Multi-contrast anatomical subcortical structures parcellation

Subcortical brain structures are often neglected in neuroimaging studies due to their small size, limited inter-regional contrast, and weak signal-to-noise ratio in functional imaging (Forstmann et al., 2016; Johansen-Berg, 2013). Yet, these small and diverse structures are prominent nodes in functional networks (Marquand et al., 2017; Ji et al., 2019), and they undergo pathological alterations already at early stages of neurodegenerative diseases (Andersen et al., 2014; Koshiyama et al., 2018). Deep brain stimulation surgery, originally performed to reduce motor symptoms in essential tremors, is now a promising therapeutic option in later stages of Parkinson’s disease and movement disorders, as well as refractory psychiatric illnesses in obsessive-compulsive disorder, anorexia, or depression (Forstmann et al., 2017; Mosley et al., 2018). Evolutionary genetics even uncovered that in modern humans, Neanderthal-inherited alleles were preferentially down-regulated in subcortical and cerebellar regions compared to other brain regions (McCoy et al., 2017), suggesting these structures to be essential in making us specifically human.

Despite their importance, these areas are particularly difficult to image. Furthermore, the size, shape, and location of these brain regions changes with development and aging (Fjell et al., 2013; Keuken et al., 2013; Yeatman et al., 2014; Herting et al., 2018). Experience-based plasticity continuously remodels myelin (Tardif et al., 2016; Hill et al., 2018; Turner, 2019), iron and other magnetic substances accumulate with age or pathology (Andersen et al., 2014; Zhang et al., 2018), both bringing changes in the MRI appearance of subcortical regions with diverse tissue characteristics (Draganski et al., 2011; Keuken et al., 2017).

Thus, mapping the structure and function of the subcortex is a major endeavor as well as a major challenge for human neuroscience. Extensive work available from animal brain models unfortunately does not translate in a straightforward way to human subcortical anatomy nor does it shed much light on its involvement in human cognition (Steiner and Tseng, 2017). Besides serious difficulties in obtaining adequate measures of subcortical neural activity in functional MRI (de Hollander et al., 2017; Miletić et al., 2020), atlases and techniques for labeling accurately and reliably individual subcortical structures have also been scarce (Frazier et al., 2005; Chakravarty et al., 2006; Ahsan et al., 2007; Yelnik et al., 2007; Qiu et al., 2010; Patenaude et al., 2011), typically labeling the thalamus, striatum (or its subdivision into caudate and putamen), and globus pallidus (internal and external segments combined), sometimes the amygdala. However, recent advances in anatomical MRI, combining multiple contrasts and/or quantitative MRI mapping and utilizing the higher resolution achievable with 7 Tesla (7T) and above have started to reduce the gap, each mapping a few additional structures or sub-structures, primarily the iron-rich substantia nigra, red nucleus and sub-thalamic nucleus (Keuken et al., 2013; Xiao et al., 2015; Visser et al., 2016a; Visser et al., 2016b; Wang et al., 2016; Makowski et al., 2018; Ewert et al., 2018; Iglesias et al., 2018; Pauli et al., 2018; Sitek et al., 2019). While these efforts generated valuable atlases, they do not yet enable to identify many subcortical structures in individual subjects. Manual delineation, on the other hand, requires extensive manual labor from highly trained experts which cannot be easily applied to large cohorts or clinical settings.

Here, we propose a new automated parcellation technique to identify and label 17 individual subcortical structures of varying size and composition in individual subjects, based on a large quantitative 7T MRI database (Alkemade et al., 2020), using quantitative maps of relaxation rates R1 and R2* (1/T1 and 1/T2*, respectively) and quantitative susceptibility maps (QSM) as anatomical contrasts. The algorithm, named Multi-contrast Anatomical Subcortical Structure Parcellation (MASSP), follows a Bayesian multi-object approach similar in essence to previous efforts (Fischl et al., 2002; Eugenio Iglesias et al., 2013; Visser et al., 2016a; Garzón et al., 2018), combining shape priors, intensity distribution models, spatial relationships, and global constraints. The main innovation of our approach is to explicitly estimate interfaces between subcortical structures based on a joint model derived from signed distance functions. Modeling interfaces in addition to the structure itself provides a rich basis to encode relationships and anatomical knowledge in shape and intensity priors. A voxel-wise Markovian diffusion regularizes the combined priors for each defined interface, lowering the imaging noise. Finally, the voxel-wise posteriors for the different structures and interfaces are further combined into global anatomical parcels by topology correction and region growing taking into account volumetric priors, which regularizes parcellation results further in smaller nuclei with low or heterogeneous contrast. To validate the results from this new method, in a thorough comparison with expert manual labeling, we show that the proposed method provides results very close from manual raters in many structures and exhibit reasonable bias across the adult lifespan. The method can easily be extended to new structures, can be applied to any quantitative MRI dataset and is available in Open Source as part of Nighres (Huntenburg et al., 2018), a neuroimage analysis package aimed at high-resolution neuroimaging.

The MASSP parcellation method presented here has been trained to parcellate the following 17 structures: striatum (Str), thalamus (Tha), lateral, 3rd and 4th ventricles (LV, 3V, 4V), amygdala (Amg), globus pallidus internal segment (GPi) and external segment (GPe), SN, STN, red nucleus (RN), ventral tegmental area (VTA), fornix (fx), internal capsule (ic), periaqueductal gray (PAG), pedunculopontine nucleus (PPN), and claustrum (Cl), see Figure 1. These structures include the most commonly defined subcortical regions (Str, Tha, Amg, LV), the main iron-rich nuclei (GPi, GPe, RN, SN, STN), as well as smaller, less studied areas (VTA, PAG, PPN, Cl), white matter structures (ic, fx), and the central ventricles (3V, 4V).

Figure 1

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MASSP uses a data set of ten expert delineations as a basis for its modeling. From the delineations, an atlas of interfaces between structures, shape skeletons, and interface intensity histograms are generated, and used as prior in a multiple-step non-iterative Bayesian algorithm, see Figure 2 and Materials and methods.

Figure 2

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Validation against manual delineations

In a leave-one-out validation study comparing performance with the manual delineations, MASSP performed above 95% of the level of quality of the raters for Str, Tha, 4V, GPe, SN, RN, VTA, ic in terms of Dice overlap, the most stringent of the quality measures (see Figures 3 and 4 and Table 1). Several of the smaller structures have lower overlap ratios likely due to their smaller size (GPi, STN, PAG, PPN). Structures with an elongated shape (fx, Cl) remain challenging, due to the fact that small differences in location can substantially reduce overlap (Bazin et al., 2016). Despite these challenges, when comparing the dilated Dice scores, all structures were above 75% of overlap, with most reaching over 90% of the manual raters ability. Note that the Dice coefficient is very sensitive to size, as smaller structures will have lower overlap ratios for the same number of misclassified voxels. The dilated Dice coefficient is more representative of the variability regardless of size, as the smaller structures can reach high levels of overlap, both in manual and automated parcellations (see Table 1). The average surface distance confirms these results, showing values generally between one and two voxels of distance at a resolution of 0.7 mm, except in the cases of Amg, LV, fx, PPN, and Cl. These structures are generally more variable (LV), elongated (fx, Cl), or have a particularly low contrast with neighboring regions (Amg, PPN).

Table 1

	Str	STN	SN	RN	GPi	GPe	Tha	LV	3V	4V	Amg	ic	VTA	fx	PAG	PPN	Cl
Dice overlap
MASSP	0.893	0.648	0.805	0.870	0.702	0.800	0.867	0.849	0.741	0.869	0.723	0.745	0.570	0.527	0.641	0.496	0.485
Manual	0.897	0.800	0.841	0.875	0.762	0.813	0.877	0.907	0.797	0.882	0.866	0.732	0.574	0.823	0.791	0.665	0.727
Ratio	0.995	0.811	0.957	0.996	0.925	0.987	0.989	0.936	0.936	0.988	0.836	1.020	0.994	0.641	0.814	0.754	0.664
Dilated overlap
MASSP	0.982	0.919	0.977	0.991	0.909	0.956	0.970	0.929	0.890	0.951	0.891	0.915	0.863	0.756	0.897	0.795	0.789
Manual	0.987	0.988	0.985	0.995	0.953	0.972	0.970	0.967	0.944	0.961	0.978	0.924	0.818	0.957	0.960	0.910	0.914
Ratio	0.995	0.930	0.992	0.995	0.955	0.984	1.000	0.961	0.946	0.991	0.911	0.992	1.059	0.790	0.935	0.879	0.863
Average surface distance
MASSP	0.750	0.911	0.676	0.491	1.140	0.863	1.058	2.690	0.994	0.817	1.476	1.275	1.074	2.950	0.955	1.484	1.685
Manual	0.723	0.508	0.571	0.482	0.902	0.804	0.971	0.615	0.637	0.671	0.779	1.045	1.204	0.703	0.555	0.801	0.670
Ratio	0.971	0.590	0.852	0.996	0.861	0.943	0.916	0.277	0.662	1.020	0.553	0.834	1.161	0.287	0.610	0.619	0.465

Figure 3

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Figure 4

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Application to new MRI contrasts

Quantitative MRI has only become recently applicable in larger studies, thanks in part to the development of integrated multi-parameter sequences (Weiskopf et al., 2013; Caan et al., 2019). Many data sets, including large-scale open databases, use more common T1- and T2-weighted MRI. In order to test the applicability of MASSP to such contrasts, we obtained the test-retest subset of the Human Connectome Project (HCP, Van Essen et al., 2013) and applied MASSP to the 45 pre-processed and skull-stripped T1- and T2-weighted images from each of the two test and retest sessions. While performing manual delineations on the new contrasts would be preferable, the model is already rich enough to provide stable parcellations. Test-retest reproducibility is similarly high for MASSP and Freesurfer, and are generally in agreement, see Figure 5 and Table 3.

Table 3

	Str	STN	SN	RN	GPi	GPe	Tha	LV	3V	4V	Amg	ic	VTA	fx	PAG	PPN	Cl
Dice overlap
MASSP test-retest	0.914	0.701	0.818	0.829	0.791	0.859	0.928	0.881	0.837	0.870	0.866	0.860	0.738	0.774	0.714	0.713	0.785
Freesurfer test-retest	0.898				0.770		0.919	0.894	0.842	0.849	0.852
MASSP – Freesurfer	0.876				0.778		0.838	0.858	0.430	0.769	0.692
Dilated overlap
MASSP test-retest	0.987	0.939	0.977	0.978	0.963	0.977	0.990	0.980	0.979	0.986	0.981	0.973	0.969	0.961	0.965	0.972	0.966
Freesurfer test-retest	0.986				0.926		0.986	0.989	0.972	0.975	0.978
MASSP – Freesurfer	0.954				0.788		0.919	0.934	0.435	0.901	0.866
Average surface distance
MASSP test-retest	0.513	0.528	0.467	0.461	0.532	0.508	0.488	0.509	0.391	0.419	0.533	0.536	0.431	0.464	0.428	0.402	0.433
Freesurfer test-retest	0.876				0.778		0.838	0.858	0.430	0.769	0.692
MASSP – Freesurfer	0.976				1.673		1.605	1.946	5.699	1.428	1.478

Figure 5

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Biases due to atlas size

A common concern of brain parcellation methods is the risk of biases, as they are typically built from a small number of manual delineations. Our data set is part of a large scale study of the subcortex, for which we obtained manual delineations of the STN, SN, RN, GPe, and GPi on 105 subjects over the adult lifespan (18–80 year old, see Alkemade et al., 2020 for details). First, we investigated the impact of atlas size. We randomly assigned half of the subjects from each decade to two groups, and built atlas priors from subsets of 3, 5, 8, 10, 12, 15, and 18 subjects from the first group. The subjects used in the atlas were taken randomly from each decade (18-30, 31-40, 41-50,51-60, 61-70, 71-80), so as to maximize the age range represented in each atlas. Atlases of increasing size were constructed by adding subjects to previous atlases, so that atlases of increasing complexity include all subjects from simpler atlases. Results applying these atlases to parcellate the second group are given in Figure 6. As in previous studies (Eugenio Iglesias et al., 2013; Bazin and Pham, 2008), performance quickly stabilized with atlases of more than five subjects (no significant difference in Welch’s t-tests between using 18 subjects or any subset of 8 or more for all structures and measures).

Figure 6

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Biases due to age differences

To more specifically test the influence of age on parcellation accuracy, we defined again six age groups by decade and randomly selected 10 subjects from each group. Each set of subjects was used as priors for the five structures above, and applied to the other age groups. Results are summarized in Figure 7. Examining this age bias, we can see a decrease in performance when parcellating subjects in the range of 60 to 80 years of age. The choice of priors seem to have a limited impact, which varies across structures. In particular, using priors from a similar age group is not always beneficial.

Figure 7

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Bias on individual measures

Finally, we investigated the impact of this decrease in performance in the estimation of anatomical quantities, see Figure 8. The bias did affect the morphometric measures of structure volume and thickness, but the effects on the local measure of thickness was reduced compared to the global measure of volume. Quantitative MRI averages were very stable even when age biases are present in the parcellations.

Figure 8

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For reference, we report structure volumes, thickness, R1, R2* and QSM values estimated from the entire AHEAD cohort for different age groups, extending our previous work based on manual delineations on a different data set (Keuken et al., 2017; Forstmann et al., 2014). Results are given in Table 4, describing average volumes, thickness, and quantitative MRI parameters for young, middle-aged, and older subjects for the 17 subcortical structures.

Table 4

Age	Str	STN	SN	RN	GPi	GPe	Tha	LV	3V	4V	Amg	ic	VTA	fx	PAG	PPN	Cl
Volume ($m{m}^3$)
18-40	10656	118	566	253	567	1366	7112	7524	1895	1391	1315	4335	254	1632	250	193	843
41-60	10572	124	583	256	586	1403	7492	8850	2024	1408	1363	4495	264	1808	255	195	830
61-80	10734	130	584	260	586	1397	7463	9142	2023	1407	1321	4407	272	1910	259	192	829
Thickness ($mm$)
18-40	5.94	1.89	2.55	4.64	3.09	3.56	8.31	4.27	2.77	4.03	4.81	4.06	1.69	2.06	1.78	1.92	1.79
41-60	5.47	1.86	2.66	4.58	2.96	3.41	8.28	5.08	2.95	3.89	4.85	4.19	1.76	1.96	1.84	1.86	1.80
61-80	5.22	1.83	2.60	4.11	2.92	3.22	8.28	4.90	3.18	4.06	4.73	4.19	1.80	1.97	1.90	1.95	1.82
qR1 ($Hz$)
18-40	0.647	0.949	0.857	0.928	0.868	0.850	0.761	0.332	0.346	0.274	0.546	0.906	0.819	0.714	0.654	0.779	0.650
41-60	0.662	0.968	0.893	0.939	0.879	0.856	0.758	0.278	0.315	0.269	0.559	0.904	0.833	0.671	0.653	0.771	0.664
61-80	0.648	0.952	0.882	0.903	0.860	0.830	0.743	0.273	0.300	0.270	0.552	0.884	0.814	0.638	0.647	0.764	0.669
qR2* ($Hz$)
18-40	43.8	67.1	67.8	63.2	75.2	79.6	38.1	14.7	18.9	9.0	25.5	36.8	39.2	37.4	25.9	32.7	32.6
41-60	50.4	74.1	74.1	77.1	80.2	87.9	40.3	8.4	12.4	11.7	28.1	38.7	42.8	37.4	28.0	33.4	36.9
61-80	51.8	77.0	72.5	73.8	77.8	87.0	40.1	8.5	10.2	12.0	30.1	39.6	52.6	35.7	28.4	34.2	35.4
QSM ($ppm$)
18-40	0.0329	0.0609	0.0738	0.0717	0.1015	0.1150	0.0138	0.0130	0.0100	0.0279	0.0036	−0.0234	0.0241	0.0079	0.0119	0.0135	−0.0122
41-60	0.0400	0.0647	0.0713	0.0829	0.0984	0.1241	0.0134	0.0115	0.0025	0.0234	0.0085	−0.0226	0.0201	0.0079	0.0089	0.0099	−0.0110
61-80	0.0411	0.0705	0.0610	0.0738	0.0925	0.1249	0.0064	0.0089	−0.0034	0.0236	0.0061	−0.0243	0.0177	0.0100	0.0039	0.0096	−0.0091

Our goal with the MASSP algorithm was to provide a fully automated method to delineate as many subcortical structures as possible on high-resolution structural MRI now available on 7T scanners. We modeled 17 distinct structures, taking into account location, shape, volume, and quantitative MRI contrasts to provide individual subject parcellations. Based on our results, we can be confident that the automated parcellation technique performs comparably to human experts, providing delineations within one or two voxels of the structure boundaries (dilated Dice overlap over 75% for all structures, including in aging groups). Results were nearly indistinguishable from expert delineations for eight major structures (Str, Tha, 4V, GPe, SN, RN, VTA, ic), and smaller structures retain high levels of overlap, comparable to trained human raters. This parcellation includes the most commonly defined structures (Str, Tha, SN, RN, STN) with overlap scores comparable to those previously reported (Garzón et al., 2018; Visser et al., 2016a; Eugenio Iglesias et al., 2013; Chakravarty et al., 2013; Patenaude et al., 2011). More importantly, it also includes structures seldom or never before considered in MRI atlases and parcellation methods, such as GPe, GPi, VTA, 3V, 4V, ic, fx, PAG, PPN, Cl. The technique handles structures of varying sizes well, as indicated by dilated overlap and boundary distance. Additional structures can be added, if they can be reliably delineated by expert raters on single-subject MRI at achievable resolutions. Some enhancement techniques such as building a multi-subject template (Pauli et al., 2018) or adding a denoising step (Bazin et al., 2019) may be beneficial. Co-registration to a high-precision atlas as in Ewert et al., 2018 may also improve the initial alignment over the MASSP group average template.

Age biases are present both in expert manual delineations and automated parcellation techniques. Age trajectories in volume and quantitative MR parameters indicate systematic shifts in contrast intensities and an increasing variability with age, associated with changing myelination, iron deposition, and brain atrophy (Draganski et al., 2011; Daugherty and Raz, 2013; Fjell et al., 2013; Keuken et al., 2017). These changes seem only to impact the parcellation accuracy for age groups beyond 60 years and age-matched priors did not provide specific improvements, thus indicating that an explicit modeling of age effects may be required to further improve parcellation quality in elderly populations. These results also point to exercising caution when applying automated parcellation methods to study morphometry in elderly or diseased populations, where measured differences may include biases. They also point out that while global volume and local thickness are indeed affected by such biases, quantitative MRI measures are much more robust. Note that this bias is likely present is many automated methods, although they have not been systematically investigated due to the extensive manual labor required. Interestingly, biases also exist in expert delineations: when the size or shape of a structure is refined in neuroanatomical studies, experts may become more or less conservative in their delineations. Automated methods provide a more objective measure in such case, as the source of their bias is explicitly encoded in the atlas prior delineations and computational model. Important applications of subcortical parcellation also include deep-brain stimulation surgery (Ewert et al., 2018), where the number of structures parcellated by MASSP can help neurosurgeons orient themselves more easily, although precise targeting will still require manual refinements, especially in neurodegenerative diseases.

We observed that dilated overlap, that is, the overlap of structures up to one voxel, provided a measure of accuracy largely independent of size, for automated or manual delineations. Imprecision in the range of one voxel in the boundary is to be expected due to partial voluming which impacts Dice overlap. The dilated overlap measure is a better representative of performance and indicates that conservative or inclusive versions of the subcortical regions can be obtained by eroding or dilating the estimated boundary by a single voxel. Such masks may be useful when separating functional MRI signals between neighboring nuclei or when locating smaller features inside a structure. Additionally, the Bayesian estimation framework provides voxel-wise probability values, which can also be used to further weight the contribution of each voxel within a region in subsequent analyses.

In summary, our method provides fast and accurate parcellation for subcortical structures of varying size, taking advantage of the high resolution offered by 7T and the specificity of quantitative MRI. The algorithm is based on an explicit model of structures given in a Bayesian framework and is free of tuning parameters. Given a different set of regions of interest or different populations, new priors can be automatically generated and used as the basis for the algorithm. If more MRI contrasts are available, the method can also be augmented to take them into account. The main requirement for the technique is a set of manual delineations of all the structures of interest in a small group of representative subjects. Performance may further improve with the number of included structures, as the number of distinct interfaces increases, refining in particular the intensity priors. In future works, we plan to include more structures or sub-structures and model the effects of age on the priors. We hope that the method, available in open source, will help neuroscience researchers to include more subcortical regions in their structural and functional imaging studies.

The tool presented in this article is available in open source on Github (https://github.com/nighres/nighres). The atlases necessary to run the algorithm have been deposited on the University of Amsterdam FigShare (https://doi.org/10.21942/uva.12074175.v1 and https://doi.org/10.21942/uva.12301106.v2). A single sample subject data set has been deposited on the University of Amsterdam FigShare (https://doi.org/10.21942/uva.12280316.v2). All the measurements used to generate the figures included in the article have been deposited on the University of Amsterdam FigShare (https://doi.org/10.21942/uva.12452444.v1).

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Author details

1. Pierre-Louis Bazin

   1. Integrative Model-based Cognitive Neuroscience research unit, University of Amsterdam, Amsterdam, Netherlands
   2. Max-Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany

   Contribution

   Conceptualization, Software, Formal analysis, Validation, Investigation, Visualization, Methodology, Writing - original draft

   For correspondence

   pilou.bazin@uva.nl

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-0141-5510

2. Anneke Alkemade

   Integrative Model-based Cognitive Neuroscience research unit, University of Amsterdam, Amsterdam, Netherlands

   Contribution

   Data curation, Formal analysis, Validation, Investigation, Methodology, Writing - review and editing

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-3234-353X

3. Martijn J Mulder

   1. Integrative Model-based Cognitive Neuroscience research unit, University of Amsterdam, Amsterdam, Netherlands
   2. Psychology Department, Utrecht University, Utrecht, Netherlands

   Contribution

   Resources, Data curation, Software, Methodology, Writing - review and editing

   Competing interests

   No competing interests declared

4. Amanda G Henry

   Faculty of Archaeology, Leiden University, Leiden, Netherlands

   Contribution

   Conceptualization, Methodology, Writing - review and editing

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-2923-4199

5. Birte U Forstmann

   Integrative Model-based Cognitive Neuroscience research unit, University of Amsterdam, Amsterdam, Netherlands

   Contribution

   Conceptualization, Resources, Formal analysis, Supervision, Funding acquisition, Project administration, Writing - review and editing

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-1005-1675

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