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Entry  Fri Feb 2 15:10:14 2024, Praveen Sripad, Projects registry for the Cogitate Project, 03/02/24, IDEA 
Initial.
    Reply  Mon Jun 24 09:02:30 2024, Praveen Sripad, Projects registry for the Cogitate Project, 03/02/24, IDEA 

Praveen Sripad wrote:
Initial.


Updated to include Co-authors and Data Used.
    Reply  Fri Aug 2 12:29:24 2024, Diptyajit Das, Projects registry for the Cogitate Project, 03/02/24, IDEA  
[quote="Praveen Sripad"]Initial. [/quote]

this a test reply
Entry  Fri Aug 2 11:12:28 2024, Diptyajit Das, Demo test project, 08/03/24, IDEA 
Entry  Fri Jun 21 14:17:41 2024, Oscar Ferrante, Gating by inhibition: do alpha oscillations modulate early visual or content-specific representations in the brain?, 12/31/25, IN PROGRESS 
Oscillatory brain activity in the alpha band (8-12 Hz) has been associated with inhibitory control [1,2,3], in the sense that alpha oscillations suppress neuronal firing in a rhythmic manner [4]. Consequently, the magnitude and phase of the pre-stimulus alpha oscillations have also been related to conscious perception [5]. It is debated whether alpha oscillations modulate neuronal firing in early sensory regions or rather reflect gating-of-information in downstream regions [6]. We will answer this question using MEG data (and secondarily ECoG data, in collaboration with the team) from Experiment 1 by examining how the phase and magnitude of pre- and post-stimulus alpha oscillations modulate early visual as well as content-specific activity. Specifically, we will use a generalized eigenvalue decomposition (GED) method [7] to identify the single trials time-course reflecting distributed activity responsive to specific stimulus categories (faces and objects). We will then test whether the single-trial activity of this category-selective source is modulated by the phase and magnitude of the alpha activity. We will compare the phasic role of alpha oscillations on activity in early visual regions, as well as on category specific activity generated in the ventral stream. This project aims at extending the current knowledge about the functional role of the alpha rhythm in human cognition and how its inhibitory control is implemented from a mechanistic point of view.

References:
1. Foxe, J. J., & Snyder, A. C. (2011). The role of alpha-band brain oscillations as a sensory suppression mechanism during selective attention. Frontiers in psychology, 2, 154.
2. Klimesch, W., Sauseng, P., & Hanslmayr, S. (2007). EEG alpha oscillations: the inhibition–timing hypothesis. Brain research reviews, 53(1), 63-88.
3. Jensen, O., & Mazaheri, A. (2010). Shaping functional architecture by oscillatory alpha activity: gating by inhibition. Frontiers in human neuroscience, 4, 186.
4. Mazaheri, A., & Jensen, O. (2010). Rhythmic pulsing: linking ongoing brain activity with evoked responses. Frontiers in human neuroscience, 4, 177.
5. Krasich K, Simmons C, O'Neill K, Giattino CM, De Brigard F, Sinnott-Armstrong W, Mudrik L, Woldorff MG. (2022) Prestimulus oscillatory brain activity interacts with evoked recurrent processing to facilitate conscious visual perception. Sci Rep. 12(1):22126. doi: 10.1038/s41598-022-25720-2.
6. Zhigalov, A., & Jensen, O. (2020). Alpha oscillations do not implement gain control in early visual cortex but rather gating in parieto‐occipital regions. Human Brain Mapping, 41(18), 5176-5186.
7. Cohen, M. X. (2022). A tutorial on generalized eigendecomposition for denoising, contrast enhancement, and dimension reduction in multichannel electrophysiology. Neuroimage, 247, 118809.
    Reply  Mon Jun 24 09:18:15 2024, Oscar Ferrante, Gating by inhibition: do alpha oscillations modulate early visual or content-specific representations in the brain?, 12/31/25, IN PROGRESS 

Oscar Ferrante wrote:
Oscillatory brain activity in the alpha band (8-12 Hz) has been associated with inhibitory control [1,2,3], in the sense that alpha oscillations suppress neuronal firing in a rhythmic manner [4]. Consequently, the magnitude and phase of the pre-stimulus alpha oscillations have also been related to conscious perception [5]. It is debated whether alpha oscillations modulate neuronal firing in early sensory regions or rather reflect gating-of-information in downstream regions [6]. We will answer this question using MEG data (and secondarily ECoG data, in collaboration with the team) from Experiment 1 by examining how the phase and magnitude of pre- and post-stimulus alpha oscillations modulate early visual as well as content-specific activity. Specifically, we will use a generalized eigenvalue decomposition (GED) method [7] to identify the single trials time-course reflecting distributed activity responsive to specific stimulus categories (faces and objects). We will then test whether the single-trial activity of this category-selective source is modulated by the phase and magnitude of the alpha activity. We will compare the phasic role of alpha oscillations on activity in early visual regions, as well as on category specific activity generated in the ventral stream. This project aims at extending the current knowledge about the functional role of the alpha rhythm in human cognition and how its inhibitory control is implemented from a mechanistic point of view.

References:
1. Foxe, J. J., & Snyder, A. C. (2011). The role of alpha-band brain oscillations as a sensory suppression mechanism during selective attention. Frontiers in psychology, 2, 154.
2. Klimesch, W., Sauseng, P., & Hanslmayr, S. (2007). EEG alpha oscillations: the inhibition–timing hypothesis. Brain research reviews, 53(1), 63-88.
3. Jensen, O., & Mazaheri, A. (2010). Shaping functional architecture by oscillatory alpha activity: gating by inhibition. Frontiers in human neuroscience, 4, 186.
4. Mazaheri, A., & Jensen, O. (2010). Rhythmic pulsing: linking ongoing brain activity with evoked responses. Frontiers in human neuroscience, 4, 177.
5. Krasich K, Simmons C, O'Neill K, Giattino CM, De Brigard F, Sinnott-Armstrong W, Mudrik L, Woldorff MG. (2022) Prestimulus oscillatory brain activity interacts with evoked recurrent processing to facilitate conscious visual perception. Sci Rep. 12(1):22126. doi: 10.1038/s41598-022-25720-2.
6. Zhigalov, A., & Jensen, O. (2020). Alpha oscillations do not implement gain control in early visual cortex but rather gating in parieto‐occipital regions. Human Brain Mapping, 41(18), 5176-5186.
7. Cohen, M. X. (2022). A tutorial on generalized eigendecomposition for denoising, contrast enhancement, and dimension reduction in multichannel electrophysiology. Neuroimage, 247, 118809.
Entry  Fri Jun 21 14:21:30 2024, Oscar Ferrante, Relating subcortical structures to the modulation of neocortical alpha and beta oscillations, 12/31/25, IN PROGRESS 
It has recently been demonstrated that the thalamus and basal ganglia are related to the modulation of neocortical oscillatory activity (Mazzetti et al., 2019). In addition, research conducted on mice and non-human primates supports the theory that cortical-thalamic-basal-ganglia circuits play a significant role in generating and controlling neocortical oscillations (Cruz et al., 2023). Meanwhile, many neurological disorders, including Alzheimer’s and Parkinson’s Disease, are linked to structural changes in the subcortical regions (Cho et al., 2014).
The aim of this study is to investigate whether changes in subcortical structures are reflected in neocortical activity, specifically the modulation of alpha and beta band oscillations, as measured by resting-state MEG. To achieve this, we will develop tools to identify alpha and beta bursting during rest in healthy participants and quantify their hemispheric asymmetries. Next, the volumetric lateralization of subcortical regions will be evaluated and correlated with neocortical oscillations to establish a link between subcortical structures and oscillatory activity. For this purpose, we would like to request having access to the resting state MEG data from experiment one and two of the COGITATE study, along with the T1 MRI scans and eyetracking data.
This study will shed light on the role of subcortical structures in cognitive functions in relation to their ability to modulat oscillatory brain activity. It also has the potential to provide non-invasive electrophysiological methodology (MEG, EEG) for early diagnosis of neurological diseases affecting subcortical structures.
Overall, this study seeks to demonstrate the relationship between subcortical structures and oscillatory activity in the neocortex. This could lead to a better understanding of neurological disorders and contribute to the development of more effective diagnostic tools for the early detection of such diseases.

Mazzetti, C., Staudigl, T., Marshall, T. R., Zumer, J. M., Fallon, S. J., & Jensen, O. (2019). Hemispheric asymmetry of globus pallidus relates to alpha modulation in reward-related attentional tasks. Journal of Neuroscience, 39(46), 9221-9236.
Cruz, K. G., Leow, Y. N., Le, N. M., Adam, E., Huda, R., & Sur, M. (2023). Cortical-subcortical interactions in goal-directed behavior. Physiological reviews, 103(1), 347-389.
Cho, H., Kim, J. H., Kim, C., Ye, B. S., Kim, H. J., Yoon, C. W., ... & Seo, S. W. (2014). Shape changes of the basal ganglia and thalamus in Alzheimer's disease: a three-year longitudinal study. Journal of Alzheimer's disease, 40(2), 285-295..
    Reply  Mon Jun 24 09:15:10 2024, Oscar Ferrante, Relating subcortical structures to the modulation of neocortical alpha and beta oscillations, 12/31/25, IN PROGRESS 

Oscar Ferrante wrote:
It has recently been demonstrated that the thalamus and basal ganglia are related to the modulation of neocortical oscillatory activity (Mazzetti et al., 2019). In addition, research conducted on mice and non-human primates supports the theory that cortical-thalamic-basal-ganglia circuits play a significant role in generating and controlling neocortical oscillations (Cruz et al., 2023). Meanwhile, many neurological disorders, including Alzheimer’s and Parkinson’s Disease, are linked to structural changes in the subcortical regions (Cho et al., 2014).
The aim of this study is to investigate whether changes in subcortical structures are reflected in neocortical activity, specifically the modulation of alpha and beta band oscillations, as measured by resting-state MEG. To achieve this, we will develop tools to identify alpha and beta bursting during rest in healthy participants and quantify their hemispheric asymmetries. Next, the volumetric lateralization of subcortical regions will be evaluated and correlated with neocortical oscillations to establish a link between subcortical structures and oscillatory activity. For this purpose, we would like to request having access to the resting state MEG data from experiment one and two of the COGITATE study, along with the T1 MRI scans and eyetracking data.
This study will shed light on the role of subcortical structures in cognitive functions in relation to their ability to modulat oscillatory brain activity. It also has the potential to provide non-invasive electrophysiological methodology (MEG, EEG) for early diagnosis of neurological diseases affecting subcortical structures.
Overall, this study seeks to demonstrate the relationship between subcortical structures and oscillatory activity in the neocortex. This could lead to a better understanding of neurological disorders and contribute to the development of more effective diagnostic tools for the early detection of such diseases.

Mazzetti, C., Staudigl, T., Marshall, T. R., Zumer, J. M., Fallon, S. J., & Jensen, O. (2019). Hemispheric asymmetry of globus pallidus relates to alpha modulation in reward-related attentional tasks. Journal of Neuroscience, 39(46), 9221-9236.
Cruz, K. G., Leow, Y. N., Le, N. M., Adam, E., Huda, R., & Sur, M. (2023). Cortical-subcortical interactions in goal-directed behavior. Physiological reviews, 103(1), 347-389.
Cho, H., Kim, J. H., Kim, C., Ye, B. S., Kim, H. J., Yoon, C. W., ... & Seo, S. W. (2014). Shape changes of the basal ganglia and thalamus in Alzheimer's disease: a three-year longitudinal study. Journal of Alzheimer's disease, 40(2), 285-295..
    Reply  Mon Jun 24 09:17:11 2024, Oscar Ferrante, Relating subcortical structures to the modulation of neocortical alpha and beta oscillations, 12/31/25, IN PROGRESS 

Oscar Ferrante wrote:
It has recently been demonstrated that the thalamus and basal ganglia are related to the modulation of neocortical oscillatory activity (Mazzetti et al., 2019). In addition, research conducted on mice and non-human primates supports the theory that cortical-thalamic-basal-ganglia circuits play a significant role in generating and controlling neocortical oscillations (Cruz et al., 2023). Meanwhile, many neurological disorders, including Alzheimer’s and Parkinson’s Disease, are linked to structural changes in the subcortical regions (Cho et al., 2014).
The aim of this study is to investigate whether changes in subcortical structures are reflected in neocortical activity, specifically the modulation of alpha and beta band oscillations, as measured by resting-state MEG. To achieve this, we will develop tools to identify alpha and beta bursting during rest in healthy participants and quantify their hemispheric asymmetries. Next, the volumetric lateralization of subcortical regions will be evaluated and correlated with neocortical oscillations to establish a link between subcortical structures and oscillatory activity. For this purpose, we would like to request having access to the resting state MEG data from experiment one and two of the COGITATE study, along with the T1 MRI scans and eyetracking data.
This study will shed light on the role of subcortical structures in cognitive functions in relation to their ability to modulat oscillatory brain activity. It also has the potential to provide non-invasive electrophysiological methodology (MEG, EEG) for early diagnosis of neurological diseases affecting subcortical structures.
Overall, this study seeks to demonstrate the relationship between subcortical structures and oscillatory activity in the neocortex. This could lead to a better understanding of neurological disorders and contribute to the development of more effective diagnostic tools for the early detection of such diseases.

Mazzetti, C., Staudigl, T., Marshall, T. R., Zumer, J. M., Fallon, S. J., & Jensen, O. (2019). Hemispheric asymmetry of globus pallidus relates to alpha modulation in reward-related attentional tasks. Journal of Neuroscience, 39(46), 9221-9236.
Cruz, K. G., Leow, Y. N., Le, N. M., Adam, E., Huda, R., & Sur, M. (2023). Cortical-subcortical interactions in goal-directed behavior. Physiological reviews, 103(1), 347-389.
Cho, H., Kim, J. H., Kim, C., Ye, B. S., Kim, H. J., Yoon, C. W., ... & Seo, S. W. (2014). Shape changes of the basal ganglia and thalamus in Alzheimer's disease: a three-year longitudinal study. Journal of Alzheimer's disease, 40(2), 285-295..
Entry  Sat Jun 22 13:58:29 2024, Urszula Górska-Klimowska, Towards improved data quality testing practices in consciousness science, 02/01/25, IN PROGRESS 
In recent years, there has been an increasing amount of multi-lab collaborative experiments in consciousness science. While this facilitates replication together with data sharing, it also reveals the need for cross-lab, standardized ways to accumulate and test the quality of the collected data, to allow its integration across labs. This work will introduce a systematic, generalizable data quality assessment framework. Initially developed for the COGITATE adversarial collaboration, it accommodates both neural datasets (fMRI, MEG/EEG, and intracranial EEG), as well as non-neural datasets (behavioral and eye-tracking data types). The framework includes three key levels: the first level assures data completeness, consistency, and anonymization. The second level tests whether the participant followed the task and if the manipulation worked. This can be done by testing behavioral or eye-tracking data, for example, independent of the hypothesis tested in an experiment. The third level checks whether neural data are of sufficient quality to test the hypotheses. In this work, we will advocate for defining clear data quality standards prior to data collection, testing that the datasets adhere to these standards prior to conducting tests on the main research hypotheses, and documenting and openly sharing the testing procedure together with the data. 
Entry  Tue Jun 18 20:45:39 2024, Aya Khalaf, Early visual perception networks, 06/18/25, IN PROGRESS 
Entry  Fri Jun 14 11:45:26 2024, Gennadiy, Exploring the role of attention in access to consciousness, 10/01/25, IN PROGRESS 
At any given point in time, a vast amount of information enters our sensory system, but only some of it is further processed and even less is subjectively perceived. Attention is one of the major phenomena selecting information for conscious processing. Yet, the exact mechanism by which attention gates access to awareness is still debated. Here, we seek to pinpoint processes of attentional selection in the context of the attentional manipulation conducted in Cogitate’s Experiment 2. We will use established markers of attention (e.g., P1, N1, N2pc) in order to test the stage at which attention has contributed to visibility in the video game. An additional goal of this experiment is to detect electrophysiological markers of subjective visibility and test their generalizability to unprobed trials using decoding. This will allow us to further explore differences between seen and unseen unprobed trials during later time windows, that are confounded by the probe in probed trials.
    Reply  Fri Jun 14 13:54:18 2024, Praveen Sripad, Exploring the role of attention in access to consciousness, 10/01/25, IN PROGRESS 

Gennadiy wrote:
At any given point in time, a vast amount of information enters our sensory system, but only some of it is further processed and even less is subjectively perceived. Attention is one of the major phenomena selecting information for conscious processing. Yet, the exact mechanism by which attention gates access to awareness is still debated. Here, we seek to pinpoint processes of attentional selection in the context of the attentional manipulation conducted in Cogitate's Experiment 2. We will use established markers of attention (e.g., P1, N1, N2pc) in order to test the stage at which attention has contributed to visibility in the video game. An additional goal of this experiment is to detect electrophysiological markers of subjective visibility and test their generalizability to unprobed trials using decoding. This will allow us to further explore differences between seen and unseen unprobed trials during later time windows, that are confounded by the probe in probed trials.
Entry  Fri Jun 14 09:18:00 2024, rony, Adventure Time: A novel paradigm for awareness manipulation, 10/31/24, IDEA 
Entry  Fri Jun 14 07:40:36 2024, Alex Lepauvre, Variational RSA applied to iEEG data, 08/31/24, IDEA 
This project aims at applying variational RSA to iEEG data. This method is a Bayesian implementation of representation similarity analysis. Using the Bayesian framework enables formal quantification of evidences for specific predictions. This in turns enables formal comparison of theory based on the amount of evidences for each. This method will be applied to iEEG data to formally compare IIT and GNW predictions. Method: Variational RSA, developped initially for fMRI by Peter and Karl, extended to EEG/MEG/iEEG for COGITATE, not published yet
Entry  Fri Jun 14 07:38:35 2024, Alex Lepauvre, A standardized procedure to test experimental setup, 08/30/24, IN REVIEW 
Required data: No data from the Cogitate project will be used. High-level summary of project: In the era of the widely accepted replication crisis, an aspect of the standard research pipeline has been systematically overlooked: the experimental setup. This crucial part of research project can malfunction in a variety of ways. Yet so far, no thorough investigation has been pursued to assess the impact of the most common malfuctions on the obtained results. More importantly, no clear testing framework exists to this day to control for experimental setup malfunction. In this project, we ambition to investigate the impact of the most common malfunctions by simulating them on published data sets to be found. Rich of our experience in testing experimental paradigms in many sites in the Cogitate project, we will develop a testing framework aimed at controlling the well functioning of experimental setup by testing only the critical part to ensure efficient, easy to implement and consistent control.
Entry  Thu Jun 13 20:02:54 2024, Tanya Brown, Testing 123, 12/31/24, IDEA 

This is just a test. :)

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