Table 2.

A
Summary of segmentation evaluation for select structures: brain rest, hippocampus (Hc), caudate putamen (CPu), substantia nigra (SN), anterior commissure (ac), corpus callosum (cc), lateral ventricles (LV). Data represent mean Dice coefficients±SEM. Minimum and maximum values are shown in bold characters.
Channel selection impacted the accuracy of segmentation.
C57BL/6	T1 (%)	T2* (%)	T1T2* (%)	T1Tr (%)	T1FA (%)	T1RA (%)	T2*FA (%)	T2*RA (%)	T2*Tr (%)	T1RD (%)	T2*RD (%)	T1E0 (%)	T2*E0(%)	F(12,39)	p
Brain rest	95.47±0.58	94.94±0.64	95.84±0.21	96.57±0.21	96.41±0.67	97.24±0.03	97.01±0.17	97.18±0.04	96.16±0.17	96.76±0.23	96.34±0.25	96.76±0.12	96.51±0.21	3.79	7.62E−04
Hc	84.37±0.71	84.14±2.62	83.43±2.40	87.29±1.51	88.67±1.62	90.64±0.50	90.53±0.77	90.75±0.71	87.85±1.19	89.62±1.67	88.69±1.46	89.29±0.83	89.75±0.91	3.13	0.0034
CPu	82.08±0.26	82.47±2.03	77.21±1.37	85.02±1.75	87.18±1.59	88.68±0.35	87.75±0.66	88.30±0.50	81.34±1.68	87.22±1.15	84.11±1.35	87.21±1.56	84.69±1.66	4.88	7.58E−05
SN	77.69±4.78	71.01±4.64	72.58±5.55	80.21±1.44	77.01±3.73	79.12±4.84	78.55±2.93	77.00±4.14	79.66±1.45	80.74±1.37	78.36±2.00	78.88±2.50	77.73±2.69	0.64	0.7945
ac	51.02±9.29	28.52±10.95	18.43±10.48	56.20±5.01	69.24±4.63	73.31±2.81	65.21±5.47	73.83±2.21	52.30±3.04	63.60±1.89	59.48±2.81	61.05±1.56	56.56±1.66	7.99	2.98E−07
cc	54.74±4.43	54.10±3.64	51.67±2.11	54.07±5.13	67.87±6.68	70.28±2.40	70.10±1.19	71.33±1.28	45.21±4.16	64.66±7.34	55.72±7.94	62.34±3.76	55.50±6.10	3.04	0.0042
LV	30.49±8.21	44.09±3.24	32.38±7.84	56.41±6.60	57.89±5.29	61.42±5.90	59.72±2.18	61.80±1.29	27.46±4.55	62.33±6.83	43.32±7.12	67.60±4.19	50.26±7.07	5.46	2.39E−05

B
Multichannel segmentation of C57BL/6mice incorporating DTI outperformed single channel segmentation using conventional contrast.
Factor 1	Factor 2	Diff (%)	CI1	CI2	p
Hc
T2*RA	T1T2*	7.32	0.11	14.53	0.04*
T1RA	T1T2*	7.21	0.00	14.42	0.05
T2*FA	T1T2*	7.10	−0.11	14.31	0.06
T2*RA	T2*	6.61	−0.60	13.82	0.10
T2*RA	T1	6.37	−0.84	13.58	0.13
CPu
T1RA	T1T2*	11.48	3.82	19.13	0.0003*
T2*RA	T1T2*	11.09	3.44	18.74	0.0006*
T2*FA	T1T2*	10.55	2.89	18.20	0.0012*
T1RD	T1T2*	10.01	2.36	17.66	0.003*
T1E0	T1T2*	10.00	2.35	17.65	0.003*
T1FA	T1T2*	9.97	2.32	17.63	0.003*
T2*RD	T1T2*	9.26	1.61	16.91	0.01*
T1Tr	T1T2*	7.81	0.16	15.46	0.04*
T2*E0	T1T2*	7.48	−0.17	15.13	0.06
T1RA	T2*Tr	7.35	−0.30	15.00	0.07
T2*RA	T2*Tr	6.96	−0.69	14.61	0.11
LV
T1E0	T2*Tr	40.14	11.22	69.06	0.001*
T1E0	T1	37.11	8.19	66.03	0.003*
T1E0	T1T2*	35.22	6.30	64.14	0.006*
T1RD	T2*Tr	34.87	5.95	63.79	0.007*
T2*RA	T2*Tr	34.34	5.42	63.26	0.01*
T1RA	T2*Tr	33.96	5.04	62.88	0.01*
T2*FA	T2*Tr	32.26	3.34	61.18	0.02*
T1RD	T1	31.84	2.92	60.76	0.02*
T2*RA	T1	31.31	2.39	60.23	0.02*
T1RA	T1	30.93	2.01	59.85	0.03*
T1FA	T2*Tr	30.43	1.51	59.35	0.03*
T1RD	T1T2*	29.96	1.03	58.88	0.04*
T2*RA	T1T2*	29.42	0.50	58.34	0.04*
T2*FA	T1	29.23	0.31	58.15	0.046*
T1RA	T1T2*	29.04	0.12	57.96	0.048*
T1Tr	T2*Tr	28.95	0.03	57.87	0.05
T1FA	T1	27.40	−1.52	56.32	0.08
T2*FA	T1T2*	27.34	−1.58	56.26	0.08
ac
T2*RA	T1T2*	55.40	26.70	84.10	<.0001*
T1RA	T1T2*	54.88	26.18	83.59	<.0001*
T1FA	T1T2*	50.81	22.11	79.51	<.0001*
T2*FA	T1T2*	46.78	18.08	75.49	<.0001*
T2*RA	T2*	45.31	16.61	74.01	0.0001*
T1RD	T1T2*	45.17	16.47	73.87	0.0001*
T1RA	T2*	44.79	16.09	73.49	0.0002*
T1E0	T1T2*	42.62	13.92	71.32	0.0004*
T2*RD	T1T2*	41.05	12.35	69.75	0.001*
T1FA	T2*	40.72	12.02	69.42	0.001*
T2*E0	T1T2*	38.13	9.43	66.83	0.002*
T1Tr	T1T2*	37.77	9.07	66.47	0.002*
T2*FA	T2*	36.69	7.99	65.40	0.004*
T1RD	T2*	35.08	6.37	63.78	0.006*
T2*Tr	T1T2*	33.87	5.17	62.58	0.009*
T1	T1T2*	32.59	3.88	61.29	0.01*
T1E0	T2*	32.53	3.82	61.23	0.01*
T2*RD	T2*	30.96	2.25	59.66	0.02*
T2*E0	T2*	28.04	−0.66	56.74	0.06
T1Tr	T2*	27.68	−1.03	56.38	0.07
cc
T2*RA	T2*Tr	26.13	2.08	50.17	0.02*
T1RA	T2*Tr	25.08	1.03	49.12	0.03*
T2*FA	T2*Tr	24.90	0.85	48.94	0.04*
T1FA	T2*Tr	22.66	−1.39	46.71	0.08
Brain rest
T1RA	T2*	2.30	0.60	4.01	0.002*
T2*RA	T2*	2.24	0.53	3.95	0.003*
T2*FA	T2*	2.07	0.36	3.78	0.01*
T1E0	T2*	1.82	0.11	3.53	0.03*
T1RD	T2*	1.82	0.11	3.53	0.03*
T1RA	T1	1.77	0.06	3.48	0.04*
T2*RA	T1	1.70	−0.01	3.41	0.05
T1Tr	T2*	1.63	−0.08	3.34	0.08
T2*E0	T2*	1.57	−0.14	3.28	0.10

C
Multichannel segmentation in test strains showed that T1 and T1T2w combinations have similar performance, and outperformed T2w in segmenting the cc (T1 vs T2w: CI [4.7 81.9]; T2w vs T1T2w: CI [−81.6 −4.3]) and VS (T1 vs T2w: CI [4.7 85.8]; T2w vs T1T2w: CI [−83.8 −2.7]).
	T1 (%)	T2(%)	T1T2w (%)	F	P
Brain rest	90.60±1.07	89.92±1.14	90.76±1.03	0.02	0.98
Hc	79.95±2.27	72.02±3.18	80.04±2.42	0.07	0.93
CPu	83.08±1.41	79.07±1.03	83.82±1.45	0.18	0.84
SN	48.63±5.11	53.69±3.88	54.70±5.00	0.04	0.96
ac	39.14±3.97	29.28±4.25	39.74±3.35	0.64	0.54
cc	53.67±3.32	39.14±2.88	53.57±3.36	5.29	0.01*
VS	46.42±2.41	31.75±3.54	44.07±3.01	5.05	0.02*

D
For C57BL/6 miceMRF classification following deformable registration (Diff), using T2* and RA images outperformed Diff only (using T2* and RA images), and differences were significant in 5 out of 8 structures labeled.
C57BL/6	Diff(%)	MRF(%)	Difference (%)	t	CI1	CI2	p
Brain rest	95.97±0.70	95.13±0.63	−0.84	−0.89	−2.94	1.26	0.39
Hc	91.39±0.39	93.61±0.28	2.22	4.65	1.16	3.29	0.001*
CPu	88.82±0.60	92.02±0.54	3.2	3.99	1.41	4.99	0.003*
SN	72.56±2.35	80.86±1.12	8.3	3.18	2.49	14.11	0.01*
ac	74.90±3.18	77.59±5.17	2.69	0.44	−10.83	16.21	0.67
cc	73.47±1.86	79.96±1.75	6.49	2.54	0.8	12.18	0.03*
LV	62.65±3.29	73.92±3.13	11.26	2.48	1.14	21.38	0.03*
V4	56.92±5.55	63.30±5.55	6.39	0.81	−11.11	23.88	0.44

E
For test strains there was a trend for MRF classification following deformable registration (Diff) to outperform Diff, with the exception of the ac, which was not reliably segmented.
Test strains	Diff (%)	MRF (%)	Difference (%)	t	CI1	CI2	p
Brain rest	90.76±0.42	90.12±0.30	−0.64	1.24	−1.57	2.85	0.34
Hc	80.04±1.88	87.37±1.91	7.32	−2.74	−18.84	4.19	0.11
CPu	83.82±1.15	86.23±4.61	2.41	−0.51	−22.87	18.05	0.66
SN	54.70±4.74	66.62±3.64	11.92	−1.99	−37.64	13.80	0.18
ac	39.74±1.98	16.83±1.69	−22.90	8.79	11.69	34.11	0.01
cc	53.57±6.51	59.81±6.77	6.24	−0.66	−46.64	34.16	0.57
VS	44.07±7.15	53.08±16.12	9.01	−0.51	−84.87	66.85	0.66

^*indicates significance at a p<0.05 level