Preregistration and data availability
The full study protocol is available in the preregistration on the OSF webpage (https://osf.io/92tbg/), including: (a) an exhaustive description of the experimental design, (b) the theories’ predictions and agreed upon interpretations of the results, (c) iEEG, MEG, and fMRI data acquisition details; (d) preprocessing pipelines; and (e) data analysis procedures. All data and code will be shared upon publication. Below, the main methods are concisely summarized.
Ethics Statement
The experiment was approved by the institutional ethics committees of each of the data-collecting labs (see supplementary for details). All volunteers and patients provided oral and written informed consent before participating in the study. All study procedures were carried out in accordance with the Declaration of Helsinki. Epilepsy patients were also informed that clinical care was not affected by participation in the study.
Participants
Healthy volunteers and patients with pharmaco-resistant focal epilepsy participated in this study. The datasets reported here consist of: (1) Behaviour, eye tracking and invasive electroencephalogram (iEEG) data collected at the Comprehensive Epilepsy Center at New York University (NYU) Langone Health, Brigham and Women’s Hospital, Boston Children’s Hospital (Harvard), and University of Wisconsin School of Medicine and Public Health (WU). (2) Behaviour, eye tracking, magnetoencephalographic (MEG) data collected at the Centre for Human Brain Health (CHBH) of the University of Birmingham (UB), and at the Center for MRI Research of Peking University (PKU). (3) Behaviour, eye tracking and functional magnetic resonance (fMRI) data collected at Yale Magnetic Resonance Research Center (MRRC) and at the Donders Centre for Cognitive Neuroimaging (DCCN), of Radboud University Nijmegen. For both the MEG and fMRI datasets, a 1/3 of the data that passed quality tests (henceforth, Optimization dataset; see preregistration for details about quality test criteria) were used to optimize the analysis methods, which were subsequently added to the preregistration as an additional amendment. These preregistered analyses were then run on the remaining 2/3 of the data (henceforth, Replication dataset) and constitute the data reported in the main study. For comparison, results from the optimization phase are reported in the supplementary material. This procedure was not used for the iEEG data due to the serendipitous nature of the recording and electrode placement, the rarity of this type of data and the increased difficulty of data collection due to the COVID-19 pandemic.
For the iEEG arm of the project, a total of 34 patients were recruited. Two patients were excluded due to incomplete data. Demographic, medical and neuropsychological scores for each patient, when available, are reported in Supplementary Table 25. Three iEEG patients whose behavior fell slightly short of the predefined behavioral criteria (i.e. hits < 70%, FA > 30%) were nonetheless included given the difficulty to obtain additional iEEG data. A total of 97 healthy subjects were included in the MEG sample (mean age 22.79 ± 3.59 years, 54 females, all right-handed), 32 of those datasets were included in the optimization phase (mean age 22.50 ± 3.43 years, 19 females, all right-handed), and 65 in the replication sample (mean age = 22.93 ± 3.66, 35 females, all right-handed). Five additional subjects were excluded from the MEG dataset: two due to failure to meet predefined behavioral criteria (i.e., hits < 80%, and/or FA > 20%), two due to excessive noise from sensors, and one due to incorrect sensor reconstruction. A total of 108 healthy participants were included in the fMRI sample (mean age 23.28 ± 3.46 years, 70 females, 105 right-handed), 35 of those datasets were included in the optimization sample (mean age 23.26 ± 3.64 years, 21 females, 34 right-handed), and 73 in the replication sample (mean age = 23.29 ± 3.37, 49 females, 71 right-handed). Twelve additional subjects were excluded from the fMRI dataset: eight due to motion artifacts, two due to insufficient coverage, and two due to incomplete data.
Experimental procedure
Experimental design
To test critical predictions of the theories, five experimental manipulations were included in the experimental design: (1) stimulus category (faces, objects, letters and false fonts), (2) stimulus identity (20 different exemplars per stimulus category), (3) stimulus orientation (front, left and right view), (4) stimulus duration (0.5 s, 1.0 s, 1.5 s), and (5) task relevance (relevant targets, relevant non-targets, irrelevant).
Stimulus category, stimulus identity and stimulus orientation served to test predictions about the representation of the content of consciousness in different brain areas by the theories. In addition, stimulus duration served to test predictions about the temporal dynamics of sustained conscious percepts and interareal synchronization between areas. Task relevance served to rule out the effect of task demands, as opposed to conscious perception per se, on the observed effects 1.
Stimuli
Four stimulus categories were used: faces, objects, letters and false fonts. These stimuli naturally fell into two clearly distinct groups: pictures (faces and objects) and symbols (letters and false fonts). These natural couplings were aimed at creating a clear difference between task relevant and task irrelevant stimuli in each trial block (see Procedure). All stimuli covered a squared aperture at an average visual angle of 6˚ by 6˚. Face stimuli were created with FaceGen Modeler 3.1; letter and false fonts stimuli were generated with MAXON CINEMA 4D Studio (RC - R20) 20.059; object stimuli were taken from the Object Databank2. Stimuli were gray-scaled and equated for luminance and size. To facilitate face individuation, faces had different hairstyles and belonged to different ethnicities and genders. The orientation of the stimuli was manipulated, such that half of the stimuli from each category had a side view (30° and -30° horizontal viewing angle, left and right orientation) and the other half had a front view (0°).
Procedure
Subjects performed a non-speeded target detection task (see supplementary video). The experiment was divided into runs, with four blocks in each run (see Trial counts below). On a given block, subjects viewed a sequence of single, supra-threshold, foveally presented stimuli belonging to four stimulus categories and presented for three stimulus durations. Within each block, half of the stimuli were task relevant and half task irrelevant. To manipulate task relevance, at the beginning of each block subjects were instructed to detect the rare occurrences of two target stimulus identities, one from each relevant category (pictures: face/object or symbols: letter/false-font), irrespective of their orientation. This was specified by presenting the instruction “detect face A and object B” or “detect letter C and false-font D”, accompanied by images for each target (See Figure 1e). Targets did not repeat across blocks. Each run contained two blocks of the Face/Object task and two blocks of the Letter/False-font task, with block order counterbalanced across runs.
Accordingly, each block contained three different trial types: i) Targets: the two stimuli being detected (e.g., the specific face and object identities); ii) Task Relevant Stimuli: all other stimuli from the task relevant categories (e.g., the non-target faces/objects); and iii) Task Irrelevant Stimuli: all stimuli from the two other categories (e.g., letters/false fonts). An advantage of this design is that the three trial types enabled a differentiation of neural responses related to task goal, task relevance, and simply consciously seeing a stimulus.
Stimuli were presented for one of three durations (0.5 s, 1.0 s or 1.5 s), followed by a blank period of a variable duration to complete an overall trial length fixed at 2.0 s. For the MEG and iEEG version, random jitter was added at the end of each trial (mean inter-trial interval of 0.4 s jittered 0.2-2.0 s, truncated exponential distribution) to avoid periodic presentation of the stimuli. The mean trial length was 2.4 s. For the fMRI protocol, timing was adjusted as follows: the random jitter between trials was increased (mean inter-trial interval of 3 s, jittered 2.5-10 s, with truncated exponential distribution), with each trial lasting approximately 5.5 s. This modification helped avoid non-linearities in BOLD signal which may impact fMRI decoding3. Second, to increase detection efficacy for amplitude-based analyses, three additional baseline periods (blank screen) of 12 s each were included per run (total = 24). The identity of the stimuli was randomized with the constraint that they appeared equally across durations and tasks conditions.
Subjects were further instructed to maintain central fixation on a black circle with a white cross and another black circle in the middle throughout each trial (see Figure 1e).
Trial counts
The MEG study consisted of 10 runs containing 4 blocks each with 34-38 trials per block, 32 non-targets (8 per category) and 2-6 targets, for a total of 1,440 trials. The same design was used for iEEG, but with half the runs (5 runs total), resulting in a total of 720 trials. For fMRI, there were 8 runs containing 4 blocks each with 17-19 trials per block, 16 non-targets (4 per category) and 1-3 targets, for a total of 576 trials. Rest breaks between runs and blocks were included.
Data Acquisition
Behavioral data acquisition
The task was run on Matlab (PKU: R2018b; DCCN, UB and Yale: R2019b; Harvard: R2020b; NYU: R2020a, WU: 2021a) using Psychtoolbox v.3 4. The iEEG version of the task was run on a Dell Precision 5540 laptop, with a 15.6" Ultrasharp screen at NYU and Harvard and on a Dell D29M PC with an Acer 19.1" screen in WU. Participants responded using an 8-button response box (Millikey LH-8; response hand(s) varied based on the setting in the patient’s room). The MEG version was run on a custom PC at UB and a Dell XPS desktop PC on PKU. Stimuli were displayed on a screen placed in front of the subjects with a PROPixx DLP LED projector (VPixx Technologies Inc.). Subjects responded with both hands using two 5-button response boxes (NAtA or SINORAD). The fMRI version was run on an MSI laptop at Yale and a Dell Desktop PC at DCCN. In DCCN, stimuli were presented on an MRI compatible Cambridge Research Systems BOLD screen 32” IPS LCD monitor, and in Yale they were presented on a Psychology Software Tools Hyperion projection system to project stimuli on the mirror fixed to the head coil. Subjects responded with their right hand using a 2x2 Current Designs response box at Yale and a 1x4 Current Designs response box at DCCN.
Eye tracking data acquisition
For the iEEG setup, eye tracking and pupillometry data were collected using a EyeLink 1000 Plus on a remote mode, sampled monocularly at 500 Hz (from the left eye at WU, and depending on the setup at Harvard), or on a Tobii-4C eye-tracker, sampled binocularly at 90 Hz (NYU). The MEG and fMRI labs used the MEG and fMRI compatible EyeLink 1000 Plus Eye-tracker system (SR Research Ltd., Ottawa, Canada) to collect data at 1000 Hz. For MEG, eye tracking data were acquired binocularly. For fMRI, data were acquired monocularly from either the left or the right eye, in DCCN and Yale, respectively. For all recordings, a nine-point calibration was performed (besides Harvard, where thirteen-point calibration was used) at the beginning of the experiment, and recalibrated as needed at the beginning of each block/run.
iEEG data acquisition
Brain activity was recorded with a combination of intracranially subdural platinum-iridium electrodes embedded in SILASTIC sheets (2.3 mm diameter contacts, Ad-Tech Medical Instrument and PMT Corporation) and/or depth stereo-electroencephalographic platinum-iridium electrodes (PMT Corporation; 0.8-mm diameter, 2.0-mm length cylinders; separated from adjacent contacts by 1.5 to 2.43 mm), or Behnke-Fried depth stereo-electroencephalographic platinum-iridium electrodes (Ad-Tech Medical, BF08R-SP21X-0C2, 1.28 mm in diameter, 1.57 mm in length, 3 to 5.5 mm spacing). Electrodes were arranged as grid arrays (either 8 × 8 with 10 mm center-to-center spacing, 8 x 16 contacts with 3 mm spacing, or hybrid macro/micro 8 x 8 contacts with 10 mm spacing and 64 integrated microcontacts with 5 mm spacing), linear strips (1 × 8/12 contacts), depth electrodes (1 × 8/12 contacts), or a combination thereof. Recordings from grid, strip and depth electrode arrays were done using a Natus Quantum amplifier (Pleasonton, CA) or a Neuralynx Atlas amplifier (Bozeman, MT). A total of 4057 electrodes (892 grids, 346 strips, 2819 depths) were implanted across 32 patients with drug-resistant focal epilepsy undergoing clinically motivated invasive monitoring. 3512 electrodes (780 grids, 307 strips, 2425 depths) that were unaffected by epileptic activity, artifacts, or electrical noise were used in subsequent analyses. To determine the electrode localization for each patient, a post-operative computed tomography scan and a pre-operative T1 MRI were acquired and co-registered.
MEG data acquisition
MEG was acquired using a 306-sensor TRIUX MEGIN system, comprising 204 planar gradiometers and 102 magnetometers in a helmet-shaped array. The MEG gantry was positioned at 68 degrees for optimal coverage of frontal and posterior brain areas. Simultaneous EEG was recorded using an integrated EEG system and a 64-channel electrode cap (EEG data is not reported here, but is included in the shared dataset). During acquisition, MEG and EEG data were bandpass filtered (0.01 and 330 Hz) and sampled at 1000 Hz. The location of the head fiducials, the shape of the head, the positions of the 64 EEG electrodes and the head position indicator (HPI) coil locations relative to anatomical landmarks were collected with a 3-D digitizer system (Polhemus Isotrack). ECG was recorded with a set of bipolar electrodes placed on the subject’s chest. Two sets of bipolar electrodes were placed around the eyes (two at the outer canthi of the right/left eyes and two above/below the center of the right eye) to record eye movements and blinks (EOG). Ground and reference electrodes were placed on the back of the neck and on the right cheek, respectively. Subjects’ head position on the MEG system was measured at the beginning and end of each run, and also before and after each resting period, using four HPI coils placed on the EEG cap, next to the left and right mastoids and over left and right frontal areas.
Anatomical MRI data acquisition
For source localization of the MEG data with individual realistic head modeling, a high resolution T1-weighted (T1w) MRI volume (3T Siemens MRI Prisma scanner) was acquired per subject. Anatomical scans were acquired either with a 32-channel coil (TR/TE = 2000/2.03ms; TI = 880 ms; 8° flip angle; FOV = 256×256×208 mm; 208 slices; 1 mm isotropic voxels, UB) or a 64-channel coil (TR/TE = 2530/2.98ms; TI = 1100 ms; 7° flip angle; FOV = 256×256×208 mm; 198 slices;1 mm isotropic voxels, PKU). The FreeSurfer standard template was used (fsaverage) for participants lacking an anatomical scan (N=5).
fMRI data acquisition
MRI data were acquired using a 32-channel head coil on a 3T Prisma scanner. A session included high-resolution anatomical T1w MPRAGE images (GRAPPA acceleration factor = 2, TR/TE = 2300/3.03 ms, 8° flip angle, 192 slices, 1 mm isotropic voxels), and a whole-brain T2*-weighted multiband-4 sequence (TR/TE = 1500/39.6 ms, 75° flip angle, 68 slices, voxel size 2 mm isotropic, A/P phase encoding direction, FOV = 210 mm, BW = 2090 Hz/Px). A single band reference image was acquired before each run. To correct for susceptibility distortions, additional scans using the same T2*-weighted sequence, but with inverted phase encoding direction (inverted RO/PE polarity) were collected while the subject was resting at multiple points throughout the experiment.
Preprocessing and analysis details
For readability, we first detail the preprocessing protocols for each of the modalities (iEEG, MEG, and fMRI) separately. Then, we describe the different analyses, combining information across the modalities, while noting any differences between them.
iEEG preprocessing
Data were converted to BIDS5 and preprocessed using MNE-Python version 0.246, and custom-written functions in Python and Matlab. Preprocessing steps included downsampling to 512 Hz, detrending, bad channel rejection, line noise and harmonic removal, and re-referencing. Electrodes were re-referenced to a Laplacian scheme7 while bipolar referencing was used for electrodes at the edge of a strip, grid or sEEG and the signal was localized at the midpoint (Euclidean distance) between the two electrodes. Electrodes with no direct neighbors were discarded. Seizure onset zone electrodes, those localized outside the brain, and/or containing no signal or high amplitude noise level were discarded. Line noise and harmonics were removed using a one pass, zero-phase non-causal band-stop FIR filter.
The high gamma power (HG, 70-150 Hz) was obtained by bandpass filtering the raw signal in 8 successive 10 Hz wide frequency bands, computing the envelope using a standard Hilbert transform, and normalizing it (dividing) by the mean power per frequency band across the entire recording. To produce a single HG envelope time-series, all frequency bands were averaged together8. Most analyses focused on the HG power as it closely correlated with neural spiking activity9 and with the BOLD signal 10. To obtain the Event Related Potentials (ERPs), the raw signal was low pass filtered at 30 Hz with a one pass, zero-phase non causal low pass FIR filter. Epochs were segmented between 1 s pre-stimulus until 2.5 s post-stimulus of interest.
Surface reconstruction and electrode localization
Electrode positions were determined based on a computed tomography scan coregistered with a pre-implant T1 weighted MRI. A three-dimensional reconstruction of each patient’s brain was computed using FreeSurfer (http://surfer.nmr.mgh.harvard.edu). For visualization, the individual subject’s electrode positions were converted to Montreal Neurological Institute (MNI)152 space. As each theory specified a set of anatomical regions of interest (ROIs), after electrode localization, electrodes were labeled according to the Freesurfer based Destrieux atlas segmentation11,12 and/or Wang atlas segmentation13.
Identification of task responsive channels
To identify task responsive electrodes, we computed the Area Under the Curve (AUC) for the baseline (-0.3-0 s) and the stimulus-evoked period (0.05-0.35s) separately for the task relevant and irrelevant conditions, and compared them per electrode using a Wilcoxon sign-rank test, corrected for False Discovery Rate (FDR14). A Bayesian t-test15 was used to quantify evidence for non-responsiveness.
Identification of category selective channels
To determine category selectivity for faces, objects, letters and false fonts on the HG, we followed the method of Kadipasaoglu and colleagues16. Per category, we computer a d’ (AUC, 0.05 -0.4 s) comparing the activation between the category-of-interest (uj) and each of the other categories (ui), normalized by the standard deviation of each category:
A permutation test (10,000 permutations) was used to evaluate significance. d’ was computed for the task relevant and irrelevant conditions, separately. An electrode was considered selective if it showed selectivity on both tasks.
Multivariate analysis electrodes combination
Due to the sparse and highly variable coverage of iEEG data, all collected electrodes were combined into a "super subject" multivariate analyses (RSA and decoding). To create a single trial matrix for the super subject, we equated the trial matrices of all our subjects by subsampling to the lowest number of trials in the relevant conditions. Subjects that did not complete the full experiment were discarded (N=3), resulting in a total of 29 subjects with 583 electrodes in posterior and 576 electrodes in prefrontal ROIs, respectively. In the case of analyses on stimuli identities, stimuli that were presented less than three times to any of the participants across intermediate and long trials in the task relevant and irrelevant trials were discarded. We then subsampled the trials for each identity to three trials per participant. The subsampling procedure was repeated 100 times to avoid random fluctuation induced by the subsampling. The analysis was computed for each repetition and average across repetitions.
MEG preprocessing
The MEG data were converted to BIDS17 using MNE-BIDS18, and preprocessed following the FLUX Pipeline19 in MNE-Python v0.24.06. Preprocessing steps included MEG sensor reconstruction using a semi-automatic detection algorithm and Signal-Space Separation (SSS)20 to reduce environmental artifacts. FastICA21 was used to detect and remove cardiac and ocular components from the data for each subject (M=2.90 components, SD=0.92). Prior to ICA, data were segmented, and segments containing muscle artifacts were removed. After preprocessing, data were epoched into a 3.5 s segment (1 s pre-stimulus to 2.5 s post-stimulus onset). Trials where gradiometers values exceeded 5000 fT/cm, magnetometers exceeded 5000 fT, and/or contained muscle artifacts were rejected from the MEG dataset.
Source modeling
MEG source modeling was performed using the dynamic statistical parametric mapping (dSPM) method22, based on depth-weighted minimum-norm estimates (MNE23,24), on epoched and baseline (-0.5 s to 0 s prior to stimulus onset) corrected data. To build a forward model, the MRI images were manually aligned to the digitized head shape. A single shell Boundary Elements Model (BEM) was constructed in MNE-Python based on the inner skull surface derived from FreeSurfer 11,12, to create a volumetric forward model (5 mm grid) covering the full brain volume. The lead field matrix was then calculated according to the head-position with respect to the MEG sensor array. A noise covariance matrix for the baseline and a covariance matrix for the active time window were calculated and the combined (i.e., sum) covariance matrix was used with the forward model to create a common spatial filter. Data were spatially pre-whitened using the covariance matrix from the baseline interval to combine gradiometer and magnetometer data 25.
fMRI Preprocessing
Source DICOM data were converted to BIDS using BIDScoin v3.6.326. This includes converting DICOM data to NIfTI using dcm2niix 27 and creating event files using custom Python codes. BIDS compliance of the resulting dataset was controlled using BIDS-Validator. Subsequently, MRI data quality control was performed using MRIQC 28 and custom scripts for data rejection. All (f)MRI data were preprocessed using fMRIPrep 20.2.329, based on Nipype 1.6.130. For further details on the fMRIprep pipeline, see preregistration.
Analysis-specific functional preprocessing
Additional, analysis-specific, fMRI data preprocessing was performed using FSL 6.0.2 (FMRIB Software Library; Oxford, UK31), Statistical Parametric Mapping (SPM 12) software32, and custom Python scripts after the above outlined general preprocessing. Functional data for univariate data analyses were spatially smoothed (Gaussian kernel with full-width at half-maximum of 5 mm), grand mean scaled, and temporal high-pass filtered (128 s). No spatial smoothing was applied for multivariate analyses.
Contrast of parameter estimates
We modeled BOLD signal responses to the experimental variables by fitting voxel-wise General Linear Model (GLM) to the data of each run using FSL FEAT. The following regressors were modeled in an event-related approach, with event duration corresponding to the stimulus duration (i.e., 0.5, 1.0, 1.5 s), and convolved with a double gamma hemodynamic response function: 12 regressors of interest (Targets, task relevant and task irrelevant stimuli per stimulus category i.e., faces, objects, letters, false fonts; and a regressors of no interest i.e., target screen display). We included the first-order temporal derivatives of the regressors of interest, and a set of nuisance regressors: 24 motion regressors (FSL’s standard + extended set of motion parameters) plus a CSF and a WM tissue regressor.
Each of the 12 regressors of interest was contrasted against an implicit baseline (used in the putative NCC analysis). Additionally, we obtained contrast of parameter estimates for ‘relevant faces vs. relevant objects’, ‘relevant letters vs. relevant false fonts’, ‘irrelevant faces vs. irrelevant objects’, ‘irrelevant letters vs. irrelevant false fonts’ (used for the definition of decoding ROIs), ‘relevant and irrelevant faces vs. relevant and irrelevant objects’ and ‘all stimuli vs. baseline’ (used for the definition of seeds for the generalized psychophysiological interaction analysis).
Data were averaged across runs per subject using FSL’s fixed effects analysis and subsequently averaged across participants using FSL’s FLAME1 mixed effect analysis. Gaussian random-field cluster thresholding was used to correct for multiple comparisons, using the default settings of FSL, with a cluster formation threshold of one sided p < 0.001 (z ≥ 3.1,) and a cluster significance threshold of p < 0.05.
Anatomical Regions-of-interest (ROIs)
ROIs were defined a priori in consultation with the adversaries. They were determined per subject based on the Destrieux atlas12 including both hemispheres, and then resampled to standard MNI space (see Extended Data Table 2). For the connectivity analysis, areas V1/V2 (combining dorsal and ventral) were defined based on the Wang cortical parcellation13.
Behavioral analyses
Log-linear corrected d’prime33, false alarms (FA) and reaction times (RT) were computed per category and stimulus duration, separately (FAs were also calculated per task relevance, without duration), and per modality (iEEG, MEG, fMRI). These measures were compared with Linear/Logistic mixed models, where appropriate. For the former, we report ANOVA omnibus F tests, and for the latter, omnibus χ² test from an analysis of deviance. We approximated degrees of freedom using the Satterthwaite method34. Pairwise t-tests following significant interactions were Bonferroni corrected. To estimate Bayesian Information Criterion (BIC) differences between the original and null logistic models, we used the p-values and sample size (35; p_to_bf package in R).
Eye-tracking analyses
For Eyelink, gaze and pupil data were segmented, and missing data were excluded. Blinks were detected using the Hershman algorithm36, and removed with 200 ms padding37. The Eyelink standard parser algorithm was used for saccade and fixation detection. Saccades were further corroborated using the Engbert & Kliegl38 algorithm. Fixations were baseline corrected (-0.25 s to 0 s). Mean fixation distance, mean blink rate, mean saccade amplitude and mean pupil size were compared in a Linear Mixed Model (LMM) with category and task relevance as fixed effects and subject and item as random effects. Separate analyses were carried out on the first 0.5 s after stimulus onset including all trials; and on the 1.5 s trials including time window (0-0.5 s, 0.5-1.0 s, 1.0-1.5 s) as fixed effects. BIC was used to test the models against the null hypothesis models. For Tobii, gaze coordinate data was segmented, missing data were excluded, and coordinates were baseline corrected to depict heatmaps of patients’ gaze. Notably, the coordinate data was not added to the LMMs due to its poorer quality with respect to the EyeLink data.
Decoding analysis
All decoding analyses were performed using a linear Support Vector Machine (SVM, scikit learn, https://scikit-learn.org/) classifier. Below we explain how this was done for each one of the predictions.
iEEG Decoding was done on the HG response, averaged over non-overlapping windows of 0.02 s separately for electrodes located in the GNWT and IIT ROIs. The top 200 electrodes (selectKbest39), as determined by F-test within a given set of electrodes from the theory ROIs, were used as features for the classifier. 200 features were selected to provide a balance between model optimization (e.g., feature selection) and subject representation (e.g., electrodes/features coming from multiple subjects). Statistical significance of decoding performance was assessed via permutation test, randomly permuting the sample labels and repeating the decoding analysis 1000 times, corrected for multiple comparisons using a cluster-based correction (cluster mass inference with cluster forming threshold at p < 0.0540,41). Also, to assess the decoding accuracy within unique ROIs (e.g., S_temporal_sup of the Destrieux atlas), separate classifiers were trained using all electrodes in a given parcel. Each classifier was fitted using all electrodes in a parcel and time window (GNWT: 0.3-0.5 s, IIT: 0.3-1.5 s) as features, resulting in a single accuracy value per parcel. SelectKbest (200 features iEEG) feature selection and 5-fold cross-validation with 3 repetitions was used. To assess the statistical significance of the decoding accuracy within unique ROIs (so only one accuracy score is obtained per ROI), p-values obtained via permutation tests were corrected for multiple comparisons across all ROIs using FDR correction (q ≤ 0.0514).
MEG Decoding was done on bandpass filtered (1-40 Hz) and downsampled (100 Hz) data. The reconstructed source-level MEG data within a subset of the predefined anatomical ROIs (GNWT: 'G_and_S_cingul-Ant','G_and_S_cingul-Mid-Ant', 'G_and_S_cingul-Mid-Post', 'G_front_middle','S_front_inf', 'S_front_sup' , IIT: 'G_cuneus', 'G_oc-temp_lat-fusifor', 'G_oc-temp_med-Lingual','Pole_occipital', 'S_calcarine','S_oc_sup_and_transversal', as they show high response to the stimulus on the optimization dataset) were extracted for further analysis (500 vertices and 800 vertices per hemisphere for each of the anatomical ROI defined by the theories). We applied temporal smoothing (0.05 s window, 0.01 sliding window), computed pseudotrials42, normalized the data, and selected the top 30 features within a given ROI as features for the different classifiers. A group-level one-sample t-test per time point was performed on the decoding accuracy results, corrected for multiple comparisons using a cluster-based correction41.
The overall decoding strategy for fMRI was similar to that used on the iEEG and MEG data, yet with some differences. A Multi-Variate Pattern Analysis (MVPA) approach was used on the pattern of BOLD activity over voxels. A non-spatially-smoothed parameter estimate map was obtained by fitting a GLM per event with that event as the regressor of interest and all the other remaining events as one regressor of no interest43 as implemented in NiBetaSeries 0.6.0 package. The model also included the 24 nuisance regressors described in the fMRI preprocessing section.
Decoding was performed using a whole-brain approach and an ROI-based approach. The whole-brain analysis was performed using a searchlight approach with 4 mm radius. For ROI-based decoding, decoding ROIs were defined based on functional fMRI contrasts (see fMRI preprocessing section) and constrained with pre-defined anatomical ROIs (see Extended Data Table 2: Anatomical Regions-of-interest (ROIs)). One-sample permutation test was used to determine if decoding significantly exceeds chance level within each ROI. FDR was used to correct for multiple comparisons across ROIs. For whole-brain decoding, a cluster-based permutation test was used to evaluate the decoding statistical significance across subjects (p < 0.05). Additionally, stimulus vs. baseline searchlight decoding was performed using leave-one-run out cross validation and the resultant decoding accuracy maps were used as input for the multivariate putative NCC analysis (see below). To perform stimulus vs. baseline decoding, we subsampled the stimuli trials to a 2:1 ratio with respect to baseline. The SVM cost function was weighted by the number of trials from each class.
Decoding schemes for the different predictions
To test GNWT and IIT decoding predictions, stimulus category (faces vs. objects and letters vs. false fonts) was decoded separately for the task relevant and task irrelevant conditions (within-task category decoding) while orientation (front view vs. left view vs. right view) was decoded on the combined data from the two task conditions. In addition, cross-task category decoding from task relevant to task irrelevant condition and vice versa was performed to test generalization by training classifiers on one condition and testing on the other condition. Both within-task category and orientation decoding were performed in a leave-one-run-out cross validation scheme for fMRI and in an k-fold cross validation scheme for MEG and iEEG.
For category decoding, trials from each task condition (i.e., task relevant, irrelevant) were extracted for each category comparison of interest: 160 face/160 objects classification, 160 letters/160 false fonts classification within each task relevance condition for MEG, and half the trials for iEEG. For fMRI, there were 64 trials for each category in each task relevance condition. For orientation decoding, task relevant and task irrelevant trials were collapsed within category to increase Signal-to-Noise Ratio (SNR), resulting in 160 Front, 80 Left, and 80 Right trials per category for MEG, and half these numbers for iEEG. For fMRI, there were 64 Front, and 32 Left and Right trials per category. Decoding was evaluated using accuracy measures, tested against 50% chance level for category decoding (binary classification) and against 33% chance level for orientation decoding (3-class classification). For orientation decoding, balanced accuracy was used due to the unbalanced number of trials for the different orientations. The SVM cost function was weighted by the number of trials per class to reduce bias to the class with the highest number.
For within-task decoding (e.g., classification of categories across time), a classifier at each time-point was trained and tested separately using a 5-fold cross-validation (with 3 separate repeats of cross-validation). For cross-task decoding (task relevant -> irrelevant & task irrelevant -> relevant), each SVM model was trained on one task (e.g., faces/objects in the task relevant condition) and tested on the second task (e.g., faces/objects in the task irrelevant one). As cross-decoding in iEEG data is performed across all pooled electrodes, an additional cross-validation step was performed on this modality data to provide a confidence metric (e.g., confidence intervals) using a 5-fold cross-validation with 3 repetitions (e.g. train on 80% of task 1, and test on held-out 20% of task 2).
Within-task temporal generalization was performed by training a classifier at each time-point (using selectKbest feature selection) and testing its performance across all time-points using the same set of selected features and 3 repetitions of 5-fold cross-validation. To generalize from one task to another across all time-points, cross-temporal generalization was used: a classifier was trained at each time-point in task 1 (e.g., task relevant) using selectKbest feature selection, and tested across all time-points in task 2 (e.g., task irrelevant) using the same set of selected features. Cross-validation was performed in the same fashion as in cross-decoding.
Additional decoding analyses were performed on all trials aligned to the stimulus onset (e.g. -0.2-2 s relative to stimulus onset), and stimulus offset (-0.5-0.5 s around stimulus offset). For the latter analysis, all trials from different durations were aligned to the stimulus offset.
To assess the specific IIT prediction that including prefrontal regions along with posterior regions to the decoding of categories will not significantly affect decoding accuracy, we performed two additional decoding analyses in which the decoding performance of electrodes from the IIT region were compared with the decoding performance when electrodes from both the posterior + PFC ROIs are included. The PFC ROI included all PFC ROIs, except for inferior frontal sulcus, as it belongs to the IIT extended ROIs. Posterior ROI included all IIT ROIs shown in Extended Data Table 2. The first analysis compared the decoding accuracy for a model including all electrodes from posterior regions to a separate model in which electrodes (features) from posterior & PFC regions were combined (e.g., feature combination). In the second analysis, the decoding accuracy of the model including all electrodes from posterior regions was compared to a combined posterior + PFC model, in which two separate classifiers were trained and calibrated on posterior & PFC regions separately using isotonic calibration44, and posterior probabilities from each classifier were combined using a softmax normalization45. Training and testing of the individual models followed all previously described cross-validation procedures and model comparison was performed using a variance-corrected paired t-test46 and complemented with Bayesian analysis. Following Benavoli and colleagues47, the prior distribution of the mean difference in decoding scores between two classifier models was modeled as a Normal-gamma distribution conjugate to a normal likelihood, and the posterior distribution was obtained as a normal distribution. This posterior distribution was utilized to calculate the probability of one classification model being better than, worse than, or equivalent to the other model. As this estimation approach is applied using resampled datasets (e.g., using 5-fold cross-validation), the performance of the model becomes dependent on the folds, and thus a variance corrected t-distribution was used46.
We also tested this prediction on the fMRI data. To select features to be used for both analyses, the face vs. object contrast for each subject was masked by a predefined anatomical posterior ROIs as well as a PFC anatomical ROIs, defined the same way as described above. Within each of the two ROIs, the 150 voxels that are most selective to each of the to-be-decoded stimuli were defined as the decoding ROIs (300 voxels total) for each subject. The first analysis compared the decoding accuracies for a model that included 300 voxels from the posterior ROIs as features to another model that included 600 voxels (300 features from each ROI). In the second analysis, two separate models were constructed, calibrated, and combined as described above. For the two analyses, model comparison was performed using a group-level one-sample permutation test to determine if accuracies obtained by combining posterior and PFC ROIs are significantly higher than the accuracies obtained based on posterior ROIs only. FDR was used to correct for multiple comparisons.
Duration analysis
Neural responses were extracted from three windows of interest (WoI) (0.8-1.0 s, 1.3-1.5 s, 1.8 -2.0 s) and compared using LMM. Four theory agnostic models were fitted: a null model, a duration model (3 durations), a WoI model, and a duration and WoI model. Two theory model were fitted: the GNWT model predicts activation (ignition) following stimulus offset (0.3-0.5 s) independent of duration, with virtually no response in between. The IIT model predicts sustained activation for the duration of the stimulus returning to baseline after stimulus offset. Both theoretical models were complemented with an interaction term between category (faces, objects, letters and false fonts) and the theories’ predictors, to account for regions showing selective responses to categories. Bayesian Integration Criterion (BIC) was used to define the winning model.
Models for iEEG were fitted per electrode on the predefined ROIs, using the HG (AUC), alpha (8-13 Hz, obtained through Morlet wavelets, f=8-13 Hz, in 1 Hz steps; f/2 cycles, AUC), and ERPs (peak to peak) as signal, separately for task relevant and irrelevant condition.
MEG models were fitted to source data on the predefined ROIs, using the gamma (60-90 Hz) and alpha band (8-13 Hz) as signal, separately for task relevant and irrelevant conditions. Time-frequency analyses were performed on source-data using Morlet wavelets (f=8-13 Hz, in 1 Hz steps; f/2 cycles; f=60-90 Hz, in 2 Hz steps, f/4 cycles), and were baseline corrected. Spectral activity was computed for each vertex, baseline corrected and then averaged across trials within each parcel included in the ROIs, yielding a unique time-course per ROI parcel. In addition, a single source time-course capturing the entire prefrontal ROI and the posterior ROI was computed by averaging the spectral activity within an ROI. Models were fitted on each parcel and ROI, as defined by the theories.
Representational Similarity Analysis (RSA)
To examine how the neural representations evolved over time in response to the different stimulus properties (i.e., category, orientation and identity representation), we performed cross-temporal RSA on source level MEG data and iEEG HG power within each of the theory-defined ROIs. Specifically, at each set of data points, we computed a Representational Dissimilarity Matrix (RDM) by calculating the correlation distance (1- Pearson’s r, Fisher corrected) between all pairs of stimuli. Next, to quantify the representational space occupied by one class vs. another, we computed the average within-class distances vs. the average between-class distances. This analysis was performed in a cross-temporal manner, in which RDMs were computed between all stimuli at time point t1 and the corresponding set of stimuli at time points t1,2,…n.
Long trials (1.5 s) were used to investigate category and orientation representation. Since specific identities were repeated a limited number of times per duration, both intermediate (1.0) and long (1.5 secs) trials were combined and equated in duration by cropping the 1-1.5s time interval for long trials. This was done to allow for the analysis of at least three (3) presentations of the same identity.
To evaluate the theoretical predictions about when significant content representation should occur, we subsampled the observed cross-temporal representational matrices in four time windows (0.3-0.5, 0.8-1.0, 1.3-1.5, 1.8-2.0 s). The subsampled matrices were correlated to the model matrices predicted by GNWT and IIT (see Figure 1a, right panel) using Kendall’s Tau correlation. If the correlation was significant (see below) for at least one of the predicted matrices, we computed the difference between the transformed correlation () to each theory; and compared this difference against a random distribution to obtain a p-value. If the correlation with the theory predicted pattern in the theory ROI was significantly higher than the other model, we considered the theory prediction to be fulfilled.
To generate a null distribution of cross-temporal RSA surrogate matrices, we repeated the procedure outlined above 1024 times, randomly shuffling the labels. Next, the observed RSA matrix was z-scored using the null distribution as:
For iEEG, the HG power per electrode within the predefined anatomical ROI was averaged in 0.02s non-overlapping windows. Electrodes were used as features for the RDM. The data were vectorized across all electrodes within a ROI (e.g., samples x significant electrodes) to compute the RDMs. 576 and 583 electrodes entered this analysis for the prefrontal and posterior ROI, respectively. The resultant RDM was subjected to a principal component analysis and the first two dimensions were plotted against each other to produce a 2-dimensional projection of dissimilarity scores across all pairs for each of the 100 subsampling repetitions. The PCA components were aligned across repetitions using Procrustes alignment and averaged together for visualization purposes49,50.
For MEG, the same analysis was run on the source reconstructed data within the predefined anatomical ROIs used for the Decoding analysis, bandpass filtered (1-40 Hz) and downsampled (100 Hz). For the category and orientation analysis, pseudo-trials and temporal moving-average methods were used to optimize the RSA analysis and improve the SNR. For identity, single trials were used. Vertices within the ROIs were used as features. The statistical testing differed from that conducted on the iEEG data, as it was performed at the subject level. Like the iEEG analysis, we first tested if the correlation between the data and the model predicted by each theory was greater than zero using the Kendall's tau measure, and then compared between the theories using the Mann-Whitney U rank test on two independent samples.
Functional Connectivity analysis
For both iEEG and MEG, pairwise phase consistency (PPC51) was computed between each category-selective time series (face- and object-selective) and either the V1/V2 or the PFC time series.
For iEEG, the PPC analysis included electrodes in V1/V2 visual areas, in PFC ROIs (see Extended Data Table 2), and face and object selective electrodes (see Identification of task responsive channels), as long as they were “active” during the task. As both theories predict different types of activation (e.g., ignition vs. sustained activation), channels were categorized as active if they showed an increase in HG power relative to baseline (-0.5 to -0.3 s, p<0.05, signed-rank test) evaluated across all trials (task relevant + irrelevant, intermediate + long trials, combined across both categories), for the 0.3-0.5 s window (GNWT), or in all time windows 0.3-0.5 s, 0.5-0.8 s, and 1.3-1.5 s (IIT).
For MEG, the category-selective single-trial time courses used to define the ROIs for PPC analysis were extracted using the Generalized Eigenvalue Decomposition (GED) method52. Two GED spatial filters were built by contrasting either faces or objects against all other categories during the first 0.5 s after stimulus onset. Single-trial covariance matrices were computed separately for signal and reference for all vertices within the fusiform ROI identified from the FreeSurfer parcellation using the Desikan atlas 53, and the Euclidean distance between them was z-scored. Trials exceeding 3 z-scores were excluded. The reference covariance matrix was regularized to reduce overfitting and increase numerical stability. The GED was then performed on the two covariance matrices, resulting in N (= rank of the data) pairs of eigenvectors and eigenvalues. The eigenvector associated with the highest eigenvalue was selected as a GED spatial filter, which in turn was applied to the data to compute the single-trial GED component time series. A GED spatial filter was extracted also for the PFC ROI, on parcels from the Destrieux atlas12, to identify the distributed pattern of sources that are responsive to visually-presented stimuli. Specifically, a spatial filter was built by contrasting source-level frontal slow-frequency activity (30-Hz low-pass filter) after stimulus onset (0 to 0.5 s) against baseline (-0.5 to 0 s). V1/V2 areas were identified using the Wang Atlas13 and a singular values-decomposition approach. For the GED, the 1.0 and 1.5 s duration trials were used to minimize overlap with the transient evoked at stimulus onset.
PPC was computed for each MEG time series/iEEG electrode pairing, for all face-trials and object-trials separately. Analyses were performed on 1.0 and 1.5 duration trials, separately on task relevant and irrelevant trials and also combined to maximize statistical power. To compute synchrony, time-frequency analysis of the broadband MEG and LFP signal was performed using Morlet wavelets (f=2-30 Hz, in 1 Hz steps; 4 cycles; f=30-180 Hz for iEEG or f=30-100 Hz for MEG, in 2 Hz steps, f/4 cycles), and PPC was then computed by taking the difference in phase angle between MEG time series/iEEG electrode at each time, t, and frequency f, for a specific trial and computing PPC across all trials in a category (e.g., faces) as:
For iEEG, PPC for each category-selective site was then averaged across all its pairings (e.g., all PFC electrodes pairings or all V1/V2 pairings within that patient). The variability in electrode coverage across patients precluded a within-subjects analysis. Therefore, to achieve sufficient statistical power, we pooled all derived PPC values from one electrode pairing (e.g., face-selective to PFC) across all patients into one ROI specific analysis. A similar approach was used on the MEG parcels.
To quantify content-specific synchrony enhancement, the difference in PPC was computed between within-category and across-category trials (e.g., for face-selective sites, the change in PPC was computed between faces vs. objects trials) using a cluster-based permutation test41. This was done for both modalities.
As an exploratory analysis, we also investigated dynamic functional connectivity using the Gaussian-Copula Mutual Information (GCMI54) approach to evaluate the dependencies between time series. This power-based measure of connectivity was implemented using the conn_dfc method from the Frites Python package 55. We used the same parameters as for the PPC analysis, with the following exceptions: For both MEG and iEEG, power was estimated through a multitaper-based method (using a frequency dependent dynamic sliding window: 2-30 Hz, T= 4 cycles; 30-100 Hz, T4/f using a 0.25-s sliding window. For iEEG the high frequency range was extended from 30-180 Hz, T=4/f cycles). DFC was performed per frequency band, 0.1 s sliding window, 0.02s steps.
For fMRI, connectivity was assessed through generalized Psycho-Physiological Interaction (gPPI) implemented in SPM56. The Fusiform Face Area (FFA) and Lateral occipital cortex (LOC) were defined as seed regions per subject based on an anatomically constrained functional contrast. Anatomically, FFA seeds were constrained to the “Inferior occipital gyrus (O3) and sulcus” and “Lateral occipito-temporal gyrus (fusiform gyrus, O4-T4)”. LOC seeds were constrained to the “Middle occipital gyrus (O2, lateral occipital gyrus)” and the “Middle occipital sulcus and lunatus sulcus” (Destrieux ROIs 2 and 21 for FFA and ROIs 19 and 57 for LOC, see Anatomical Regions-of-interest (ROIs)).
Candidate seed voxels within the above-mentioned anatomical ROIs were defined as those with a z value > 1 in the contrast of parameter estimates of all stimuli vs. baseline. Three subjects with less than 300 candidate seed voxels were excluded from the analysis. This was done to ensure that the seed voxels were visually driven. Next, using an unthresholded contrast of parameter estimates between ‘relevant and irrelevant faces’ and ‘relevant and irrelevant objects’, the 300 voxels most responsive to faces within the FFA anatomical ROIs were selected for the FFA seed, and the 300 voxels most responsive to objects within the LOC anatomical ROIs were selected for the LOC seed.
gPPI analysis was performed per subject and seed region separately, including an interaction term between the seed time series regressor (physiological term) and the task regressor (psychological term) at the subject-level GLM56, separately for task relevant and irrelevant conditions, and also combining across tasks to increase statistical power. For combined conditions, the model design matrix for each subject included regressors for task relevant and task irrelevant faces, objects, letters, and false fonts collapsed across conditions (four regressors) as well as a regressor for targets (irrespective of their category), yielding five regressors in total. As for separated conditions, the model design matrix included regressors for task relevant and task irrelevant faces, objects, letters, and falsefonts (eight regressors) as well as a regressor for targets (irrespective of their category), yielding nine regressors in total. For each seed, group level analysis was performed using a cluster-based permutation test to evaluate the statistical significance of face > object contrast parameter estimates across subjects (p < 0.05).
Putative NCC analyses
A series of conjunction analyses were performed on the fMRI data to identify a) areas responsive to task goal, b) areas responsive to task relevance, and c) areas putatively involved in the neural correlate of consciousness. We note that the contrasts proposed below might overestimate the neural correlates of consciousness and that the fast event-related design adopted here might be suboptimal to detect activity changes in the salience network57, i.e., potentially underestimating some regions that might be involved in conscious processing. We therefore have adopted a conservative approach that distinguishes between areas that might participate in consciousness vs. those that definitely do not.
The conjunction defining areas responsive to task goals was defined as [TaskRelTar > bsl] & [(TaskRelNonTar = bsl) & (TaskIrrel = bsl)]. This contrast captures areas that show an increase of BOLD signal for targets but not for other stimuli. The following conjunction identified areas responsive to task relevance: [(TaskRelTar > bsl) & (TaskRelNonTar ≠ bsl)] & [TaskIrrel = bsl]. This contrast identifies areas displaying differential activity for all task relevant stimuli, but are insensitive to non-task relevant ones. Finally, the following conjunction was used to identify the putative NCC areas: [(TaskRelNonTar (stim id) > bsl) & (TaskIrrel (stim id) > bsl)] OR [(TaskRelNonTar (stim id) < bsl) & (TaskIrrel (stim id) < bsl)], critically detecting areas that responsive to any stimulus category irrespective of task, with consistent activation or deactivation.
To compute conjunctions, we first ran a GLM (see above) corrected for multiple comparisons (Gaussian random-field cluster-based inference). Equivalence to baseline was established using a JZS Bayes Factor test, with a Cauchy prior (r scale value of 0.707). Evidence maps were thresholded at BF01 > 3. The thresholded z maps and the Bayesian evidence maps on the group level were used for the conjunction analysis. For conjunctions including an ‘unequal to’, a ‘logical and’ operation was used between the directional z maps, after thresholded maps were binarized. For the putative NCC contrast, conjunctions were performed separately for activations and deactivations, using a ‘logical and’ operator for the task relevant and irrelevant z maps. The resulting maps were combined using a ‘logical or’ operation to discard areas showing effects of opposite direction for task relevant and task irrelevant stimuli. This analysis was also done at the subject level, masked using the anatomical ROIs, to account for inter-subject variability. For each ROI, the proportion of subjects with voxels included in the conjunction is reported. The multivariate version of the putative NCC analysis was done using the thresholded statistical maps obtained from the whole-brain searchlight decoding based on a subject-level stimulus vs. baseline decoding accuracy maps (for details regarding the decoding approach used, see Decoding Analysis).
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