Measurement of Cortical Thickness and Volume of Subcortical Structures in Multiple Sclerosis: Agreement between 2D Spin-Echo and 3D MPRAGE T1-Weighted Images

A. Vidal-Jordana; D. Pareto; J. Sastre-Garriga; C. Auger; E. Ciampi; X. Montalban; A. Rovira

doi:10.3174/ajnr.A4999

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Fig 1.
FreeSurfer and FIRST outputs from 3D-GE and 2D-SE T1-weighted images. The 2D-SE and 3D-GE T1-weighted image inputs for the same patient (A and E, respectively), the cortical parcellation and subcortical segmentation obtained with FreeSurfer for each input (B and F), and the subcortical segmentation overlaid onto the original T1-weighted images obtained with FIRST for each input (C, D, G, and H) are shown.

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Table 1:

Intraclass correlation coefficients for 2D-SE and 3D-GE cortical thickness estimates using FreeSurfer^{^a}

Structure	ICC	Structure	ICC
None	≥0.81	L supramarginal	0.395
R superior temporal	0.663	R parahippocampal	0.393
R temporal pole	0.605	L inferior parietal	0.391
L superior temporal	0.59	L superior frontal	0.363
R inferior temporal	0.589	R lateral orbitofrontal	0.35
R superior parietal	0.58	R postcentral	0.343
L superior parietal	0.54	R isthmus cingulate	0.342
L inferior temporal	0.519	L precuneus	0.334
L fusiform	0.512	L precentral	0.329
R rostral middle frontal	0.508	R insula	0.328
R inferior parietal	0.503	L temporal pole	0.327
L lingual	0.501	L isthmus cingulate	0.325
L pars orbitalis	0.489	R entorhinal	0.324
R frontal pole	0.483	L parahippocampal	0.322
L middle temporal	0.481	R lateral occipital	0.319
R mean thickness	0.479	L transverse temporal	0.305
L caudal middle frontal	0.476	L lateral occipital	0.299
L pars triangularis	0.473	L entorhinal	0.293
L pars opercularis	0.465	R posterior cingulate	0.281
R pars opercularis	0.465	R caudal anterior cingulate	0.274
R caudal middle frontal	0.462	L pericalcarine	0.265
R fusiform	0.46	L posterior cingulate	0.251
R middle temporal	0.442	R medial orbitofrontal	0.248
R precuneus	0.439	L bankssts	0.223
L mean thickness	0.438	R pericalcarine	0.199
L rostral middle frontal	0.431	L paracentral	0.179
R supramarginal	0.431	L frontal pole	0.177
R pars orbitalis	0.429	R lingual	0.16
R precentral	0.428	R paracentral	0.159
L lateral orbitofrontal	0.418	R rostral anterior cingulate	0.156
L cuneus	0.409	L insula	0.128
R superior frontal	0.405	L rostral anterior cingulate	0.12
R pars triangularis	0.402	L medial orbitofrontal	0.103
L postcentral	0.401	R transverse temporal	0.04
R bankssts	0.399	L caudal anterior cingulate	0.016
R cuneus	0.399

Note:—L indicates left; R, right; bankssts, banks of the superior temporal sulcus.
↵a ICCs for 2D-SE and 3D-GE cortical thickness estimates using FreeSurfer are shown. The ICC values are grouped in 5 categories. Zero percent of the structures had almost perfect agreement, 1.4% had substantial agreement, 40% had a moderate agreement, 42.9% had fair agreement, and 15.7% had slight agreement.

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Table 2:

Intraclass correlation coefficients for 2D-SE and 3D-GE subcortical volume estimates using FreeSurfer and FIRST^{^a}

FreeSurfer Software		FIRST Software
Structure	ICC	Structure	ICC
Estimated TIV	0.942	R caudate	0.914
Subcortical gray volume	0.93	L caudate	0.899
R thalamus	0.903	L hippocampus	0.864
Brain stem	0.865	R thalamus	0.85
L putamen	0.861	L putamen	0.826
L caudate	0.833	R putamen	0.815
R putamen	0.82	R hippocampus	0.814
L ventral diencephalon	0.801	Brain stem	0.784
R ventral diencephalon	0.765	L pallidum	0.781
R pallidum	0.762	L thalamus	0.773
R caudate	0.743	R pallidum	0.605
L thalamus	0.737	R amygdala	0.456
L pallidum	0.71	L amygdala	0.406
R accumbens	0.694	L accumbens	0.25
R hippocampus	0.654	TIV^{^b}	0.175
R cerebellum cortex	0.616	R accumbens	0.009
L cerebellum cortex	0.579
L hippocampus	0.568
L accumbens	0.511
R amygdala	0.397
L amygdala	0.321

Note:—L indicates left; R, right.
↵a The ICCs for 2D-SE and 3D-GE subcortical volume estimates using FreeSurfer and FIRST are shown. The ICC values are grouped in 5 categories: 33.3% and 43.8% of the structures with an almost perfect agreement using FreeSurfer and FIRST respectively, 42.9% and 25% of the structures with a substantial agreement using FreeSurfer and FIRST respectively, 14.3% and 12.5% of the structures with a moderate agreement using FreeSurfer and FIRST respectively, 9.5% and 6.25% of the structures with a fair agreement using FreeSurfer and FIRST respectively, and 0% and 12.5% of the structures with a slight agreement using FreeSurfer and FIRST respectively.
↵b FIRST total intracranial volume was calculated with the following formula: (FIRST template volume/matrix determinant) × 1000.

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Table 3:

Clinicoradiologic correlation using 3D-GE and 2D-SE normalized subcortical structure values obtained with FreeSurfer software

Subcortical Structure	FreeSurfer 3D-GE				FreeSurfer 2D-SE
	Disease Duration		EDSS		Disease Duration		EDSS
	r	P	ρ	P	r	P	ρ	P
Brain stem	−0.258	.123	−0.408^{^a}	.012^{^a}	−0.143	.400	−0.545^{^a}	<.001^{^a}
L thalamus	−0.249	.137	−0.268	.109	−0.301	.070	−0.313^{^b}	.059^{^b}
L caudate	−0.304^{^b}	.068^{^b}	−0.285^{^b}	.088^{^b}	−0.316^{^b}	.057^{^b}	−0.283	.090
L putamen	−0.443^{^a}	.006^{^a}	−0.494^{^a}	.002^{^a}	−0.466^{^a}	.004^{^a}	−0.510^{^a}	.001^{^a}
L pallidum	−0.489^{^a}	.002^{^a}	−0.409^{^a}	.012^{^a}	−0.315^{^b}	.057^{^b}	−0.404^{^a}	.013^{^a}
L hippocampus	−0.191	.256	−0.122	.472	−0.144	.397	−0.085	.615
L amygdala	−0.083	.627	−0.335^{^a}	.043^{^a}	0.001	.997	−0.141	.404
L accumbens	−0.332^{^a}	.045^{^a}	−0.418^{^a}	.010^{^a}	−0.358^{^a}	.030^{^a}	−0.096	.571
R thalamus	−0.409^{^a}	.012^{^a}	−0.402^{^a}	.014^{^a}	−0.386^{^a}	.018^{^a}	−0.376^{^a}	.022^{^a}
R caudate	−0.455^{^a}	.005^{^a}	−0.365^{^a}	.02^{^a}	−0.29^{^b}	.074^{^b}	−0.230	.171
R putamen	−0.505^{^a}	.001^{^a}	−0.490^{^a}	.002^{^a}	−0.472^{^a}	.003^{^a}	−0.494^{^a}	.002^{^a}
R pallidum	−0.459^{^a}	.004^{^a}	−0.395^{^a}	.016^{^a}	−0.220	.192	−0.28^{^b}	.093^{^b}
R hippocampus	−0.262	.118	−0.302^{^b}	.069^{^b}	−0.238	.157	−0.220	.190
R amygdala	−0.181	.285	−0.294^{^b}	.077^{^b}	−0.183	.279	−0.323^{^b}	.051^{^b}
R accumbens	−0.330^{^a}	.046^{^a}	−0.416^{^a}	.011^{^a}	−0.215	.202	−0.216	.199

Note:—r indicates the Pearson correlation coefficient; ρ, the Spearman correlation coefficient; L, left; R, right.
↵a Significant correlations.
↵b Trend toward a significant correlation.

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Table 4:

Clinicoradiologic correlation using 3D-GE and 2D-SE normalized subcortical structure values obtained with FIRST software

Subcortical Structure	FIRST 3D-GE				FIRST 2D-SE
	Disease Duration		EDSS		Disease Duration		EDSS
	r	P	ρ	P	r	P	ρ	P
Brain stem	−0.133	.433	−0.160	.345	0.079	.674	−0.150	.420
L thalamus	−0.424^{^a}	.009^{^a}	−0.226	.170	0.053	.777	0.080	.671
L caudate	−0.410^{^a}	.012^{^a}	−0.302^{^b}	.069^{^b}	−0.297	.105	−0.065	.728
L putamen	−0.383^{^a}	.019^{^a}	−0.364^{^a}	.027^{^a}	−0.056	.767	−0.262	.154
L pallidum	−0.308^{^b}	.063^{^b}	−0.430^{^a}	.008^{^a}	−0.073	.696	−0.002	.991
L hippocampus	−0.429^{^a}	.008^{^a}	−0.170	.313	−0.226	.222	−0.083	.658
L amygdala	−0.276^{^b}	.098^{^b}	−0.029	.864	0.195	.294	0.230	.213
L accumbens	−0.234	.164	−0.30^{^b}	.071^{^b}	0.384^{^a}	.033^{^a}	0.023	.901
R thalamus	−0.496^{^a}	.002^{^a}	−0.235	.162	−0.022	.905	−0.092	.621
R caudate	−0.501^{^a}	.002^{^a}	−0.270^{^a}	.106^{^a}	−0.419^{^a}	.019^{^a}	−0.188	.310
R putamen	−0.406^{^a}	.013^{^a}	−0.454^{^a}	.005^{^a}	−0.043	.817	−0.286	.119
R pallidum	−0.288^{^b}	.08^{^b}	−0.36^{^b}	.029^{^b}	−0.005	.980	0.013	.945
R hippocampus	−0.384^{^a}	.019^{^a}	−0.002	.988	−0.082	.662	−0.064	.731
R amygdala	−0.253	.131	0.046	.785	0.027	.887	0.331	.069
R accumbens	−0.316^{^b}	.057^{^b}	−0.322	.052	0.233	.208	−0.014	.941

Note:—L indicates left; R, right; r, the Pearson correlation coefficient; ρ, the Spearman correlation coefficient.
↵a Significant correlations.
↵b Trend toward a significant correlation.