalcord/data/Physio/ 

        %define log input

        data_path_physio = fullfile(data_path, 'Physio');

        data_path_physio_sub = dir(fullfile(data_path_physio, sprintf('subx%d*threat*.eeg', sub))) ; %CHANE FORMAT       

        filenames = {data_path_physio_sub.name};

        filenames = filenames';  

        filefolder = {data_path_physio_sub.folder};

        filefolder = filefolder';

        filename_folder = cellfun(@(folder, name) fullfile(folder, name), filefolder, filenames, 'UniformOutput', false);

 

        %define vhdr

        data_path_physio_sub = dir(fullfile(data_path_physio, sprintf('subx%d*threat*.vhdr', sub))) ; %CHANE FORMAT       

        filenames = {data_path_physio_sub.name};

        filenames = filenames';  

        filefolder = {data_path_physio_sub.folder};

        filefolder = filefolder';

        filename_folder_vhdr = cellfun(@(folder, name) fullfile(folder, name), filefolder, filenames, 'UniformOutput', false);

 

        %define vmkr

        data_path_physio_sub = dir(fullfile(data_path_physio, sprintf('subx%d*threat*.vmrk', sub))) ; %CHANE FORMAT       

        filenames = {data_path_physio_sub.name};

        filenames = filenames';  

        filefolder = {data_path_physio_sub.folder};

        filefolder = filefolder';

        filename_folder_vmrk = cellfun(@(folder, name) fullfile(folder, name), filefolder, filenames, 'UniformOutput', false);

 

        %define trials

        cfg = [];

        cfg.headerfile = char(filename_folder_vhdr);

        cfg.eventfile = char(filename_folder_vmrk);

        cfg.trialdef.eventtype = 'Stimulus';  

        cfg.trialdef.eventvalue = 'S  1';   

        cfg.trialdef.prestim = 0;             

        cfg.trialdef.poststim = 0; 

        %cfg.trialfun = 'ft_trialfun_show';

        trials = ft_definetrial(cfg);

        

 

      

        %run regressor estimation

               

        clear matlabbatch

        matlabbatch{1}.spm.tools.physio.save_dir = {fullfile(data_path_tos_brain,'physio_regressors')};

        matlabbatch{1}.spm.tools.physio.log_files.vendor = 'BrainProducts';

        matlabbatch{1}.spm.tools.physio.log_files.cardiac = filename_folder;

        matlabbatch{1}.spm.tools.physio.log_files.respiration = filename_folder;

        matlabbatch{1}.spm.tools.physio.log_files.scan_timing = {''};

        matlabbatch{1}.spm.tools.physio.log_files.sampling_interval = [];

        matlabbatch{1}.spm.tools.physio.log_files.relative_start_acquisition = 0;

        matlabbatch{1}.spm.tools.physio.log_files.align_scan = 'last';

        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nslices = 44;

        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.NslicesPerBeat = [];

        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.TR = 3.39;

        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Ndummies = 0;

        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nscans = 147;

        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.onset_slice = 1;

        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.time_slice_to_slice = [];

        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nprep = [];

        matlabbatch{1}.spm.tools.physio.scan_timing.sync.nominal = struct([]);

        matlabbatch{1}.spm.tools.physio.preproc.cardiac.modality = 'ECG';

        matlabbatch{1}.spm.tools.physio.preproc.cardiac.filter.no = struct([]);

        matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_matched.min = 0.4;

        matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_matched.file = 'initial_cpulse_kRpeakfile.mat';

        matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_matched.max_heart_rate_bpm = 90;

        matlabbatch{1}.spm.tools.physio.preproc.cardiac.posthoc_cpulse_select.off = struct([]);

        matlabbatch{1}.spm.tools.physio.preproc.respiratory.filter.passband = [0.01 2];

        matlabbatch{1}.spm.tools.physio.preproc.respiratory.despike = false;

        matlabbatch{1}.spm.tools.physio.model.output_multiple_regressors = 'multiple_regressors.txt';

        matlabbatch{1}.spm.tools.physio.model.output_physio = 'physio.mat';

        matlabbatch{1}.spm.tools.physio.model.orthogonalise = 'none';

        matlabbatch{1}.spm.tools.physio.model.censor_unreliable_recording_intervals = false;

        matlabbatch{1}.spm.tools.physio.model.retroicor.yes.order.c = 3;

        matlabbatch{1}.spm.tools.physio.model.retroicor.yes.order.r = 4;

        matlabbatch{1}.spm.tools.physio.model.retroicor.yes.order.cr = 1;

        matlabbatch{1}.spm.tools.physio.model.rvt.no = struct([]);

        matlabbatch{1}.spm.tools.physio.model.hrv.no = struct([]);

        matlabbatch{1}.spm.tools.physio.model.noise_rois.no = struct([]);

        matlabbatch{1}.spm.tools.physio.model.movement.no = struct([]);

        matlabbatch{1}.spm.tools.physio.model.other.no = struct([]);

        matlabbatch{1}.spm.tools.physio.verbose.level = 2;

        matlabbatch{1}.spm.tools.physio.verbose.fig_output_file = '';

        matlabbatch{1}.spm.tools.physio.verbose.use_tabs = false;

        matlabbatch{1}.spm.tools.physio.model.event.trials = trials.trl(:,1);

 

        spm_jobman('run', matlabbatch)

    end

 

 

If anybody has some tips, it would be greatly appreciated.

Best,
Evelyne

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From janmathijs.schoffelen at donders.ru.nl  Fri Jun 23 17:37:34 2023
From: janmathijs.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Fri, 23 Jun 2023 15:37:34 +0000
Subject: [FieldTrip] malfunction if ft_icabrowser
In-Reply-To: <8acbe7242728b7728bf3f56a16b91b00f43f033f.camel@uni-muenster.de>
References: <8acbe7242728b7728bf3f56a16b91b00f43f033f.camel@uni-muenster.de>
Message-ID: <07AAC343-73DC-418A-997C-7405732925B6@donders.ru.nl>

Dear Andreas,

Thanks for bringing this up. The ft_icabrowser function resides in a corner of the codebase that is a bit outside the scope of the ‘waan van de dag’, so it is not optimally maintained. It’s a bit surprising that you run into this only now, because the function does not seem to have been changed in the past two years or so. I guess the issue results from some interaction between the code and your local OS/matlab version etc.

We look forward to a PR on github with the suggested fix :).

Best wishes,
Jan-Mathijs


On 23 Jun 2023, at 15:52, Andreas Wollbrink via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Dear All,
I recently encountered a malfunction of ft_icabrowser:
(at least) under Linux the TopoPlots of the components do not open in the intended locations but in their own figures.
This means that the entire layout and the otherwise excellent functionality of the ICA browser is then lost.
The behaviour is due to the fact that ft_topoplotIC opens a new figure for each plot by default.

I therefore suggest adding the entry 'cfgtopo.figure = subcomp{3}{row};' to the ft_icabrowser function in lines 218.

Then everything works as intended.

Best, Andreas


--

________________________________
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MEG / EEG Lab Manager

Institute for Biomagnetism and Biosignalanalysis
University Hospital, University of Muenster

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From janmathijs.schoffelen at donders.ru.nl  Fri Jun 23 18:32:00 2023
From: janmathijs.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Fri, 23 Jun 2023 16:32:00 +0000
Subject: [FieldTrip] trial error
In-Reply-To: <000f01d9a5e4$bb848110$328d8330$@kpnmail.nl>
References: <001001d99ad2$d5bfd970$813f8c50$@kpnmail.nl>
 <B2AB9349-E2D5-4D37-B5A8-F4D80C607816@donders.ru.nl>
 <000f01d9a5e4$bb848110$328d8330$@kpnmail.nl>
Message-ID: <8B28B902-9B20-48DF-A8A1-397ECE892A1E@donders.ru.nl>

Good stuff Evelyne,

I am glad that it works for you now.

Best wishes, and have a good weekend,
Jan-Mathijs


On 23 Jun 2023, at 17:09, Evelyne Fraats via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Dear all,

This was indeed the case!
Within the tapas_physio_read_physlogfiles_brainproducts.m function, I could indeed define the event value.

Goodluck to you all.

Best,
Evelyne

Van: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> Namens Schoffelen, J.M. (Jan Mathijs) via fieldtrip
Verzonden: zaterdag 10 juni 2023 11:31
Aan: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
CC: Schoffelen, J.M. (Jan Mathijs) <janmathijs.schoffelen at donders.ru.nl<mailto:janmathijs.schoffelen at donders.ru.nl>>
Onderwerp: Re: [FieldTrip] trial error

Dear Evelyne,

Hmmm, I think that your question is a bit out of scope for the fieldtrip discussion list, because your problem seems constrained to the a problem with the  PhysIO toolbox (which uses SPM, which uses Fieldtrip). It’s great that you already have identified that calling ft_definetrial directly works fine, which makes it unlikely that there’s a bug in the fieldtrip codebase.

I have never worked with this PhysIO toolbox myself, and the combination with the matlabbatch functionality of SPM does not make the detective work straightforward.

My first hunch would be that the (possibly hardcoded) definition of the eventtype/eventvalue is incorrect for your data. I checked the TAPAS code on github, and found the following function: https://urldefense.com/v3/__https://github.com/translationalneuromodeling/tapas/blob/master/PhysIO/code/readin/tapas_physio_read_physlogfiles_brainproducts.m__;!!HJOPV4FYYWzcc1jazlU!-85bvSn00Ld6WnQtIlikYDeMbrwLX4vgQ5LpuM0eRIw4VcbZMHs2xlgrHcsQB7tYnPRDbcEYn9p4WUi0DwCb8DzjihfhZKTLKazcKw$ <https://urldefense.com/v3/__https:/github.com/translationalneuromodeling/tapas/blob/master/PhysIO/code/readin/tapas_physio_read_physlogfiles_brainproducts.m__;!!HJOPV4FYYWzcc1jazlU!5H90oiOLBBCjs7OHHJjplyfnTinW865-Zaby40nl4EbZ9Bda9wsf7NqLgE9m8mYrIAP9JANXm36nW5J0LyH6YNuL50-nLh9h6Ob8-w$> , which looks as if this is the one where things might go wrong. Specifically, starting from line 54 in said function, the eventvalue that defines the ’trials’ within PhysIO is defined hardcoded as ‘R128’, which does not seem to be present in your data.

Could this be what is causing your issue? Given that the eventvalue is hardcoded (i.e. non configurable as an option in your matlabbatch) you can not get it to run without making a change to your version of the code. I would assume that - if this is indeed the cause of the problem - the change of ‘R128’ into ‘R  1’ would be sufficient, and that this will work for all of your recorded subjects. A more principled solution would be to liaise with the PhysIO developers (or to submit a Pull Request) to discuss the possibility of making the eventvalue for the brainproducts data configurable.

If things are unclear, or on the off chance that my suggestions don’t address the problem, please feel free to drop by at the office (01.158) with some data, code and versnaperingen, so that we can have a look at it together.

Best wishes,
Jan-Mathijs





On 9 Jun 2023, at 15:03, Evelyne Fraats via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Dear all,

My name is Evelyne and I am just started to explore fieldtrip.
I use fieldtrip to define trials in physiological recordings to estimate physiological regressors for MRI preprocessing.
However, when using the physio toolbox, no trials are detected within my data.
When I run the separate ft_definetrial function, I get trials, but I seem to fail to include this in my matlabbatch.
This is my output with error message:

evaluating trial function 'ft_trialfun_general'
reading the header from '/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'
reading the events from '/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'
found 169 events
created 20 trials
the call to "ft_definetrial" took 0 seconds and required the additional allocation of an estimated 0 MB
Item model: No field(s) named
event


------------------------------------------------------------------------
09-Jun-2023 15:02:40 - Running job #41
------------------------------------------------------------------------
09-Jun-2023 15:02:40 - Running 'TAPAS PhysIO Toolbox'
Warning: cfg.trialdef.eventtype='?' is deprecated, please specify cfg.trialfun='ft_trialfun_show'
evaluating trial function 'ft_trialfun_show'
reading the events from '/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'
the following events were found in the data
event type: 'New Segment'
with event values:

event type: 'Response'
with event values: 'R  1'

event type: 'Stimulus'
with event values: 'S  1' 'S 97'

no trials have been defined yet, see FT_DEFINETRIAL for further help
found 169 events
the call to "ft_definetrial" took 0 seconds and required the additional allocation of an estimated 0 MB
evaluating trial function 'ft_trialfun_general'
reading the header from '/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'
reading the events from '/home/affneu/evefra/Spinalcord/data/Physio/subx19_new_threat_SPINAL.vhdr'
09-Jun-2023 15:02:41 - Failed  'TAPAS PhysIO Toolbox'
Error using ft_definetrial
no trials were defined, see FT_DEFINETRIAL for help

The following modules did not run:
Failed: TAPAS PhysIO Toolbox

Error using MATLABbatch system
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the
exact #job as displayed in this error message)
------------------
Running job #41
------------------


This is my code:

if physio_regressor == 1
        %cd /home/affneu/evefra/Spinalcord/data/Physio/
        %define log input
        data_path_physio = fullfile(data_path, 'Physio');
        data_path_physio_sub = dir(fullfile(data_path_physio, sprintf('subx%d*threat*.eeg', sub))) ; %CHANE FORMAT
        filenames = {data_path_physio_sub.name};
        filenames = filenames';
        filefolder = {data_path_physio_sub.folder};
        filefolder = filefolder';
        filename_folder = cellfun(@(folder, name) fullfile(folder, name), filefolder, filenames, 'UniformOutput', false);

        %define vhdr
        data_path_physio_sub = dir(fullfile(data_path_physio, sprintf('subx%d*threat*.vhdr', sub))) ; %CHANE FORMAT
        filenames = {data_path_physio_sub.name};
        filenames = filenames';
        filefolder = {data_path_physio_sub.folder};
        filefolder = filefolder';
        filename_folder_vhdr = cellfun(@(folder, name) fullfile(folder, name), filefolder, filenames, 'UniformOutput', false);

        %define vmkr
        data_path_physio_sub = dir(fullfile(data_path_physio, sprintf('subx%d*threat*.vmrk', sub))) ; %CHANE FORMAT
        filenames = {data_path_physio_sub.name};
        filenames = filenames';
        filefolder = {data_path_physio_sub.folder};
        filefolder = filefolder';
        filename_folder_vmrk = cellfun(@(folder, name) fullfile(folder, name), filefolder, filenames, 'UniformOutput', false);

        %define trials
        cfg = [];
        cfg.headerfile = char(filename_folder_vhdr);
        cfg.eventfile = char(filename_folder_vmrk);
        cfg.trialdef.eventtype = 'Stimulus';
        cfg.trialdef.eventvalue = 'S  1';
        cfg.trialdef.prestim = 0;
        cfg.trialdef.poststim = 0;
        %cfg.trialfun = 'ft_trialfun_show';
        trials = ft_definetrial(cfg);



        %run regressor estimation

        clear matlabbatch
        matlabbatch{1}.spm.tools.physio.save_dir = {fullfile(data_path_tos_brain,'physio_regressors')};
        matlabbatch{1}.spm.tools.physio.log_files.vendor = 'BrainProducts';
        matlabbatch{1}.spm.tools.physio.log_files.cardiac = filename_folder;
        matlabbatch{1}.spm.tools.physio.log_files.respiration = filename_folder;
        matlabbatch{1}.spm.tools.physio.log_files.scan_timing = {''};
        matlabbatch{1}.spm.tools.physio.log_files.sampling_interval = [];
        matlabbatch{1}.spm.tools.physio.log_files.relative_start_acquisition = 0;
        matlabbatch{1}.spm.tools.physio.log_files.align_scan = 'last';
        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nslices = 44;
        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.NslicesPerBeat = [];
        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.TR = 3.39;
        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Ndummies = 0;
        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nscans = 147;
        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.onset_slice = 1;
        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.time_slice_to_slice = [];
        matlabbatch{1}.spm.tools.physio.scan_timing.sqpar.Nprep = [];
        matlabbatch{1}.spm.tools.physio.scan_timing.sync.nominal = struct([]);
        matlabbatch{1}.spm.tools.physio.preproc.cardiac.modality = 'ECG';
        matlabbatch{1}.spm.tools.physio.preproc.cardiac.filter.no = struct([]);
        matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_matched.min = 0.4;
        matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_matched.file = 'initial_cpulse_kRpeakfile.mat';
        matlabbatch{1}.spm.tools.physio.preproc.cardiac.initial_cpulse_select.auto_matched.max_heart_rate_bpm = 90;
        matlabbatch{1}.spm.tools.physio.preproc.cardiac.posthoc_cpulse_select.off = struct([]);
        matlabbatch{1}.spm.tools.physio.preproc.respiratory.filter.passband = [0.01 2];
        matlabbatch{1}.spm.tools.physio.preproc.respiratory.despike = false;
        matlabbatch{1}.spm.tools.physio.model.output_multiple_regressors = 'multiple_regressors.txt';
        matlabbatch{1}.spm.tools.physio.model.output_physio = 'physio.mat';
        matlabbatch{1}.spm.tools.physio.model.orthogonalise = 'none';
        matlabbatch{1}.spm.tools.physio.model.censor_unreliable_recording_intervals = false;
        matlabbatch{1}.spm.tools.physio.model.retroicor.yes.order.c = 3;
        matlabbatch{1}.spm.tools.physio.model.retroicor.yes.order.r = 4;
        matlabbatch{1}.spm.tools.physio.model.retroicor.yes.order.cr = 1;
        matlabbatch{1}.spm.tools.physio.model.rvt.no = struct([]);
        matlabbatch{1}.spm.tools.physio.model.hrv.no = struct([]);
        matlabbatch{1}.spm.tools.physio.model.noise_rois.no = struct([]);
        matlabbatch{1}.spm.tools.physio.model.movement.no = struct([]);
        matlabbatch{1}.spm.tools.physio.model.other.no = struct([]);
        matlabbatch{1}.spm.tools.physio.verbose.level = 2;
        matlabbatch{1}.spm.tools.physio.verbose.fig_output_file = '';
        matlabbatch{1}.spm.tools.physio.verbose.use_tabs = false;
        matlabbatch{1}.spm.tools.physio.model.event.trials = trials.trl(:,1);

        spm_jobman('run', matlabbatch)
    end


If anybody has some tips, it would be greatly appreciated.
Best,
Evelyne
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From ivaylo.iotchev at gmail.com  Sun Jun 25 12:32:06 2023
From: ivaylo.iotchev at gmail.com (Ivaylo Iotchev)
Date: Sun, 25 Jun 2023 12:32:06 +0200
Subject: [FieldTrip] Anyone a thorough example of applying
 ft_artifact_zvalue?
Message-ID: <CAO-ud37GjcuwpXEfxyZLYhKHAsApiHWzCLnLfiuujL_RgLKujg@mail.gmail.com>

Dear community,

does anyone have actual example lines of how any of the outputs of
ft_artifact_zvalue are applied back on the data for which they were
calculated?

The function returns a cfg and an artifact matrix... because of the
constant switching between structure and matrix representation so typical
of Fieldtrip I am not yet able to apply any of the two with my current
understanding of what is going on. It is bordering on mockery that you
don't specify the functions that can use the cfg output neither in the
examples nor in the help-text description of the function itself, like
seriously? I had to find out by trial-and-error that ft_redefinetrial
cannot use the cfg output... thanks I guess.

I am  steaming a bit here, but don't mind me, maybe the answers can also be
helpful for others in the community, so don't be discouraged by my mood

Bests,

Ivo
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From arnodelorme at gmail.com  Mon Jun 26 11:01:48 2023
From: arnodelorme at gmail.com (Arnaud Delorme)
Date: Mon, 26 Jun 2023 11:01:48 +0200
Subject: [FieldTrip] Anyone a thorough example of applying
 ft_artifact_zvalue?
In-Reply-To: <CAO-ud37GjcuwpXEfxyZLYhKHAsApiHWzCLnLfiuujL_RgLKujg@mail.gmail.com>
References: <CAO-ud37GjcuwpXEfxyZLYhKHAsApiHWzCLnLfiuujL_RgLKujg@mail.gmail.com>
Message-ID: <DDF4252D-BB23-4423-864E-48524BA8A72C@gmail.com>

Dear Ivo,

Here is one.

https://urldefense.com/v3/__https://github.com/sccn/eeg_pipelines/blob/master/fieldtrip/process_fieldtrip_template.m__;!!HJOPV4FYYWzcc1jazlU!4T5A5bjLbdQbrdgU3OaYNc7GiIaMUUXB606LMB60aZmgDXsqr1ooSZoAqqVIqceV_6XpbpAbEEVX6NHRX7myGJgYQQ$ 

And there is the Fieldtrip tutorial

https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/automatic_artifact_rejection/__;!!HJOPV4FYYWzcc1jazlU!4T5A5bjLbdQbrdgU3OaYNc7GiIaMUUXB606LMB60aZmgDXsqr1ooSZoAqqVIqceV_6XpbpAbEEVX6NHRX7lz--5-GA$ 

Arno

> On Jun 25, 2023, at 12:32 PM, Ivaylo Iotchev via fieldtrip <fieldtrip at science.ru.nl> wrote:
> 
> Dear community,
> 
> does anyone have actual example lines of how any of the outputs of ft_artifact_zvalue are applied back on the data for which they were calculated?
> 
> The function returns a cfg and an artifact matrix... because of the constant switching between structure and matrix representation so typical of Fieldtrip I am not yet able to apply any of the two with my current understanding of what is going on. It is bordering on mockery that you don't specify the functions that can use the cfg output neither in the examples nor in the help-text description of the function itself, like seriously? I had to find out by trial-and-error that ft_redefinetrial cannot use the cfg output... thanks I guess.
> 
> I am  steaming a bit here, but don't mind me, maybe the answers can also be helpful for others in the community, so don't be discouraged by my mood
> 
> Bests,
> 
> Ivo
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!4T5A5bjLbdQbrdgU3OaYNc7GiIaMUUXB606LMB60aZmgDXsqr1ooSZoAqqVIqceV_6XpbpAbEEVX6NHRX7n5bFOHJA$ 




From arnodelorme at gmail.com  Mon Jun 26 11:33:42 2023
From: arnodelorme at gmail.com (Arnaud Delorme)
Date: Mon, 26 Jun 2023 11:33:42 +0200
Subject: [FieldTrip] High pass filtering before epoching
In-Reply-To: <AD2CABFD-08AD-4E80-A9A6-AE4BC66285B5@donders.ru.nl>
References: <CAEWorwAo_QBKL-j3ZnGzWv6iNXO=K8esQThsbnki3vJV6fYPWA@mail.gmail.com>
 <328D7710-EB1C-40D2-9E70-63518FF85B14@donders.ru.nl>
 <D83E571C-0489-428D-87BD-2C3E917C0EFA@ens.psl.eu>
 <AD2CABFD-08AD-4E80-A9A6-AE4BC66285B5@donders.ru.nl>
Message-ID: <BADB3652-ED6F-4DDC-90CE-292DBD8D53F0@gmail.com>

Hi Jan and Alain,

>> You are right that with proper precautions one can epoch then filter with no ill effects. 

In my testing in the paper “EEG is better left alone” the decrease in significance associated with high pass filtering data epochs was large (only half of the electrodes are significant when filtering data epochs instead of the raw data for the oddball dataset in figure S2). Using 3-second epochs instead of 1-second epochs did not fix the issue. 10-second might do it, but I think that would be overkill.

Unfortunately, the ERP tutorial of Fieldtrip still uses the one-step preprocessing approach of epoching first and then filtering

https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/preprocessing_erp/__;!!HJOPV4FYYWzcc1jazlU!-kwcDOKyZcbjid93QHIVl1OP_hwvIe18FTa-pbZGJ_z_5BurltCT28oHIPU10dFHM6ih8xQcDXhJVpNsA3tr2CqcQA$ 

The continuous data tutorial uses the ft_redefinetrial method, which is a two-step approach of filtering continuous data and then epoching.

https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/continuous/__;!!HJOPV4FYYWzcc1jazlU!-kwcDOKyZcbjid93QHIVl1OP_hwvIe18FTa-pbZGJ_z_5BurltCT28oHIPU10dFHM6ih8xQcDXhJVpNsA3vynCHXUA$ 

Cheers,

Arno

>> Alain
>> 
>>> On 23 Jun 2023, at 07:54, Schoffelen, J.M. (Jan Mathijs) via fieldtrip <fieldtrip at science.ru.nl> wrote:
>>> 
>>> Hi Frans,
>>> 
>>> Historically, due to RAM constraints etc. a tradition FieldTrip pipeline started with epoching, then filtering. However, currently there is no reason to load in the continuous data first, then do the filtering, and then do the epoching. Although I didn’t read Julian’s reply in detail, I suspect that his code is doing exactly that.
>>> 
>>> There is just still a lot of documentation online which reverses this optimal order.
>>> 
>>> Note, in addition, that if one uses a filter with a finite impulse response, the filtered signal will not depend on the overall length of the data segment that you supply to the filter, once you get sufficiently far away from the edges. In other words, for instance, the center piece a one minute data segment that has been filtered will look exactly the same as a filtered version of the exact same center piece obtained from the 1-hour continuous recording. 
>>> 
>>> Fieldtrip allows for cfg.padding in ft_preprocessing, which will allow you to obtain epoched and filtered data in a single call to ft_preprocessing, without suffering from the edge effects of the filter. Once the value for cfg.padding exceeds the maximum epoch length + the filter order (and provided you use a finite impulse response filter) then you should be good.
>>> 
>>> Best wishes,
>>> Jan-Mathijs
>>> 
>>> 
>>>> On 15 Feb 2023, at 11:33, Frans Nord via fieldtrip <fieldtrip at science.ru.nl> wrote:
>>>> 
>>>> Hello mailing-list,
>>>> 
>>>> I have a question regarding the comment about Fieldtrip in the recently published paper "EEG is better left alone" [1]. While I don't agree with the conclusions of the paper there is a specific comment regarding Fieldtrip that I would like some comments about:
>>>> 
>>>> "We realized that the FieldTrip preprocessing function extracts data epochs before filtering the data when provided with both filter settings and epoch information. After consulting with FieldTrip developers, for all analyses using FieldTrip, we used an alternate multi-step implementation allowing us to extract epochs after the raw data had been filtered."
>>>> 
>>>> Looking through the code of ft_preprocessing and how the preproc function is used in my own preprocessing pipeline i realized that I seem to do the filtering on raw data epochs with this code:
>>>> 
>>>> cfg = [];
>>>> cfg.continuous ='yes';
>>>> cfg.trialfun = 
>>>> 
>>>> 'ft_trialfun_general'
>>>> ;
>>>> cfg.trialdef.eventtype = 
>>>> 
>>>> 'STATUS'
>>>> ;
>>>> cfg.trialdef.eventvalue = {1,2,3,4}; 
>>>> 
>>>> % Trigger values
>>>> 
>>>> cfg.trialdef.prestim =.5; 
>>>> 
>>>> % -500 ms before the stimulation
>>>> 
>>>> cfg.trialdef.poststim = 2; 
>>>> 
>>>> % +2000ms after the stimulation
>>>> 
>>>> cfg.dataset = path_to_dataset; 
>>>> 
>>>> % set the name of the dataset
>>>> 
>>>> cfg = ft_definetrial(cfg); 
>>>> 
>>>> % read the list of the specific stimulus
>>>> cfg.hpfilter
>>>> =
>>>> 
>>>> 'yes';
>>>> cfg.hpfreq = 1;[data] =ft_preprocessing(cfg);
>>>> 
>>>> 
>>>> I did however think that the code above would apply the high pass filter on the continuous data and not on the epochs but it seems that I was wrong. Or am I? So I'm now consulting the E-mail list to get some clarity about this and a potential recommendation on what to do instead. Basically, how to implement the "multi-step implementation" within Fieldtrip.
>>>> 
>>>> Thank you for providing the Fieldtrip toolbox
>>>> Best
>>>> Frans
>>>> 
>>>> [1] Delorme, A. EEG is better left alone. Sci Rep 13, 2372 (2023). https://urldefense.com/v3/__https://doi.org/10.1038/s41598-023-27528-0__;!!HJOPV4FYYWzcc1jazlU!49ARQZhij07QcXbznLgyQvIp4PNcdVSoZ2EsDDB043TbF0wd09QCDkgHP7DO1BXEz9jwCWU0q6yBAjm91FJ0WtPuFdr4qia6CZo$ 
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>> https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!-_6L05NY4jlsfrP8C3I8I2jFQwOMSiDKS1tqSQ21aLsqyTB_rndzUnLg-8WiMQbKsVsuFCrx5lJzqbdD1tXsy2Tu8f4-RQxPapetqA$ 
>>> 
>>> _______________________________________________
>>> fieldtrip mailing list
>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>> https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!49ARQZhij07QcXbznLgyQvIp4PNcdVSoZ2EsDDB043TbF0wd09QCDkgHP7DO1BXEz9jwCWU0q6yBAjm91FJ0WtPuFdr4zPBfgKQ$ 
>> 
>> 
>> _______________________________________________
>> fieldtrip mailing list
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!61hGn_iqSQTqOUy5TR8ASuo3th2U8mj2LiIj1gmQhqZt2NtnKDt3WqoEVWCmSIHMFnolsu2de5rRpkJnjxYJ4TTv0myofG2Rlu5zVg$
> 
> _______________________________________________
> fieldtrip mailing list
> https://urldefense.com/v3/__https://mailman.science.ru.nl/mailman/listinfo/fieldtrip__;!!Mih3wA!AVtHBHat3jUEF6ka5zCGkFNZBaQyq5gtgZHurR6WTN74wSjFfJMyVNeSvKoJUTCbcpE-ay-MQwAQIHEs78xR$ 
> https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!Mih3wA!AVtHBHat3jUEF6ka5zCGkFNZBaQyq5gtgZHurR6WTN74wSjFfJMyVNeSvKoJUTCbcpE-ay-MQwAQIKYOBOjn$ 




From petr.jezdik at fel.cvut.cz  Tue Jun 27 13:49:32 2023
From: petr.jezdik at fel.cvut.cz (Petr Jezdik)
Date: Tue, 27 Jun 2023 13:49:32 +0200
Subject: [FieldTrip] troubles with ftbuffer compilation under windows,
 please help
Message-ID: <8f7186b3-1f22-db57-f5b1-cf25217028ce@fel.cvut.cz>

hello,

sorry to bother, but after many trials I am stucked. My task was to 
create a proxy from Natus amplifier to Ftbuffer. At the beginning, quite 
simple, under linux, not such a big troubles. But unfortunately our PCs 
in hospital are mostly running windows.

I tried xdks from ubuntu, mingw, cygwin, VS2019, Borland CPP, I reckon 
all what you mention in 
https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/development/realtime/reference_implementation/*compiling-the-code__;Iw!!HJOPV4FYYWzcc1jazlU!4AKBR5RmEnjRrIY6TO3MnTA10Snd7Y2xjyjQuvCY30N2LSNbpM4O_roKtWr6KpS01OwitcoCk16tOqr-TNQTVyu9TALkp9A$  


but with no success, mostly troubles with platform definitions, 
sys/time, pthread, winsock ...

could you please help me?

I am not really a programmer, mostly working with matlab instead of c, 
is there a way to provide me compiled libbufer.lib so I could use it in 
my windows code in similar way as libbufer.a in linux? could it work 
like that in windows?

or, even better don't you have an image or virtual 
machine/docker/whatever where the compilation for windows works?

thanks for any help

Petr

PS in attachment you can see my simple proxy, from Natus to FTbuffer, 
feel free to use it, I did not break the NDA, mostly reverse engineering 
and network sniffing of the communication

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From neoneuroimaging at gmail.com  Wed Jun 28 16:21:59 2023
From: neoneuroimaging at gmail.com (matt g)
Date: Wed, 28 Jun 2023 09:21:59 -0500
Subject: [FieldTrip] Tutor request.
Message-ID: <CADy4JMta6=--=nGJ2CcDZSC+nJNDjkVK-SqH1JuSDVvjsggYPw@mail.gmail.com>

Hello,

I am hoping that someone would be willing to teach me how to use fieldtrip
over zoom. I would be willing to compensate /pay for the lessons. Just for
added context I am starting out with ".set" files and am familiar with
EEGlab and CONN. Please let me know what time would work best for you in
your message along with the time zone. My email is  neoneuroimaging@
gmail.com .

Best,
MG
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From judy.zhu at mq.edu.au  Fri Jun 30 04:09:19 2023
From: judy.zhu at mq.edu.au (Judy Zhu)
Date: Fri, 30 Jun 2023 02:09:19 +0000
Subject: [FieldTrip] BIOMAG 2024 in Sydney
Message-ID: <SY4PR01MB5753C93EC81C6D95F701915ACD2AA@SY4PR01MB5753.ausprd01.prod.outlook.com>

Dear all,

We are excited to announce that the 23rd International Conference on Biomagnetism (BIOMAG) will take place in Sydney, Australia, on 26-29 August 2024. The conference will be held at the International Convention Centre, located within the beautiful Darling Harbour. We are looking forward to bringing together scientists, clinicians and professionals to exchange knowledge and ideas and forge new collaborations. Confirmed keynote speakers include Prof Aina Puce (Indiana University), Prof Huan Luo (Peking University) and Dr Alexandre Gramfort (Meta). Call for Abstracts and information on registrations will follow.

Please bookmark the conference website for further updates:
https://urldefense.com/v3/__https://www.biomag2024.org/__;!!HJOPV4FYYWzcc1jazlU!9oP_2XjLHo6EmIAkyaO9SeNpgefpYKM7oC9n4yZ8DXkZQaijanmJtwnUEI-0SGpqVEPOLwJnvNLTno-SqygYgXmu$ <https://urldefense.com/v3/__https://www.biomag2024.org/__;!!HJOPV4FYYWzcc1jazlU!9oP_2XjLHo6EmIAkyaO9SeNpgefpYKM7oC9n4yZ8DXkZQaijanmJtwnUEI-0SGpqVEPOLwJnvNLTno-SqygYgXmu$ >

We look forward to seeing you in Sydney!

Kind regards,
BIOMAG2024 Local Organising Committee

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From eelke.spaak at donders.ru.nl  Fri Jun 30 11:35:04 2023
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Fri, 30 Jun 2023 11:35:04 +0200
Subject: [FieldTrip] PhD position open on information seeking, active vision,
 and Rapid Invisible Frequency Tagging in MEG
Message-ID: <CABPNLUpg9N7cLWr=5vrrdn+3x_YP9zgKmaY1HLQXHNW119iV1Q@mail.gmail.com>

Dear colleagues,

Some of you may be interested in, or know others who may be interested
in, the below fully-funded PhD position I currently have open at the
Donders Institute (note deadline: **next Tuesday 4 July**!).

Details and application:
https://www.ru.nl/en/working-at/job-opportunities/phd-candidate-in-quantitative-visual-cognitive-neuroscience-at-the-donders-centre-for-cognition

All the best,
Eelke

---
PhD Candidate in Quantitative Visual Cognitive Neuroscience at the
Donders Centre for Cognition

Are you fascinated by how our brains construct our conscious visual
reality? By how our eyes move around several times per second, our
brains apparently always knowing where to look? If that applies to
you, and you furthermore are excited about developing new experimental
neuroimaging and analytical methods (including deep learning), then
this PhD position may be right for you!

As part of this job, you will conduct research testing several key
hypotheses (related to the 'Bayesian' brain) about information
sampling during visual perception. What types of visual information
are dominant in determining where we look? Which brain structures are
involved in processing this information? How is this related to what
we know about neural motivational control in general?

Studying such questions requires taking visual cognitive neuroscience
beyond its traditional paradigms of having people fixate on computer
screens and presenting visual information rather passively. This is
challenging, yet two recent developments offer a promising way
forward: Rapid Invisible Frequency Tagging (RIFT) in
magneto-encephalography (MEG) recordings, and deep learning models
from Artificial Intelligence (AI) in quantifying visual information.
You will be involved in advancing the state of the art in these
techniques (especially RIFT), and combining them to yield novel
scientific insights.

In addition, you will gain hands-on experience in research design, MEG
recordings, scientific writing, and presenting at international
conferences. In all aspects of the scientific process, you will be
guided and supervised by a diverse and experienced supervision team.
We anticipate that there will be ample room for your own creative
input, especially as your expertise and interests mature.

All PhD candidates at the Donders Centre for Cognition are involved in
0.1 FTE of teaching, which helps them prepare optimally for the
academic job market.

Profile:
- You should hold an MSc degree (or similar) in
cognitive/computational neuroscience, artificial intelligence,
experimental psychology, or a similar discipline (candidates with
experience in other fields may be considered if well motivated).
- You have a keen interest in the mechanistic basis of conscious
visual perception.
- You have strong analytical skills, and experience with programming
(in Python and/or Matlab, or any other language plus a willingness to
learn Python/Matlab).
- You are excited about pushing the boundaries of both scientific
knowledge and methodology.
- You ideally have experience with collecting experimental
(neuroimaging/physiological/eye-tracking/behavioural) data from human
subjects, or a strong willingness to learn.
- You are fluent in spoken and written English.

Further details and application:
https://www.ru.nl/en/working-at/job-opportunities/phd-candidate-in-quantitative-visual-cognitive-neuroscience-at-the-donders-centre-for-cognition


