From histology to macroscale function in the human amygdala

Reviewer #1 (Public review):

The paper by Auer et. makes several contributions:

(1) The study developed a novel approach to map the microstructural organization of the human amygdala by applying radiomics and dimensionality reduction techniques to high-resolution histological data from the BigBrain dataset.

(2) The method identified two main axes of microstructural variation in the amygdala, which could be translated to in vivo 7 Tesla MRI data in individual subjects.

(3) Functional connectivity analysis using resting-state fMRI suggests that microstructurally defined amygdala subregions had distinct patterns of functional connectivity to cortical networks, particularly the limbic, frontoparietal, and default mode networks.

(4) Meta-analytic decoding was used to suggest that the superior amygdala subregion's connectivity is associated with autobiographical memory, while the inferior subregion was linked to emotional face processing.

(5) Overall, the data-driven, multimodal approach provides an account of amygdala microstructure and possibly function that can be applied at the individual subject level, potentially advancing research on amygdala organization.

Although these are meritorious contributions there are some concerns that I will summarize below.

(1) The paper makes little-to-no contact with the monkey literature regarding the anatomy of amygdala subregions, their functionality, and their patterns of anatomical connectivity. This is surprising because such literature on non-human primates is a very important starting point for understanding the human amygdala. I recommend taking a careful look at the work by Helen Barbas, among others. There are too many papers to cite but a notable example is: Ghashghaei, H. T., Hilgetag, C. C., & Barbas, H. (2007). Sequence of information processing for emotions based on the anatomic dialogue between prefrontal cortex and amygdala. Neuroimage, 34(3), 905-923. The work of Amaral is also highly relevant. Furthermore, the authors subscribe to a model with LB, CM, and SF sectors. How does the SF sector relate to monkey anatomy?

(2) The authors use meta-analytical decoding via NeuroSynth. If the authors like those results of course they should keep them but the quality of coordinate reporting in the literature is insufficient to conclude much in the context of amygdala subregion function in my opinion. I believe the results reported are at most "somewhat suggestive".

(3) Another significant concern has to do with the results in Figure 3. The red and yellow clusters identified are quite distinct but the differences in functional connectivity are very modest. Figure 3C reveals very similar functional connectivity with the networks investigated. This is very surprising, and the authors should include a careful comparison with related findings in the literature. Overall, there is limited comparison between the observed results and those obtained via other methods. On a more pessimistic note, the results of Figure 3 seem to question the validity of the general approach.

(4) Some statements in the Discussion feel unwarranted. For example, "significant dissociation in functional connectivity to prefrontal structures that support self-referential, reward-related, and socio-affective processes." This feels way beyond what can be stated based on the analyses performed.

Reviewer #2 (Public review):

Summary:

This study bridges a micro- to macroscale understanding of the organization of the amygdala. First, using a data-driven approach, the authors identify structural clusters in the human amygdala from high-resolution post-mortem histological data. Next, multimodal imaging data to identify structural subunits of the amygdala and the functional networks in which they are involved. This approach is exciting because it permits the identification of both structural amygdalar subunits, and their functional implications, in individual subjects. There are, however, some differences in the macro and microscale levels of organization that should be addressed.

Strengths:

The use of data-driven parcellation on a structure that is important for human emotion and cognition, and the combination of this with high-resolution individual imaging-based parcellation, is a powerful and exciting approach, addressing both the need for a template-level understanding of organization as well as a parcellation that is valid for individuals. The functional decoding of rsfMRI permits valuable insight into the functional role of structural subunits. Overall, the combination of micro to macro, structure, and function, and general organization to individual relevance is an impressive holistic approach to brain mapping.

Weaknesses:

(1) UMAP 1, as calculated from the histological data, appears to correlate well across individuals, and decently with the MRI data, although the medial-lateral coordinate axis is an outlier. UMAP 2, on the other hand, does not appear to correlate well with imaging data or across individuals. This does pose a problem with the claim that this paper bridges micro- and macroscale parcellations. One might certainly expect, however, that different levels of organization might parcellate differently, but the authors should address this in the discussion and offer ways forward.

(2) It would be interesting to see functional decoding for the right amygdala. This could be included in the supplementary material. A discussion of differences in the results in the two hemispheres could be illuminating.

(3) The authors acknowledge that this mapping matches some but not all subunits that have been previously described in the amygdala. It would be helpful to neuroanatomists if the authors could discuss these differences in more detail in the discussion, to identify how this mapping differs and what the implications of this are.

(4) The acronym UMAP is not explained. A brief explanation and description would be useful to the reader.