Psilocybin induces spatially constrained alterations in thalamic functional organization and connectivity

This neuroimaging study (n=38) uses a novel Independent Component Analysis (ICA) approach and fMRI to examine psilocybin-induced changes in intrathalamic (within the thalamus) functional organization and thalamocortical connectivity. Several intrathalamic components showed significant psilocybin-induced alterations in intrathalamic spatial organization primarily localised to the mediodorsal and pulvinar nuclei, and correlated with reported subjective effects, but didn’t survive correction for multiple comparisons.


Background: Classic psychedelics, such as psilocybin and LSD, and other serotonin 2A receptor (5-HT2AR) agonists evoke acute alterations in perception and cognition. Altered thalamocortical connectivity has been hypothesized to underlie these effects, which is supported by some functional MRI (fMRI) studies. These studies have treated the thalamus as a unitary structure, despite known differential 5-HT2AR expression and functional specificity of different intrathalamic nuclei. Independent Component Analysis (ICA) has been previously used to identify reliable group-level functional subdivisions of the thalamus from resting-state fMRI (rsfMRI) data. We build on these efforts with a novel data-maximizing ICA-based approach to examine psilocybin-induced changes in intrathalamic functional organization and thalamocortical connectivity in individual participants.

Methods: Baseline rsfMRI data (n=38) from healthy individuals with a long-term meditation practice was utilized to generate a statistical template of thalamic functional subdivisions. This template was then applied in a novel ICA-based analysis of the acute effects of psilocybin on intra- and extra-thalamic functional organization and connectivity in follow-up scans from a subset of the same individuals (n=18). We examined correlations with subjective reports of drug effect and compared with a previously reported analytic approach (treating the thalamus as a single functional unit).

Results: Several intrathalamic components showed significant psilocybin-induced alterations in spatial organization, with effects of psilocybin largely localized to the mediodorsal and pulvinar nuclei. The magnitude of changes in individual participants correlated with reported subjective effects. These components demonstrated predominant decreases in thalamocortical connectivity, largely with visual and default mode networks. Analysis in which the thalamus is treated as a singular unitary structure showed an overall numerical increase in thalamocortical connectivity, consistent with previous literature using this approach, but this increase did not reach statistical significance.

Conclusions: We utilized a novel analytic approach to discover psilocybin-induced changes in intra- and extra-thalamic functional organization and connectivity of intrathalamic nuclei and cortical networks known to express the 5-HT2AR. These changes were not observed using whole-thalamus analyses, suggesting that psilocybin may cause widespread but modest increases in thalamocortical connectivity that are offset by strong focal decreases in functionally relevant intrathalamic nuclei.”

Authors: Andrew Gaddis, Daniel E. Lidstone, Mary B. Nebel, Roland R. Griffiths, Stewart H. Mostofsky, Amanda Mejia & Frederick S. Barrett

Further Notes

A Corrigendum to this article came out in May 2023, stating, “Upon further analysis, while several effects are significant before multiplicity correction, none of the reported correlations survive correction for multiple comparisons at alpha = 0.05, assessed using Bonferonni correction, correction for False Discovery Rate, and permutation analysis. This is likely due to a lack of power in our dataset (n=18), combined with the large number of comparisons being made (98 in Figure 5, 252 in Figure 7). We find more significant (uncorrected) associations (approximately 11%) than what would be expected by chance at alpha = 0.05 (5%), which suggests that a subset of the reported associations likely reflect relationships between subjective effects and psylocibin-associated changes in intra-thalamic and thalamo-cortical connectivity. However, it is not possible to distinguish which of those association are real versus spurious. Our analysis requires verification and replication in a well-powered sample.”


Psilocybin and LSD (classic psychedelics) alter perception and cognition by altering thalamocortical connectivity. A novel data-sparing ICA approach was used to examine psilocybin-induced changes in intrathalamic functional organization and thalamocortical connectivity.

A novel ICA-based analysis was conducted on rsfMRI data to evaluate the acute effects of psilocybin on intra- and extra-thalamic functional organization and connectivity.

Results: The mediodorsal and pulvinar nuclei showed significant psilocybin-induced alterations in intrathalamic spatial organization, and thalamocortical connectivity, largely with visual and default mode networks.

Psilocybin causes widespread but modest increases in thalamocortical connectivity, offset by strong focal decreases in functionally relevant intrathalamic nuclei.

Psychedelic compounds can induce perceptual and cognitive effects that may be deeply impactful to the individuals experiencing them. These effects are thought to be mediated primarily through activation of the serotonin 2A receptor (5-HT2AR).

The thalamus is among the subcortical structures that demonstrate significant expression of 5-HT2AR, and there is growing evidence that thalamocortical connectivity plays a key role in psychosis and other altered perceptual and cognitive states with potential clinical relevance.

The thalamus is a crucial “relay center” through which sensory information reaches the cortex. It is also involved in the mediation and regulation of cortical signaling beyond sensory input, and might have clinical relevance in cognitive processes and states less directly related to sensory perception, such as meditation and hypnosis.

Two fMRI studies in humans have reported differences in thalamic function during the acute effect of psilocybin, and one study has suggested potential decreases as well.

After acute LSD administration, thalamocortical connectivity increases in all regions, with increases in somatosensory regions and decreases in associative regions. However, there are also reports of decreases in connectivity, as well as increased thalamocortical activation in certain regions.

Thalamic function is diverse, and many thalamic nuclei are connected to higher-order cortical regions. 5-HT2AR signaling may alter the function of these circuits, but the thalamus is commonly treated as a unitary structure in functional neuroimaging studies with psychedelics.

In this study, we used a hierarchical Template Independent Component Analysis (tICA) model of resting-state fMRI to examine changes in thalamic functional organization and thalamocortical connectivity during psilocybin-induced acute effects.

40 participants with long-term meditation practices were enrolled in a multi-phase study of the acute and enduring subjective and neural effects of psilocybin. They provided written informed consent, were medically and psychologically healthy, and had attended at least 1 meditation retreat.

Participants were excluded if they had a history of cardiac abnormalities, substance use disorders, or a standard MRI contraindication. Half of the participants had previous experience with a hallucinogen, but none had used a psychedelic drug within 5 years of enrollment.

The Johns Hopkins Medicine Institutional Review Board approved all procedures, and no serious adverse events were encountered.

Forty healthy volunteers underwent screening and baseline MRI procedures, followed by administration of 25 mg/70 kg oral psilocybin two to four months later. They completed 8 hours of meetings with study staff to build rapport and prepare for psilocybin administration.

Twenty healthy volunteers from Phase 1 were enrolled in Phase 2, which was a single-blind, within-subjects, placebo-controlled study of the acute effects of 10 mg/70 kg oral psilocybin on brain function.

Participants completed 4 hours of preparation before their drug administration sessions, were closely monitored during acute effects of psilocybin, and completed a debriefing with study staff.

To minimize expectancy effects, participants received placebo or a very low dose of psilocybin, but the second dose was always 10 mg oral psilocybin. Psilocybin administration occurred in an aesthetic living-room environment at the Center for Psychedelic and Consciousness Research at the Johns Hopkins Bayview Medical Center. Participants completed MRI scanning procedures beginning 90 min after capsule administration. Scans were acquired on 3T Philips Achieva MRI scanners at the Kennedy Krieger Institute in Baltimore, MD, using echo planar imaging, and participants were instructed to not meditate during task-free scans. Other imaging procedures were completed during these scanning sessions and will be reported elsewhere.

Participants rated the strength of subjective drug effects experienced during each task-free fMRI scan from 0 (“none”) to 10 (“strongest imaginable”). They also rated three measures related to mindfulness, the mystical experience questionnaire, and two dimensions of general emotional experience.

fMRI datasets were minimally preprocessed using SPM 12 and custom code written in MATLAB. Resting-state scans were slice time corrected and spatial normalized using the Montreal Neurological Institute (MNI) EPI template.

The template ICA model uses empirical priors to estimate component loadings, and allows greater flexibility to deviate from the population mean in estimating component loading for voxels with large between-subject variance.

We used spatially constrained group ICA to create template mean and variance maps for the Phase II data, using minimally preprocessed baseline data.

A probabilistic Harvard-Oxford atlas was used to generate a mask of 2,268 voxels, and ICA was used to decompose the voxels into temporally coherent, spatially independent components. The between-subject variance was estimated using dual regression, and templates were generated using template ICA.

The template ICA model was fitted using fMRI data from 18 subjects. The template maps were applied to generate subject-level TICs for both placebo and psilocybin sessions.

To identify voxels showing statistically significant session-specific differences in TIC “engagement” as compared to baseline, voxelwise t-tests were performed. Multiplicity correction was performed by controlling the false discovery rate at 0.01.

We counted the number of significantly engaged voxels within the whole thalamus for each TIC and compared the number of engaged voxels between sessions using non-parametric Wilcoxon paired two-sided t-tests.

We generated probabilistic effect maps of TIC engagement to identify voxels showing a meaningful between-session effect at the group level. These maps were used to identify voxels where at least 25% of participants showed more engagement during the placebo session as compared to the psilocybin session.

We calculated the percentage of voxels in the between-session effect maps that fall into the pre-defined Morel ROIs. These ROIs were used to identify the effect of psilocybin on TIC engagement.

The following section details methods used to examine psilocybin-induced alterations in intra and extra-thalamic connectivity, including intra-cortical connectivity for large-scale resting state networks.

Using group ICA-derived template spatial maps, DR was applied to minimally preprocessed subject- and session-specific resting-state data to obtain subject-level TIC timecourses and cortical ICA-derived network timecourses. Nuisance regression was used to remove the influence of non-neural signal estimated from white matter and cerebrospinal fluid. Thalamocortical and intra-cortical connectivity were measured between sessions and compared using paired two-sided t-tests. Between-session changes in functional connectivity were associated with between-session changes in subjective-effects using Spearman rank correlations.

To examine the impact of our thalamic parcellation on our results, we calculated whole-thalamus seed connectivity with cortical ICA-derived networks and performed two-sided t-tests to examine between-session differences in thalamocortical connectivity.

Two approaches were taken to examine the loading of intra-thalamic voxels onto each TIC. The first approach used mean component loadings at baseline for each voxel, while the second approach used thresholds to identify voxels demonstrating robust mean component loading at baseline.

The results above demonstrate that the thalamus is a structure comprised of bilaterally symmetrical and functionally distinct nuclei, and that each TIC demonstrates best fit to a unique Morel ROI.

Thalamic independent components showed decreased engagement during psilocybin administration compared to placebo administration. TIC02 and TIC07 also showed decreased engagement during psilocybin administration.

The thresholded between-session effect maps of four TICs showed that differences in intrathalamic engagement were primarily localized to the Mediodorsal or Medial Pulvinar nuclei.

Six associations between the change in engagement voxel counts (placebo-psilocybin) and subjective-effects (placebo-psilocybin) were found. These associations included larger decreases in engagement of TIC03 during psilocybin sessions compared to placebo, and larger increases in engagement of TIC07 during psilocybin sessions.

During psilocybin sessions, thirteen edges showed significantly decreased connectivity compared to only five edges showing significantly increased connectivity.

Participants showing larger decreases in connectivity between TIC02-TIC03 during psilocybin sessions showed larger decreases in “fusion”, “sacredness”, “peace”, “timelessness”, “joy”, and “overall effect”. Further, participants showing larger decreases in connectivity between TIC05-TIC07 during psilocybin sessions showed larger decreases in “letting go” and “negative valence”.

The occipital-pole showed the largest change in connectivity with the thalamus seed during psilocybin sessions, and the left FPN showed the largest increase in connectivity with the thalamus seed.

The direction of between-session connectivity differences using the seed-based approach was opposite that observed for the significant TIC thalamocortical edges. This finding provides an explanation for why the seed-based approach produced opposite findings as compared to the ICA-based approach.

We used ICA to generate functional parcellations of the thalamus from baseline resting state data, and compared the resulting parcellations before and after the acute administration of psilocybin. We found several significant changes in both intra- and extra-thalamic patterns of functional organization and connectivity.

Psilocybin administration causes significant changes in both intrathalamic and thalamocortical connectivity, with the principal effect of focally reducing intrathalamic and thalamo-cortical connectivity. These changes are also associated with reported acute subjective effects.

Through the use of a novel data-sparing approach, we have revealed that the mediodorsal and pulvinar nuclei are the most impacted by the acute administration of psilocybin, and that these two nuclei are spatially aligned with nuclei previously implicated in the psychedelic state.

After administration of psilocybin, specific components of the thalamus showed decreased connectivity with large-scale cortical networks, whereas overall thalamo-cortical connectivity increased, although these increases did not reach statistical significance.

Our study reports on the engagement and connectivity of specific thalamic subregions during acute administration of psilocybin, and suggests that whole-thalamus masking may be less effective than ICA-based parcellation at detecting certain focal patterns of altered thalamo-cortical connectivity.

Psilocybin appears to increase thalamo-cortical connectivity, but decreases it in specific thalamic nuclei and cortical networks that express 5-HT2AR receptors and are implicated in the acute effects of the classic psychedelics.

When analyzing thalamocortical connectivity, whole-thalamus masking may obscure nuanced nuclei-specific effects associated with acute psilocybin exposure. A data-sparing approach can be used to reveal focal underlying effects during acute drug exposure.

Study details

Compounds studied

Topics studied

Study characteristics

18 Humans


Authors associated with this publication with profiles on Blossom

Roland Griffiths
Roland R. Griffiths is one of the strongest voices in psychedelics research. With over 400 journal articles under his belt and as one of the first researchers in the psychedelics renaissance, he has been a vital part of the research community.

Frederick Barrett
Frederick Streeter Barrett is an Assistant Professor of Psychiatry and Behavioral Sciences and works at the Johns Hopkins University Center for Psychedelic and Consciousness Research.


Institutes associated with this publication

Johns Hopkins University
Johns Hopkins University (Medicine) is host to the Center for Psychedelic and Consciousness Research, which is one of the leading research institutes into psychedelics. The center is led by Roland Griffiths and Matthew Johnson.

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