Participants. The study was approved by the Institutional Review Board at Baylor College of Medicine (IRB: H-18112), in compliance with the international standard of the Declaration of Helsinki. All participants provided written informed consent. Participants consisted of 10 patients (Nfemale=5; mean age = 41 years; Supplementary Table 1) undergoing intracranial stereo-EEG (sEEG) monitoring for medically refractory epilepsy evaluation. sEEG probes were placed based on clinical criteria.
Auditory Oddball Paradigm. Participants completed an active ‘count’ auditory oddball (AOB) task in which they mentally counted the number of ‘oddball’ tones they heard. The count was reported verbally after each experimental block. Stimuli were 250-ms long pure tones at two frequencies (1 and 2 kHz) representing the standard and oddball sounds (Fig. 1a). The assignment of tone frequency to condition (standard or oddball) was counterbalanced across blocks within each participant. Each block consisted of 160 total trials. A trial included the auditory presentation of the tone followed by inter-trial intervals (ITIs) randomly varying between 1.0 and 1.2 seconds. The first ten trials of each block were always standard stimuli. The remaining 150 trials consisted of 80–85% standard tones with 15–20% pseudo-randomly interleaved oddball tones, which resulted in approximately 128–136 standard trials and 24–32 oddball trials per test block. The pseudo-randomization for oddball stimuli was necessary to ensure that there would be enough time to allow the pupil to return to baseline before presenting another oddball trial (6.0–9.0 seconds inter-oddball interval). Each block lasted approximately 3–4 minutes and each participant completed 2–7 blocks per session. Sounds were played binaurally from speakers situated directly behind the patient at an intensity adjusted based on individual comfort (~ 68–82 dB).
Electrode localization. FSL was employed to align post-implantation CT brain scans from each patient, showing the location of the intracranial electrodes, to their pre-operative structural T1 MRI scans. We used FreeSurfer to reconstruct the brain surface from the MRI volume. BioImage Suite 35 and iELVis52 were used to obtain electrode coordinates and determine the position of the electrode with respect to anatomical landmarks. The anatomical assignment was based on the proximity to the cortical surface and labeled based on the Destrieux cortical parcellation atlas, which was then confirmed based on independent expert visual inspection. Electrodes were included if they were located within 5 mm of the grey matter boundary of the posterior Supratemporal Gyrus (pSTG). The auditory cortex was identified based on major sulci along the supratemporal gyrus (pSTG)53–55. More specifically, ROIs were within Heschl’s Gyrus bounded by the anterior temporal sulcus, through the second transverse gyrus bounded posteriorly by Heschl’s sulcus (Fig. 1b). A total of 80 electrodes were identified in the ROI. After the exclusion of electrodes contaminated by noise or artifacts, 73 electrodes remained for analyses.
Pupil Recording and Pre-Processing. Pupil diameter was recorded using an EyeLink 1000 system (SR-Research, Osgoode, ON, Canada) while participants fixated on a cross presented at the center of a display monitor (Viewsonic VP150, 1920 x 1080) positioned at a comfortable distance (22–24 in) during the AOB task. Each block of data was sampled at 1,000 Hz (n = 1, Desktop Mode) or 500 Hz (n = 9, Remote Mode) after the successful completion of a 5-point calibration, validation, and single-point drift correction paradigm.
Blinks and artifacts were isolated using the findpeaks.m 56 function in MATLAB (R2021a) and confirmed by visual inspection. Peaks were identified as maximal points in the pupil diameter Z-score time series with a minimum peak height of 10 S.D., and a minimum distance of 50 samples between peaks. Peak points were padded by 200 ms and linearly interpolated. Due to the minimum peak distance parameter, not all blinks or artifacts were detected in just one iteration of the pipeline. The findpeaks.m function was used until it could no longer detect any peaks, indicating that all artifacts had been eliminated. This was confirmed via visual inspection on each iteration, with a maximum of 7 iterations of the artifact elimination pipeline for a single patient. Two patients were eliminated due to excessive blinks and artifacts.
The pupil time series was down-sampled to 500 Hz and low-pass filtered at 50 Hz. Trial onsets were identified using event markers sent from the computer generating the standard and oddball sequence to the EyeLink 1000 system. The pupil time series was epoched between 1,000 ms before and 3,000 ms after sound onset. Maximum pupil size values were identified for each run per patient, and time series were normalized to the percentage of the maximum pupil size (% of max) to standardize the time series across patients and runs. Responses were calculated as the difference between the average % of max in the response window (first 2,500 ms) versus the baseline window. Single trials were eliminated if they contained greater than 40% interpolated values, or response average values were greater than or equal to five median absolute deviations from other epochs at that sample location within the task block (see Supplementary Table 1 for final trial counts across all runs electrodes within each condition).
Intracranial EEG Recording and Preprocessing. Neural signals were recorded from stereo EEG probes (Ad-Tech Medical Instrument Corporation or PMT Corporation) connected to a Cerebus data acquisition system (Blackrock Neurotech). All recording signals were amplified, filtered (high-pass 0.3 Hz first-order Butterworth, low-pass 500 Hz fourth-order Butterworth), and digitized at 2,000 Hz. Acoustic stimulation was synchronized with neural signals using an audio analog input which copied the sound waveform to the Cerebus system.
Visual inspection was used to exclude recordings from electrodes with excessive noise, artifacts, and/or interictal activity. Recordings from included electrodes were then re-referenced using a common average reference of all valid electrodes, and notch filtered to remove line noise (60 Hz, first harmonic, second harmonic, and third harmonic). Finally, all recordings were downsampled to 500 Hz using a low-pass Chebyshev type 1 IIR filter of order 8.
The signals obtained were transformed from the time domain into the frequency domain using a wavelet transformation (Morlet, 7 cycles per wavelet; frequencies equally spaced on a linear scale from 2 to 200 Hz). This provided an electrode-by-time matrix of power values for each data run. The analog recorded acoustic signal was used to identify sound onsets. The neural signals of interest (from the electrode-by-time matrix) were obtained by extracting values for each trial (between 1,000 ms before and 2,000 ms after sound onset). Trial power values were normalized to a baseline period (-250 ms to 0 ms; preceding stimulus onset) by calculating % signal change from baseline for the early intra-stimulus (0 ms to 350 ms) and late (250 ms to 750 ms)57 post-stimulus time windows. While the stimulus playback only occurred between 0-250 ms, the early intra-stimulus time window was expanded to 0-350 ms to capture high gamma salience-related activity, which has been reported to cluster between 200–300 ms in the human auditory cortex 58. We compute percent power change across canonical neural frequency bands (High Gamma [70–150 Hz]; Low Gamma [32–70 Hz]; High Beta [20–30 Hz]; Low Beta [12–20 Hz]; Alpha [8–10 Hz]; Theta [4–8 Hz]; Delta [2–4 Hz]) when investigating the shift in aperiodic 1/f activity between pre-and post-stimulus periods. We focus on our apriori hypotheses surrounding high gamma, low beta, and alpha bands in the correlational and linear mixed-effects modeling analyses. Cortical excitability was quantified in the pre (-250–0 ms) and post (0–750 ms) stimulus time windows using the delta power fraction (delta power / total power), or the aperiodic (1/f) slope estimate, which was calculated using a linear fit (MATLAB function polyfit.m, degree 1, MathWorks™ 2023b) over the 20–45 Hz spectral range. The intermediate frequencies (20–45 Hz) reflect the region of transition from high-to-low frequencies, such that increased delta power and decreased gamma power will have a steep slope in the transition region, whereas low delta power and increased gamma power should have a flatter slope59.
Statistical Analyses. Pupil response profiles were assessed at the group level between subjects, and the trial level within subjects. Pupil diameter responses and cortical responses for both conditions were calculated for each task block in each canonical frequency band. A Pearson correlation was conducted for each LFP response component-condition pair, and Benjamini-Hochberg correction was performed for a total of six correlational analyses. Linear mixed-effects (LME) modeling was used to examine the trial-by-trial relationship within subjects for the significant group-level relationships (high gamma, low beta, alpha). Average high gamma, low beta, and alpha component responses were extracted for each electrode per trial and then averaged over all electrodes per trial, such that there was one value per trial, per test block. The LME was constructed with pupil response as the dependent variable, cortical response (high gamma, low beta, or alpha) and condition (standard vs. oddball) as interacting fixed effects, and subject ID as a random effect. Benjamini-Hochberg correction was performed for a total of three high gamma LMEs (see Table 1 for model notations). All LME modeling was completed using the lmer package in R, notations provided in results tables reflect lmer model notations.
State dependence was assessed at the group level between subjects, and the trial level within subjects. Trials were averaged over all electrodes such that each task block only had one value per trial. Pre-stimulus slope or delta fraction (delta fraction = delta power/total power) was computed in the baseline (-250–0 ms) window for each trial. These values were then sorted into evenly spaced bins per condition, except for the extremes which were extended to ensure adequate bin size (Nbin > 5, bin cutoffs for 1/f slope = [-8.5, -5.5,-5.0,-4.5,-4.0,-3.5,-3.0,-2.5,-2,-2.5] and delta fraction = [0, 0.05, 0.1, 0.15, 0.20, 0.25, 0.3, 0.35, 0.40, 0.45, 0.5]). Average pre-stimulus slope values per task block were examined using the MATLAB isoutlier.m function. One subject (Subject 10) was identified as an outlier for both task blocks (falling greater than three median absolute deviations from the group mean) and was excluded from group analyses but included in within-subjects trial-level analyses. A regression line was fit to the binned dataset using the MATLAB lmfit.m function. A quadratic (high gamma responses, pupil-oddball responses) or linear (pupil-standard responses) depending on which fit was most appropriate for each relationship based on R-squared values. Cortical trial-level analyses were conducted using LME modeling within subjects per electrode per subject. Pupil trial-level analyses also utilized LME modeling, though (pre- or post-stimulus) slope values were averaged over all pSTG electrodes per task block for each trial and only fit per subject to avoid pupil response redundancy.
Cortical response profiles were assessed at the group level. Epoched spectra were averaged over all trials for each condition (standard vs. oddball) for a given task block, and early (0–350 ms) and late (250–750 ms) time windows were extracted for each canonical frequency band. Wilcoxon signed-rank tests were first used to assess if each condition-frequency band pair exhibited a significant change from zero, and Benjamini-Hochberg correction was used to adjust for 14 total tests per time window. Then average oddball and average standard responses for each time window were matched by task block and the difference was computed for each pair (Oddball amplitude – Standard amplitude) for each canonical frequency band. Wilcoxon signed-rank tests were again used to assess if each band amplitude was different from zero, and Benjamini-Hochberg correction was used for seven total tests for each time window. This method was also used for assessing the effect of tone frequency (1,000 vs 2,000 Hz) rather than salience condition, and a Kruskal-Wallis test was used to compare group means.
Pre-, post-early, and post-late stimulus slope estimates were averaged over all trials per condition within a given task block. An LME was fit with aperiodic slope estimate as the dependent variable, time window (pre, post-early, post-late) and condition as interacting fixed effects, and subject ID as a random effect. Estimated Marginal Means (EMMs) were computed using the emmeans60 function in R, and pairwise comparisons were made between each condition-time window pair. Corrections were made using the Benjamini-Hochberg method. After-oddball responses were identified, and an LME was fit with high gamma responses as the dependent variable and condition (standard, oddball, after oddball) as the dependent variable, and subject ID as a random effect. EMMs were computed, and pairwise comparisons were made across condition.