Figures and data in Multi-contrast anatomical subcortical structures parcellation

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Tables
Additional files

11 figures, 4 tables and 1 additional file

Figures

Figure 1

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The 17 subcortical structures currently included in the parcellation algorithm in axial (A), sagittal (B), and coronal (C) views.

Figure 2

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The MASSP parcellation pipeline.

Atlas priors for interfaces between structures are combined to the MRI data, regularized via probability diffusion and topology correction, and the final structure posteriors are jointly estimated by region growing.

Figure 3

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Leave-one-out validation of the structures parcellated by MASSP, compared to the human rater with most neuroanatomical expertise.

Scores for the left and right side are computed separately and then combined into box-and-whisker plots.

Figure 4

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Inter-rater variability for the human expert raters.

Scores for the left and right side are computed separately and then combined into box-and-whisker plots.

Figure 5

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Parcellation with Freesurfer (top, on T1w image) and MASSP (bottom, on T2w image) on Human Connectome Project data.

MASSP priors were not derived from the contrasts, but transferred via a spatial mapping of the quantitative MRI intensities from AHEAD subjects.

Figure 6

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MASSP parcellation scores as a function of increasing number of subjects included in the atlas.

Scores for the left and right side are computed separately and then combined into box-and-whisker plots.

Figure 7

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MASSP parcellation scores over the lifespan.

Each matrix show the average Dice overlap (top), dilated Dice overlap (middle), and average surface distance (bottom) for using one age group as prior (’train’) to parcellate another age group (’test’).

Figure 8

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Regression of volume (log scale), structure thickness, R1, R2*, and QSM MRI parameters estimated using manual delineations versus MASSP automated parcellations.

Circles show individual data points, linear regression is indicated by a straight line, and 95% confidence interval is given as the shaded area. Pearson correlation coefficients are indicated when significant (p-value<0.01).

Figure 9

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MP2RAGEME maps and delineations: quantitative R1 (left), quantitative R2* (middle), QSM (right).

Manual delineations for the 17 structures of interest are overlaid on all images.

Figure 10

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Anatomical interface (A) and skeleton (B) priors derived from the 10 manually delineated subjects.

Figure 11

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Successive parcellation results: (A) voxel-wise posteriors and parcellation, (B) diffused posteriors and parcellation, (C) topology-corrected posteriors and final region-growing parcellation.

Tables

Table 1

Mean overlap and distance measures for the leave-one-out validation.

	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

Table 2

Comparison with multi-atlas registration, Freesurfer, and FSL FIRST.

	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
Multi-atlas	0.855	0.662	0.760	0.820	0.742	0.796	0.859	0.734	0.660	0.691	0.761	0.718	0.626	0.478	0.674	0.539	0.398
Freesurfer	0.876				0.778		0.838	0.858	0.430	0.769	0.692
FSL FIRST	0.875				0.813		0.839				0.653
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
Multi-atlas	0.976	0.938	0.968	0.989	0.947	0.968	0.970	0.920	0.920	0.908	0.921	0.939	0.924	0.798	0.943	0.871	0.811
Freesurfer	0.975				0.922		0.946	0.974	0.562	0.911	0.857
FSL FIRST	0.976				0.946		0.950				0.843
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
Multi-atlas	0.961	0.891	0.858	0.675	0.992	0.882	1.083	1.417	0.932	1.249	1.359	1.129	0.813	1.362	0.794	1.055	1.273
Freesurfer	0.770				1.211		1.405	0.685	4.071	1.361	1.749
FSL FIRST	0.867				1.143		1.675				1.746
Volume bias
MASSP	0.041	0.017	-0.038	0.007	0.066	0.089	0.040	0.0470	0.121	0.047	0.078	0.183	0.032	-0.016	0.026	0.009	0.023
Multi-atlas	0.020	-0.087	-0.009	0.031	0.009	0.014	0.020	-0.003	-0.007	-0.092	-0.038	0.055	-0.067	-0.264	-0.090	-0.269	-0.376
Freesurfer	0.017				0.087		0.163	0.122	-0.551	0.351	0.468
FSL FIRST	-0.100				-0.021		0.165				-0.249

Table 3

Test-retest comparison with Freesurfer on Human Connectome Project data.

	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

Table 4

Mean volume and quantitative MRI values for each age group.

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 ( $m m$ )
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 ( $H z$ )
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* ( $H z$ )
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 ( $p p m$ )
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

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Transparent reporting form: https://cdn.elifesciences.org/articles/59430/elife-59430-transrepform-v2.docx
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Pierre-Louis Bazin
Anneke Alkemade
Martijn J Mulder
Amanda G Henry
Birte U Forstmann

(2020)

Multi-contrast anatomical subcortical structures parcellation

eLife 9:e59430.

https://doi.org/10.7554/eLife.59430

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The 17 subcortical structures currently included in the parcellation algorithm in axial (A), sagittal (B), and coronal (C) views.

The MASSP parcellation pipeline.

Leave-one-out validation of the structures parcellated by MASSP, compared to the human rater with most neuroanatomical expertise.

Inter-rater variability for the human expert raters.

Parcellation with Freesurfer (top, on T1w image) and MASSP (bottom, on T2w image) on Human Connectome Project data.

MASSP parcellation scores as a function of increasing number of subjects included in the atlas.

MASSP parcellation scores over the lifespan.

Regression of volume (log scale), structure thickness, R1, R2*, and QSM MRI parameters estimated using manual delineations versus MASSP automated parcellations.

MP2RAGEME maps and delineations: quantitative R1 (left), quantitative R2* (middle), QSM (right).

Anatomical interface (A) and skeleton (B) priors derived from the 10 manually delineated subjects.

Successive parcellation results: (A) voxel-wise posteriors and parcellation, (B) diffused posteriors and parcellation, (C) topology-corrected posteriors and final region-growing parcellation.

Mean overlap and distance measures for the leave-one-out validation.

Comparison with multi-atlas registration, Freesurfer, and FSL FIRST.

Test-retest comparison with Freesurfer on Human Connectome Project data.

Mean volume and quantitative MRI values for each age group.

Transparent reporting form

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)