November 2018 – Finally the EEG experiment

So, it’s beginning of January and only now I have time and energy to write the wrap up of November (and December). In general November has been very creative in research, teaching and outreach. But let’s take it from the top.

Research

November started with unresolved issues in the Matlab script, related to stimulus presentation. I have extensive notes of the first couple of days, because I had to keep track of the solutions I’ve already tried, in order to avoid losing time on re-trying things that didn’t work out. Looking into Matlab code generally makes me dizzy, but at least I managed to navigate and eventually solve the issues. I ran the whole experiment on myself and discovered some missing files and some typos that needed to be fixed. One of the audio files needed to be re-recorded, as it included a mispronunciation of a name in only one part of the story. Luckily, the speaker was available in Maastricht, so he passed by and we wrapped up the recording in 15 minutes. Then I normalized that file and included it to the list of audio files. I also fixed the typos and balanced the correct answers to half option a and the other half option b.

My initial experimental script was doing the normalization in the stimulus presentation script and the resulting normalized files were only peak-normalized. This ended up not having the same loudness across files. With the valuable help of my collaborator Thanos, who explained how to do a two-step normalization, I made a short script which normalized the files in peak and loudness externally from the experimental script. Then, in the experimental script I only load and play the files without needing to normalize them anymore. In mid November I sent the normalized files to Thanos, so that he runs his auditory analysis algorithms on the signal.

We then determined how to analyze the audio signal, based on Thanos’s previous research and its relevance for cognitive functions. In my email to Thanos I wrote:

I see that the most prominent features given the theory on speech rhythm, such as the period of the strongest peak (beat), do not perform so well in the automatic language identification task in all the corpora you tested. This might at first be surprising, but the difference should be viewed, as you already discussed in the paper, under the task performed by the classification algorithm and the fact that the algorithm might not be reflecting cognitive processes.

Given these, I would like to suggest that we take all the beat histogram features for our analysis and use them in two ways:

  1. to test whether the algorithm can discriminate between conditions, poem vs. story and which features are the most prominent in this classification.
  2. then, to take the most cognitively motivated features, e.g. amplitude and F0, and compare their fit to the EEG data.

We decided to compute all the novelty functions based on the beat histograms, as laid out in Thanos’s 2015 paper. We would then discuss that we can do with features like spectral flux or spectral flatness, which do not seem to be relevant for cognition, at least for the moment, but seemed to contribute very much to the classification between languages.

On November 20th, I had a second project proposal meeting with the TMS group, in which I outlined the details of the experimental setup. The group recommended me to be cautious about: preparation of the subject (the gel would dry out when applying the TMS), how to optimize procedures so that we are fast and effective, use a TMS compatible cap, how to localize the pre-SMA for each participant. In my meeting with Teresa on November 23rd, she stressed that the most important thing is how we localize the pre-SMA, whether we need a structural MRI and look in each brain for the specific co-ordinates, or whether it is an easy area to localize, such as other motor regions, and does not need an MRI scan. She advised me to look into previous studies which have targeted the pre-SMA and check the methodological details. I have to complete and send back the NIBS Project Proposal Form before we start measuring for NERHYMUS.

Teaching

Most of the students of the writing skills course submitted their Introduction on time on November 9th. I was amazed at the general low quality of the essays. However, after I visited the course on how to evaluate and give feedback for writing skills and theses, I realized that the students are just starting to understand how scientific writing is expressed and how to write in this form themselves. So, I re-evaluated my initial evaluation, and made an effort to give my students meaningful feedback on how to improve, rather than dismissive general comments. From the individual short meetings for providing this feedback I had the impression that the students truly appreciated my effort and that it helped them understand what they did wrongly and how to improve.

With regard to the mentoring course, I had the impression that the second mentor meeting was a disaster. Even though I did my best to follow the instructions of the course administrator, I felt that the students were not interested, as the session was very much just repeating the content of the first session. The general impression was that what we did in the scheduled 2 hours, could have easily been done in 1 hour without needing to overtire the students with repetition. Maybe it was also the wrong time of the day for such a task, as 4-6pm in the late afternoon is quite late. I have forwarded this feedback to the colleagues who planned the course and hope that this session will be planned differently for next year.

Outreach

We’ve made a lot of progress with Pint of Science Maastricht. In mid November, Lena and I met with Danielle Vogt and Flore Clerx from the Marketing and Communications of the FHML, who really helped us to pitch our call for volunteers in a fun manner. They were also very supportive of Pint of Science Maastricht in general and they suggested to hold a general info session in the Turnzaal in January and have media coverage and possibly interviews to spread the word about the festival. Lena worked with them on the text for the university-wide call for participation and we sent it out at the end of November.

On November 27th I held the first info meeting in a small circle with people from NP&PP and CN. The goal of this meeting was not only to inform, but also to recruit volunteers for the taster event, which will introduce Pint of Science to Maastricht on February 27th, 2019.

On November 28th, I went to the Societal Engagement event, organized by the University of Maastricht, representing Pint of Science Maastricht with my own stand in the “market”.

Many people showed interest in the initiative, especially because they found the idea of bringing science to the pubs cool. I also got some important contacts, such as the organizers of TEDx Maastricht Gonny Willems and Sophie Kells. Sophie works in the press office of the university and came to my stand to offer her enthusiastic support to Pint of Science Maastricht. I approached Gonny at the bar and we decided to meet in January in order to discuss collaborating on the level of training speakers for public speaking and on organizing an event with the topic “Redefining Europe” for the Pint of Science festival in May.

Last, on November 13th I went to the launch event of the Female Empowerment Maastricht initiative. This album has some amazing photos.

Photo by: Brian Megens Photography (www.brianmegens.com)

I took part in the Work-Life balance workshop, together with my colleague and friend Alex Emmendorfer, see us both in the picture.

Photo by: Brian Megens Photography (www.brianmegens.com)

That was a decent summary of November.

KDK

September 2018 – Delays and disappointments, BUT Pint Of Science

This month’s progress can be categorized in advances, delays, teaching and outreach.

Advances

In research, I made the experimental lists of the materials, in order to assign the text material to the four different speakers. The lists are here. In these lists I have estimated 30min of auditory material, of which roughly half is poems and the other half is stories. Also, in each list, each speaker is heard 2-3 times, which assures that every list has at least 20% auditory material for each of the four speakers. Given the naturalness of the stimuli, and the speed of the speaker, I cannot have a more precise estimate yet. This will be finalized when the audio files are finalized.

Delays

The construction of the speech labs was delayed up until the middle of September. In the BAND-LAB meeting I was informed that I could use the EEG lab for my recordings instead. So I informed the speakers and organized meetings for recordings. I was in need of a mic stand, as there was no proper support for the microphone we have in the lab. I went to Instrumentation to ask for help, but it was difficult to solve the issue on the spot. I had to rely on them to find a solution with mic stand, which took another couple of days. When finally a provisional stand was there, clearly not ideal for the mic, but for the moment suitable enough, I could start the recordings. I started with the female speakers, as they are based in Maastricht. Here is a little video of recording a funny story.

In the first couple of meetings with the female speakers, we realized that the speed of the speech was quite fast. I asked my colleague’s opinion as a native speaker (Michael Schwartze) and he confirmed my suspicion. The poems were consistently too fast to visualize for the listener. The stories were on the boarder of being too fast, as non-metered speech sounded more natural in faster speed. However we decided to re-do everything, in order to assure a listener-friendly pace. In the beginning of October I am planning some more recordings.

Teaching

As I had decided to become a mentor for first year bachelor students, I went to the mentor instruction meeting on the 11th of September. In that meeting all mentors were instructed about their role in the course “Skills II: Observing Others and Yourself, under which the mentoring takes place. We were instructed that our main task is to listen and, if necessary, refer to the academic adviser (Aimee Coenen: UM link, better link). I was assigned a group of 13 perople, group number 21. Before October 2nd, I had to meet individually with every student in order to get to know them a bit. Before the meeting they were required to send me their portfolio, for which they were encouraged to be as creative as they liked. I received a variety of portfolios, which included a website, a poem, graphical art and some philosophical reflections.

I met with each student for about 30min in the last two weeks of September. Some of them were shy, some didn’t know what to expect, some others were already overwhelmed with their studies. Some have extended international experience, some others have difficulties with the language. Most of them live in Maastricht, but the one or two who don’t live in town, are a bit more distant also within the group. In every meeting I did my best to create a safe and comfortable environment and I was very thankful for their openness and trust. Even though this mentoring task took a lot of time, I liked the process of meeting different students and understanding their backgrounds. I am very motivated to support them with their study-struggles, especially in their first few months at university, because I know that I would have welcomed such help in my first few months in every new study (and new university).

Outreach

We are bringing Pint of Science to Maastricht in 2019!

Pint of Science is an international science festival, which takes place every year in May in pubs/bars. The friendly and relaxed atmosphere of a pub, along with the consumption of a pint of beer (or other alcohol) is making science accessible to the public. Our team in the official Pint of Science Netherlands page.

In this initiative, I am City Coordinator for Maastricht and Lena Liapi is Communications Officer, assisted by Claudia Spierings and Thom Frijns of the Marketing & Communication Office of the Faculty of Psychology and Neuroscience. We are planing two events, one main event in May 20-22 2019 as well as a taster event in February 2019.

Stay tuned by following us on twitter (@pintofscienceNL or @KaterinaDKand )!

I already have 7 volunteers, after a short announcement in our department, and the team is planning the next actions. I am looking forward to launching this event in Maastricht and thereby fulfill another of my plans, as written in my MSC application.

These were the most important things that happened in September.

KDK

August 2018 – Change of plans

This month I officially changed the timeline of the project to include two experiments (1. EEG+TMS, adn 2. fMRI+TMS) instead of one, which would combine all three methods.  The reasons for that are documented in the July blog post “NOT concurrent and why”. The developments during August can be categorised in research, outreach, grant writing, and teaching. Let’s get this going.

Research

  1. Order of experiments: We decided to start with the combined EEG and TMS experiment.
  2. Stimuli texts: Anna and I selected the stimuli texts, and this is our final selection. There is a variety of poems and stories, both serious and amusing, from old time classic writers like J. W. von Goethe, Heinrich Böll, and Heinrich Heine, as well as more contemporary writers like Jorge Bucay, and Petra Müller. I then continued into making the experimental lists in order to assign the stimuli to the different speakers. Each experimental list contains 50% of each stimulus condition poem/story and 25% of each of the four speakers (2 female and 2 male voices). The order of the stimuli will be as much as possible counterbalanced, only between stories/poems but not within a story/poem.
  3. Online questionnaire: Anna and I also worked on the modification of the online questionnaire (MMHQ). We included Sonja’s previously used language background questionnaire, which comprises of how many languages one speaks, understands, writes and reads and documents at which level for competence and language. Anna then had to leave the project, because of her study obligations.
  4. Speakers: I had a meeting with an actress, who responded to my advert for professional speakers in the theater mailing list. In the beginning I was positive that this collaboration is meaningful. However, after I realized how precise I need to instruct the actors on how to speak out the stimuli, how prompt they were to express them with strong emotion, as well as how much the costs would be for 4 speakers, I was discouraged to choose that path. A rough estimate showed that the costs would rise up to 800-1000 euro per speaker, and that was definitely way out of our budget. Sonja and I decided to go natural and just employ native speakers who have good voices. Lisa Goller and Francesca Bolk were the ones that came to mind immediately and they also agreed to perform this task upon payment. Anna offered the solution for the male voices by suggesting Tobias and Johannes Weinhold. They sent me sample recordings and I agreed to have them as the male voices of the NERHYMUS experiments.
  5. Audio recordings: Since the speakers were found so miraculously and we also had the stimuli texts, I could proceed to the audio recordings. However, the speech lab(s), in which I was supposed to record the stimuli were under construction, so I couldn’t start the recordings immediately. The construction was first delayed to the end of August and then further to the middle of September. I therefore could not start the recordings in August.
  6. EGI system training: on August 28th I participated in a one-day training on how to use the EGI system for EEG recordings, which is compatible with MRI scanner. I found very interesting that they do not use caps but nets, which are called geodesic sensor nets. This following picture is a closeup of the net, which comprises of sealed wet sponges for each of the 128 sensors. Definitely a promising setup, but I am not sure until I actually test it in my own experiments.
Closeup of the Geodesic Sensor Net of the EGI system.

Outreach

  1. Talks at schools: I had another meeting with Ellen Krijnen and Isabelle Grosch in which we discussed the specifics of my visit to schools. We decided to target the age group 15-18 years, which covers grades 4th, 5th and 6th of secondary school. We decided to frame it as an interdisciplinary talk, which combines the arts (language) and the sciences (neurobiology) and would be interesting to pupils of different directions (arts and sciences). I have stated my availability from February on and I have sent an email with a catchy title and some sentences that explain my talk.
  2. Pint of Science (PoS): I contacted Pint of Science Netherlands in order to start organizing how to bring this festival to Maastricht in 2019. On August 31st I met with Taichi Ochi, the director of PoS Netherlands, Lena Liapi, an enthusiastic Cardiology PhD student, Claudia Spierings, head of Marketing and Communications at the Faculty of Psychology and Neuroscience and Thom Frijns, a colleague of Claudia, in Dadawan for lunch. Thaichi explained the roles that are needed in each city and the timeline of the events and organization.

Grant writing

In the last two weeks of August I spontaneously decided to apply for the VENI grant of the NWO. Even though I didn’t want to apply in the first place, I reconsidered because this year would be my last chance, given the eligibility criteria. There should be no more than 3 years after PhD graduation date and on 28th of January 2019 I would complete 3 years. This process took one whole weekend, half a working week and another Sunday to complete. I enjoyed the creation of the new ideas and hypotheses, based on Sonja’s recent TICS paper and on Alex’s 2017 paper on new advances on stimulation technologies. I was happy with the end result and with the smooth communication with the involved people (Sonja, Alex, and Rense). Let’s see what comes out of this attempt, fingers crossed, and hopefully more news in October.

Teaching

  1. Mentoring for skills II Observing yourself and others: for my teaching hours, I have decided to become a mentor for a group of bachelor students. This entails 5 group meetings within 3 years of their study, as well as individual meetings with the students and support in their questions or concerns with their studies. On the 29th of August I participated in team building activities together with a group of students, as part of my mentoring duties.
  2. Tutoring for Skills IV Writing: I am passionate about teaching people how to write properly and how to structure their thoughts, texts and paragraphs accordingly to formal instructions. I want to use this passion in tutoring 2nd year bachelor students in their writing skills.

In the end of August I had to say goodbye to my dear “sister sealy”, who was accepted for a PhD in the South of France and left Maastricht to start her new adventure. You are greatly missed, Giusy, hope you can visit us!

Giusy in watermelon shirt eating watermelon.

That’s basically all for August. Bye bye summer.

July 2018 – NOT concurrent and why

July was generally busy with: TMS-relevant training and decisions, choosing suitable texts for stimuli, modifying the MMHQ for NERHYMUS, and the individualized Dutch course at the Language Center of Maastricht University.

In the beginning of July I presented my project proposal to the Brain Stimulation and Cognition group (BSC, led by Alexander Sack). Sonja was present. The group gave me very useful comments/suggestions of what to think about when applying TMS.

  1. As previously suggested by the fMRI group, the BSC group also suggested I separate the acquisition of EEG and fMRI data into two experiments. In the previous blog post (about June) I have outlined the reasons that this separation would make sense. The main advantage is the better data quality for both methods. We therefore decided to do two experiments: first, one with EEG-TMS and next another one with fMRI-TMS combination.
  2. TMS protocol: We will use continuous Theta Burst Stimulation (cTBS), once before measurement. This protocol comprises of 50Hz pulses (every 2s) for 40s in total. This is a classical inhibitory rTMS protocol, which will be applied on the right preSMA (for right-handed people).
  3. What is the exact hypothesis. The up/down-regulation of theta activity in the preSMA should interfere with rhythm perception, in specific the subpart of beat extraction.
  4. What is the best control condition: sham or a control site? For the moment we decide for sham. In this way our results would be able to conclude about brain stimulation interfering with the rhythm network, not in specific with the preSMA. As it is the first study to stimulate rhythm perception during story comprehension, we start by establishing the effect of the network. Next steps (possibly in a VENI grant) could target other nodes of this network and investigate their co-ordination for rhythm perception. Remaining open question: what would a good control site be?
  5. How to define the stimulation site individually? We will use a structural MRI scan and the Neuronavigation system. The preSMA region will be anatomically localized.
  6. The specific procedure: first do the EEG setup in the EEG lab at UNS40, then go to the TMS lab at UNS40 (floor -1) for the rTMS and then go back up to the EEG lab for the measurements. This procedure was suggested by Theresa Schumann and approved by Franc Donkers.
  7. I was put in contact with Stefano Gallotto and I helped him a couple of times with his experiment in order to familiarize myself with the neuronavigation system and with the TMS application.
  8. After I have settled the details of the procedure, I will present to this group again when the set up is finalized.

Anna (Otta) and I have been working closely on choosing suitable stimuli, but are not yet done in the end of July. Vacation followed so we continued with this task in August, see update on this in the August blog post.

I modified the MMHQ; I inserted a checkbox (default unchecked) with which participants agree to their anonymized data to be stored in encrypted university servers. This is the exact wording of the information “Experiment Information: This questionnaire will collect non-identifiable data on e.g. language background, music experience, dance performance. This data will be anonymized, encrypted and safely stored in servers of Maastricht University. Please confirm that you are aware of and agree with the following data collection and with the mentioned conditions of data storage.” and of the checkbox: “I confirm that I have read the abovementioned conditions and agree with the outlined data collection and its storage conditions.”. Participants also need to fill in their participant number or code and the date they completed the questionnaire. This is how it looks like:

 

The Dutch course was a real blast. I participated in this together with Anna Sagana, a new assistant professor in Forensic Psychology at UM. Our teacher was Petrie Roefs, she did a very good job in individualizing the course to our needs. On the last day I gave a 5-minute laymen presentation of NERHYMUS in Dutch. It was good fun and I realized I can speak and explain more if I am given enough time to think and if the topic is my own research.

In the end of July I left for Italy (Lecce) for vacation.

Then I flew from there to England (Chichester) for the MMM summer school. I came back on the 8th of August. The next blog post on August will take it from here.

 

 

June 2018 – The traveling month

This post comes a little bit delayed than normal, because during this month I was traveling a lot and I needed time to settle back at the end of the month. From 2-10/6 I went to Athens to teach a course entitled “Introduction to eye-tracking for psycholinguistics” at the 1st summer school of Experimental Methods in Pscycholinguistics (Empsy).

The students of the 1st Empsy

Then, I worked one full week in Maastricht 11-15/6. The next traveling for work was on the 18/6, when I was on my way to the 1st international Workshop on Predictive Processing (WoPP).

View from the workshop location, Miramar Palace.

From San Sebastian I flew directly to Crete for my friend’s wedding, which was a real blast. And when I came back on the 27/6 and worked for the last two days of June, there was only as much time to re-calibrate and get back to my list of tasks for NERHYMUS. There are therefore not many developments on the practical aspects of NERHYMUS this month, but more on the development of my own research agenda and personal character.

My impressions and reflections on my first intensive teaching experience at the summer school will be the topic of a separate post. I am therefore moving on to the developments on NERHYMUS, which happened the week of 11-15/6.

On June 12th I gave a presentation in a project proposal meeting of the fMRI group lead by Elia Formisano at the Cognitive Neuroscience department. The main comments on my proposal were:

  1.  Why do concurrent EEG-fMRI? If we want to go through the hassle of noisy EEG data and complicated set up, we should have a hypothesis that can only be answered with a concurrent design. Our design up to now does not motivate concurrent data acquisition.
  2. Think about how to model the fMRI response with the beats extracted from the audio signal, because of the different time resolution.
  3. Check sparse sampling as a possible solution to comment Nr. 2.

On June 13th I skyped with Emily Coffey in order to get a short overview of the Montreal Music History Questionnaire, which I will use for quantifying musical and dance expertise. I will add one section on language expertise and a clarification about ethics and data management, according to the EU GDPR.

Update on the Stimuli: Anna (the intern who is helping select the stimuli texts) has chosen poems that should suffice for 50 minutes of poem materials for the experiment. In beginning of July she is going to select stories and then I will take it from there on, to find speakers and calculate the budget for recording the audio stimuli.

Concurrent or not

Since the fMRI PPM I have been thinking about the pros and the cons of concurrent or non concurrent EEG-fMRI data acquisition. I have summarized these in the following table:

I discussed these points with Lars Hausfeld on Skype while I was at the WoPP in San Sebastian. His advice was similar to that which came up at the fMRI PPM; unless there is a clear hypothesis to be answered only with the concurrent design, there is not enough motivation to go for it. He favored a step-by-step build-up approach, in which I would combine EEG and offline TMS first and then continue with the combination of fMRI and offline TMS. With regard to comment Nr. 2 from the fMRI PPM, he suggested averaging the BOLD response within 1 minute, thereby creating a mini-block design.

The first WoPP was very interesting and scientifically stimulating. There were experts of different fields, who discussed their research of predictive processing under their understanding and following different frameworks. I observed inconsistencies in the terminology, which essentially arise from the adoption of different theoretical frameworks, but I would have welcomed a critical summary of all the presented approaches, at least of the ones that were included in the Symposia. It seems easy to me that each speaker tells their own story, but the most interesting part would have been an amalgamation of the available expertise into conclusions about predictive processing.

So this was June, in short. In July I aim to develop the experiment in more detail and progress on the stimuli and questionnaire. Also, I have planned a Dutch course which will take a significant part of my time, but it will be a good investment for the future.

KDK