index.md

Number	Formatted reference	Reference	Species	Pathology	Tissue structure	Post-mortem time	Regions / tissue types of interest	ROI definition	MRI modality	MRI metrics	T	Resolution (in mm)	Tissue state	Temperature	Tissue preparation histology	Slice thickness	Myelin histology	Iron	Axons	Histology metric	Correlation	Coregistration	N Subjects per group	N Total subjects	N ROIs	Variance/Statistical Design	Correlation Method	Result	Linear equation	included in MA	qualifies for MA
1	Abe, Y., Komaki, Y., Seki, F., Shibata, S., Okano, H., & Tanaka, K. F. (2019). Correlative study using structural MRI and super-resolution microscopy to detect structural alterations induced by long-term optogenetic stimulation of striatal medium spiny neurons. Neurochemistry International, 125(2018), 163–174.	Abe2019	Mouse	MSN-ChR2 mice	Whole brain	NA	dGM, CT	manual	DWI	AD, FA, RD	7	0.125 x 0.125 x 0.125 mm	perfusion fixed	not reported	cryosectioning	25 µm	PLP	-	+	staining fraction	ROI to ROI	No coregistration	8	8	96 (in total across subjects)	Mixed (not modelled)	Pearson	FA: r = .32 (p = .012), RD: r= -.41 (p = .001), AD: r = -.11 (p = .39)	NA	-	- (statistical design)
2	Aojula, A., Botfield, H., Patterson, J., Ii, M., Gonzalez, A. M., Abdullah, O., … Sinclair, A. (2016). Diffusion tensor imaging with direct cytopathological validation: characterisation of decorin treatment in experimental juvenile communicating hydrocephalus. Fluids and Barriers of the CNS, 13(9).	Aojula2016	Rat	Kaolin-induced hydocephalus and Controls	Whole brain	NA	CC and PVWM	manual for histology, coordinate-based for MRI	DWI	AD, FA, MD, RD	7	0.195 x 0.195 x 1mm	in vivo	body temperature	perfusion fixation, cryosectioning	15 µm	MBP	-	-	staining fraction	ROI to ROI	No coregistration	4 kaolin-only, 6 kaolin + PBS (control intervention), 5 kaolin + decorin, 4 controls,	19	2	Between-subject	Spearman	AD: r = .159, p = .541 (CC); r = -.360, p = 0.155 (PVWM); FA: r = .091, p = .729 (CC); r = .346, p = .174 (PVWM); MD: r = -.031, p = .903 (CC); r = -.495, p = .043 (PVWM); RD: r = -.115, p = .66 (CC); r = -.458, p = .064 (PVWM)	NA	+	BS Pearson
3	Argyridis, I., Li, W., Johnson, G. A., & Liu, C. (2014). Quantitative magnetic susceptibility of the developing mouse brain reveals microstructural changes in the white matter. NeuroImage, 88, 134–142.	Argyridis2014	Mouse	Different neonatal stages	Whole brain	NA	EC	manual	QSM	Susceptibility	9.4	0.06 mm isotropic	perfusion fixed	not reported	not reported	2 µm	LFB	+	-	contrasted and normalised luminance	ROI to ROI	Not reported	18	18	3 (pooled into 1 weighted measure)	Between-subject	Not reported (likely linear regression)	susceptibility: R2 = .93, p = .004	Susceptibility = -0.14 * myelin + 0.14	+	BS Pearson
3	Argyridis, I., Li, W., Johnson, G. A., & Liu, C. (2014). Quantitative magnetic susceptibility of the developing mouse brain reveals microstructural changes in the white matter. NeuroImage, 88, 134–142.	Argyridis2014	Mouse	Different neonatal stages	Whole brain	NA	EC	manual	DWI	MD	9.4	unclear	perfusion fixed	not reported	not reported	2 µm	LFB	+	-	contrasted and normalised luminance	ROI to ROI	Not reported	18	18	3 (pooled into 1 weighted measure)	Between-subject	Not reported (likely linear regression)	MD: R2 = .003, p = .46	MD = -0.09 * myelin + 0.69	+	BS Pearson
4	Bagnato, F., Hametner, S., Boyd, E., Endmayr, V., Shi, Y., Ikonomidou, V., … Welch, E. B. (2018). Untangling the R2* contrast in multiple sclerosis: A combined MRI-histology study at 7.0 Tesla. PLoS ONE, 13(3), e0193839.	Bagnato2018	Human	MS	1 cm coronal slices	4-83 hours	NAWM, DWMI, WM-Ls, thalamus, dGM, normal cortex	manual	Relaxometry	R2*	7	0.7 mm isotropic	fixed	room temperature	not reported	10 µm	LFB and PLP	+	-	staining intensity	ROI to ROI	No coregistration	7	7	429 (in total across subjects)	Within-subject (mixed, modelled)	Pearson; linear regression	R2* and LFB: r = -.09, p < .01 (NAWM); r = -.05, p < .01 (DWMI); r = .99, p<.01 (WM-Ls); r = .83, p < .01 (thalamus); r = .82, p < .01 (dGM); shadow plaques: not significant; R2=0.014 (all ROIs combined); R2* and PLP: only CT reported, r = 0.57 p < .01	R2* = 0.02 * myelin	-	WS Pearson
5	Beckmann, N., Giorgetti, E., Neuhaus, A., Zurbruegg, S., Accart, N., Smith, P., … Shimshek, D. R. (2018). Brain region-specific enhancement of remyelination and prevention of demyelination by the CSF1R kinase inhibitor BLZ945. Acta Neuropathologica Communications, 6(1), 9.	Beckmann2018	Mouse	Cuprizone	Whole brain	NA	CC, EC (within same ROI)	not reported	MT	MTR	7	0.094 × 0.094 x 0.5 mm	in vivo	body temperature	paraffin embedding	3 µm	LFB	-	-	staining intensity	ROI to ROI	Not reported	5	20	1	Between-subject	Pearson	MTR: R2 = .7669 (p < .0001)	NA	+	BS Pearson
6	Bot, J. C. J., Blezer, E. L. A., Kamphorst, W., Lycklama, G. J., Ader, H. J., Castelijns, J. A., & Ig, K. N. (2004). The spinal cord in multiple sclerosis: relationship of high-spatial-resolution quantitative MR imaging findings to histopathologic results. Neuroradiology, 233, 531–540.	Bot2004	Human	MS and Controls	Cervical spinal cord	8.2±1.7 hours	WM-Ls, NAWM, WM	manual	Relaxometry	T1, T2	4.7	0.007 x 0.007 x 1 mm	fixed	not reported	not reported	5 µm	LFB	-	+	normalised staining intensity	ROI to ROI	No coregistration	11 MS, 2 controls	13	222 (in total across subjects)	Mixed (unclear)	Spearman; linear regression	T1: r = .71 (p < .001); T2: r = .77 (p < .001)	See paper	-	- (statistical design)
6	Bot, J. C. J., Blezer, E. L. A., Kamphorst, W., Lycklama, G. J., Ader, H. J., Castelijns, J. A., & Ig, K. N. (2004). The spinal cord in multiple sclerosis: relationship of high-spatial-resolution quantitative MR imaging findings to histopathologic results. Neuroradiology, 233, 531–540.	Bot2004	Human	MS and Controls	Cervical spinal cord	8.2±1.7 hours	WM-Ls, NAWM, WM	manual	MT	MTR	4.7	0.007 x 0.007 x 1 mm	fixed	not reported	not reported	5 µm	LFB	-	+	normalised staining intensity	ROI to ROI	No coregistration	11 MS, 2 controls	13	222 (in total across subjects)	Mixed (unclear)	Spearman; linear regression	MTR: r = -.76, p < .001	See paper	-	- (statistical design)
7	Chandran, P., Upadhyay, J., Markosyan, S., Lisowski, A., Buck, W., Chin, C. L., … Day, M. (2012). Magnetic resonance imaging and histological evidence for the blockade of cuprizone-induced demyelination in C57BL/6 mice. Neuroscience, 202, 446–453.	Chandran2012	Mouse	Cuprizone	Whole brain	NA	WM	atlas-based	DWI	FA, RD	7	0.2 x 0.2 x 1 mm	in vivo	body temperature	paraffin embedding	5 µm	LFB, MBP	-	-	staining intensity	ROI to ROI	Not reported	5 to 6 per group	20	1	Between-subject	Linear regression	FA: R2 = .27, p = .016 (LFB), R2 = .50, p = .0003 (MBP); RD: R2 = .34, p = .005 (MBP), R2=0.05; p = .31 (LFB)	not reported	+	BS Pearson
8	Chang, E. H., Argyelan, M., Aggarwal, M., Chandon, T. S. S., Karlsgodt, K. H., Mori, S., & Malhotra, A. K. (2017). The role of myelination in measures of white matter integrity: Combination of diffusion tensor imaging and two-photon microscopy of CLARITY intact brains. NeuroImage, 147, 119–124.	Chang2017	Mouse	Controls	Whole brain	NA	Various WM tracts	manual	DWI	FA, AD, RD	11.7	0.1 mm isotropic	perfusion fixed	28°C	CLARITY	3D	MBP	-	-	staining intensity	ROI to ROI	Linear registration (12 dof affine)	4	4	14 (in total across subjects)	Mixed (not modelled)	Spearman; linear regression	AD: p = .61; FA: p < .01; RD: p = .83	Not reported	-	- (statistical design)
9	Chang, E. H., Argyelan, M., Aggarwal, M., Chandon, T. S. S., Karlsgodt, K. H., Mori, S., & Malhotra, A. K. (2017). The role of myelination in measures of white matter integrity: Combination of diffusion tensor imaging and two-photon microscopy of CLARITY intact brains. NeuroImage, 147, 119–124.	Chang2017a	Mouse	Thy1-eYFP-H mice and Controls	Whole brain	NA	Various WM tracts	manual	DWI	FA, AD, RD, MD	11.7	0.1 mm isotropic	perfusion fixed	28°C	CLARITY	3D	MBP	-	-	normalised staining intensity	ROI to ROI	Unclear	4	4	14 (in total across subjects)	Mixed (not modelled)	Spearman	AD: r = .0385; FA: r = .446, p <.05; MD: r = -.114; RD: r = -.195	NA	-	- (statistical design)
10	Chen, H. S. M., Holmes, N., Liu, J., Tetzlaff, W., & Kozlowski, P. (2017). Validating myelin water imaging with transmission electron microscopy in a rat spinal cord injury model. NeuroImage, 153, 122–130.	Chen2017	Rat	SCI	3 mm spinal cord sections	NA	Fasciculus gracilis	manual	Relaxometry	MWF	7	0.07 x 0.07 x 05 mm	perfusion fixed	not reported	ultrasectioning	1 µm	EM	-	+	staining fraction	ROI to ROI	NA	3 to 6 per group	14	1	Between-subject	not reported	MWF: r = .823, p < .001	NA	-	- (statistical measure)
11	Choi, J., Dickson, P., Calabrese, E., Chen, S., White, L., Ellingwood, M., & Provenzale, J. M. (2015). Predicting degree of myelination based on diffusion tensor imagining of canines with mucopolysaccharidosis type I. The Neuroradiology Journal, 28(6), 562–573.	Choi2015	Dog	MPS type 1 and Control	Whole brain	NA	ROIs across the brain, including WM and GM	manual	DWI	FA, RD	7	0.1 mm isotropic	fixed	not reported	cryosectioning	50 µm	Gold chloride	-	+	staining intensity	ROI to ROI	Linear registration (affine, in Matlab)	2 MPS brains, 1 control	3	16	Within-subject	Correlation coefficient type not reported; Multivariate linear regression	FA: p = 1.9 × 10E-5 (control), p = .989 and p = .776 (MPS); RD: p < .0001 (control), p = .917 and p = .459 (MPS)	Not reported	-	- (statistical measure)
12	Duhamel, G., Prevost, V. H., Cayre, M., Hertanu, A., Mchinda, S., Carvalho, V. N., … Girard, O. M. (2019). Validating the sensitivity of inhomogeneous magnetization transfer (ihMT) MRI to myelin with fluorescence microscopy. NeuroImage, 199, 289–303.	Duhamel2019	Mouse	plp-GFP mice and Controls	Whole brain	NA	ROIs across the brain, including WM and GM	manual	MT	ih-MTR	11.75	0.3125 x 0.3125 x 1 mm	in vivo	37°C	perfusion fixation, cryosectioning	20 µm	PLP-GFP fluorescence	-	-	normalised (background) staining intensity	ROI to ROI	No coregistration	3	3	8 (7 ROIs + 1 "ROI" of relative GM/WM contrast)	Mixed (not modelled)	Pearson; linear regression	ih-MTR: between r = .93 and r = .98, p < .0001, depending on the specific sequence	See paper	-	- (statistical design)
13	Fatemi, A., Wilson, M. A., Phillips, A. W., McMahon, M. T., Zhang, J., Smith, S. A., … Johnston, M. V. (2011). In vivo magnetization transfer MRI shows dysmyelination in an ischemic mouse model of periventricular leukomalacia. Journal of Cerebral Blood Flow and Metabolism, 31(10), 2009–2018.	Fatemi2011	Mouse	Ischemic injury and control	Whole brain	NA	CC, IC, CP	manual	MT	MTR	9.4	0.083 x 0.81 x 0.8 mm	in vivo	body temperature	perfusion fixation, paraffin embedding / cryosectioning	20 µm / 40 µm	LFB, MBP	-	+	staining intensity	ROI to ROI	Not reported	29 ischemic injury, 33 controls	61	25 (in total across subjects)	Unclear (likely mixed, not modelled)	Linear regression	MTR: R2 = .695, p < .0001; correlations with LFB not reported	not reported	-	- (statistical design)
14	Fjær, S., Bø, L., Lundervold, A., Myhr, K., Pavlin, T., Torkildsen, Ø., & Wergeland, S. (2013). Deep gray matter demyelination detected by magnetization transfer ratio in the cuprizone model. PLoS ONE, 8(12), e84162.	Fjaer2013	Mouse	Cuprizone and Controls	Whole brain	NA	CC, dGM, olfactory bulb, cerebellum and CT	manual	MT	MTR	7	0.2 x 0.2 x 0.23 mm	in vivo	body temperature	fixation, paraffin embedding	7 µm	PLP	-	-	staining fraction	ROI to ROI	No coregistration	6 controls, 48 cuprizone at varying stages	54	4	Between-subject	Linear regression	MTR: R2 = .338, p < .0001 (medial CC); R2 = .426, p < .0001 (lateral CC); R2 = .208, p < .001 (dGM); R2 = .052, p = .1048 (CT)	intercept = -3.002, slope 0.004 (medial CC); intercept -2.910, slope = 0.002 (lateral CC); intercept= -1.414, slope = 0.018 (dGM); intercept = -1.273, slope = 0.347 (CT)	+	BS Pearson
15	Fjær, S., Bø, L., Myhr, K. M., Torkildsen, O., & Wergeland, S. (2015). Magnetization transfer ratio does not correlate to myelin content in the brain in the MOG-EAE mouse model. Neurochemistry International, 83–84, 28–40.	Fjaer2015	Mouse	EAE	Whole brain	NA	CC, dGM, olfactory bulb, cerebellum, CT	semi-automated	MT	MTR	7	0.2 x 0.2 x 0.23 mm	in vivo	body temperature	fixation, paraffin embedding	7 µm	LFB, PLP	+	-	manual scoring, staining fraction	ROI to ROI	Not reported	6	24	5	Between-subject	Linear regression	MTR and LFB: not reported. MTR and PLP: R2 = 0.01, p = .63 (CC), R2 = .08, p = .2 (dGM), R2 < .01, p = .97 (CT);	not reported	+	BS Pearson
16	Gareau, P. J., Rutt, B. K., Karlik, S. J., & Mitchell, J. R. (2000). Magnetization transfer and multicomponent T2 relaxation measurements with histopathologic correlation in an experimental model of MS. Journal of Magnetic Resonance Imaging, 11(6), 586–595.	Gareau2000	Guinea pig	EAE and Controls	Brain slice	NA	NAWM in CC	manual	MT	MTR	4	0.160 x 0.3 x 0.5 mm	in vivo	body temperature	not reported	5 µm	Solochrome-R-cyanine	-	-	score of estimated 'myelin pallor'	unclear (likely ROI to ROI)	No coregistration	6x4 EAE at different time points, 6 controls	24	1	Between-subject	Spearman	MTR: R2 = .45, p < .001	NA	+	BS Spearman
17	Grussu, F., Schneider, T., Tur, C., Yates, R. L., Tachrount, M., Deluca, G. C., & Wheeler-kingshott, C. A. M. G. (2017). Neurite dispersion: a new marker of multiple sclerosis spinal cord pathology? Annals of Clinical and Translational Neurology, 4(9), 663–679. https://doi.org/10.1002/acn3.445	Grussu2017	Human	MS and Controls	Upper thoraric and upper lumbar spinal cord	not reported	GM, WM, lesional vs nonlesional	manual	DWI	AD, FA, MD, RD	9.4	0.2 x 0.2 x 2 mm	fixed	35°C	paraffin embedding	10 µm	PLP	-	+	staining fraction	ROI to ROI	Landmark-based nonlinear registration	2 MS, 2 controls	4	48 (in total across subjects)	Mixed (not modelled)	Pearson; linear regression	AD: r = .75, p < .001; FA: r = .42, p = .025; MD: r = .67; p < .001; RD: r = .61; p < .001	See paper	-	- (statistical design)
18	Hakkarainen, H., Sierra, A., Mangia, S., Garwood, M., Michaeli, S., Gröhn, O., & Liimatainen, T. (2016). MRI relaxation in the presence of fictitious fields correlates with myelin content in normal rat brain. Magnetic Resonance in Medicine, 75(1), 161–168.	Hakkarainen2016	Rats	Controls	Whole brain	NA	ROIs across the brain	not reported	Relaxometry	RAFFn, T1, T2	9.4	0.156 x 0.156 x .35 mm	perfusion fixed	not reported	cryosectioning	30 µm	Gold chloride	+	-	normalised staining intensity	ROI to ROI	Not reported	5 to 6 per group	5	60 (in total across subjects)	Not reported (likely mixed, not modelled)	Pearson	T1: r =.77; T2: r = .18; TRAFF 1: r = .33; T RAFF2: r =.47; T RAFF3: r = .56; T RAFF4: r = .83; T RAFF5: r = .84 (all p < .001)	NA	-	- (statistical design)
18	Hakkarainen, H., Sierra, A., Mangia, S., Garwood, M., Michaeli, S., Gröhn, O., & Liimatainen, T. (2016). MRI relaxation in the presence of fictitious fields correlates with myelin content in normal rat brain. Magnetic Resonance in Medicine, 75(1), 161–168.	Hakkarainen2016	Rats	Controls	Whole brain	NA	ROIs across the brain	not reported	MT	MTR	9.4	0.0293 x 0.0293 x 0.7 mm	perfusion fixed	not reported	cryosectioning	30 µm	Gold chloride	+	-	normalised staining intensity	ROI to ROI	Not reported	5 to 6 per group	5	60 (in total across subjects)	Not reported (likely mixed, not modelled)	Pearson	MTR: r = .34 (p < .001)	NA	-	- (statistical design)
19	Hametner, S., Endmayr, V., Deistung, A., Palmrich, P., Prihoda, M., Haimburger, E., … Grabner, G. (2018). The influence of brain iron and myelin on magnetic susceptibility and effective transverse relaxation - A biochemical and histological validation study. NeuroImage, 179(June), 117–133.	Hametner2018	Human	Controls	Whole brain	range: 72-192 hours	WM, CT, Th, BG	manual	Relaxometry	T1, R2*	7	0.43 x 0.43 x 0.65 mm	in situ	room temperature (20 deg)	fixation, cutting, paraffin embedding	10 µm	LFB	+	-	staining intensity	ROI to ROI	No coregistration	6	6	2870 (in total across subjects) for R2*, 2809 (in total across subjects) for T1	Within-subject (mixed, modelled)	Linear regression	R2*: r = .027; T1 (log): r = -.583; for results separate for tissue class see paper	R2* = 44.7355 – 0.002942 * myelin; T1 (log) = 7.2738 – 0.001928 * myelin	-	WS Pearson
19	Hametner, S., Endmayr, V., Deistung, A., Palmrich, P., Prihoda, M., Haimburger, E., … Grabner, G. (2018). The influence of brain iron and myelin on magnetic susceptibility and effective transverse relaxation - A biochemical and histological validation study. NeuroImage, 179(June), 117–133.	Hametner2018	Human	Controls	Whole brain	range: 72-192 hours	WM, CT, Th, BG	manual	QSM	Susceptibility	7	0.43 x 0.43 x 0.65 mm	in situ	room temperature (20 deg)	fixation, cutting, paraffin embedding	10 µm	LFB	+	-	staining intensity	ROI to ROI	No coregistration	6	6	2809 (in total across subjects)	Within-subject (mixed, modelled)	Linear regression	Susceptibility: r = -.352; for results separate for tissue class see paper	Susceptibility = 0.008758 – 0.000196 * myelin	-	WS Pearson
20	Janve, V. A., Zu, Z., Yao, S. Y., Li, K., Zhang, F. L., Wilson, K. J., … Gochberg, D. F. (2013). The radial diffusivity and magnetization transfer pool size ratio are sensitive markers for demyelination in a rat model of type III multiple sclerosis (MS) lesions. NeuroImage, 74, 298–305. https://doi.org/10.1016/j.neuroimage.2013.02.034	Janve2013	Rat	LPS and control	Whole brain	NA	CC	not reported	DWI	AD, FA, RD	9.4	0.167 x 0.167 x 0.167 mm	perfusion fixed	not reported	paraffin embedding	10 µm	LFB	-	-	normalised staining intensity	ROI to ROI	Manual coregistration	8 LPS, 1 control	9	6	Mixed (not modelled)	Pearson	AD: r = .03 (lesion), r = -.08 (combined); FA: r = .16 (lesion), r = .27 (combined); RD: r = -.40 (lesion), r= -.49 (combined)	NA	-	- (statistical design)
20	Janve, V. A., Zu, Z., Yao, S. Y., Li, K., Zhang, F. L., Wilson, K. J., … Gochberg, D. F. (2013). The radial diffusivity and magnetization transfer pool size ratio are sensitive markers for demyelination in a rat model of type III multiple sclerosis (MS) lesions. NeuroImage, 74, 298–305. https://doi.org/10.1016/j.neuroimage.2013.02.034	Janve2013	Rat	LPS and control	Whole brain	NA	CC	not reported	MT	MP ('PSR')	9.4	0.167 x 0.167 x 0.167 mm	perfusion fixed	not reported	paraffin embedding	10 µm	LFB	-	-	normalised staining intensity	ROI to ROI	Manual coregistration	8 LPS, 1 control	9	6	Mixed (not modelled)	Pearson	MP: r = .87 (lesion), r = .85 (all)	NA	-	- (statistical design)
21	Jelescu, I. O., Zurek, M., Winters, K. V., Veraart, J., Rajaratnam, A., Kim, N. S., … Fieremans, E. (2016). In vivo quantification of demyelination and recovery using compartment-specific diffusion MRI metrics validated by electron microscopy. NeuroImage, 132, 104–114.	Jelescu2016	Mouse	Cuprizone and controls	Whole brain	NA	CC splenium	semi-automated	DWI	RD, RK	7	0.112 x 0.112 x 0.8 mm	in vivo	body temperature	perfusion fixation, nanosectioning	2.36 nm	EM	-	+	staining fraction	ROI to ROI	NA	2 x 12 Cuprizone, 10 controls	34	1	Between-subject	Partial Spearman (weight as covariate)	RD: r = -.71, p = .0004; RK: r = .14, p = .5638	NA	+	BS Spearman
21	Jelescu, I. O., Zurek, M., Winters, K. V., Veraart, J., Rajaratnam, A., Kim, N. S., … Fieremans, E. (2016). In vivo quantification of demyelination and recovery using compartment-specific diffusion MRI metrics validated by electron microscopy. NeuroImage, 132, 104–114.	Jelescu2016	Mouse	Cuprizone and controls	Whole brain	NA	CC splenium	semi-automated	Relaxometry	T2	7	0.112 x 0.112 x 0.8 mm	in vivo	body temperature	perfusion fixation, nanosectioning	2.36 nm	EM	-	+	staining fraction	ROI to ROI	NA	2 x 12 Cuprizone, 10 controls	34	1	Between-subject	Partial Spearman (weight as covariate)	T2: r = -.64, p = .0024	NA	+	BS Spearman
21	Jelescu, I. O., Zurek, M., Winters, K. V., Veraart, J., Rajaratnam, A., Kim, N. S., … Fieremans, E. (2016). In vivo quantification of demyelination and recovery using compartment-specific diffusion MRI metrics validated by electron microscopy. NeuroImage, 132, 104–114.	Jelescu2016	Mouse	Cuprizone and controls	Whole brain	NA	CC splenium	semi-automated	MT	MTR	7	0.112 x 0.112 x 0.8 mm	in vivo	body temperature	perfusion fixation, nanosectioning	2.36 nm	EM	-	+	staining fraction	ROI to ROI	NA	2 x 12 Cuprizone, 10 controls	34	1	Between-subject	Partial Spearman (weight as covariate)	MTR: r =.32, p = .1821	NA	+	BS Spearman
22	Jespersen, S. N., Bjarkam, C. R., Nyengaard, J. R., Chakravarty, M. M., Hansen, B., Vosegaard, T., … Vestergaard-Poulsen, P. (2010). Neurite density from magnetic resonance diffusion measurements at ultrahigh field: Comparison with light microscopy and electron microscopy. NeuroImage, 49(1), 205–216.	Jespersen2010	Rat	Controls	Whole brain	NA	ROIs across the brain, including WM and GM	manual	DWI	FA	16.4	0.1 x 0.1 x 0.5 mm	perfusion fixed	21°C	cryosectioning	40 µm	AMG	-	+	staining intensity	ROI to ROI	No coregistration	3	3	8	Mixed (not modelled)	Pearson	FA: r = .78, p = 7 × 10E-8	NA	-	- (statistical design)
23	Jito, J., Nakasu, S., Ito, R., Fukami, T., Morikawa, S., & Inubushi, T. (2008). Maturational changes in diffusion anisotropy in the rat corpus callosum: Comparison with quantitative histological evaluation. Journal of Magnetic Resonance Imaging, 28(4), 847–854.	Jito2008	Rats	6 postnatal stages	Whole brain	NA	CC	manual	DWI	FA	7	0.117 x 0.24 x 1 mm	in vivo	body temperature	perfusion fixation, semithin sectioning	750 nm	Toluidine blue	-	+	staining fraction	ROI to ROI	NA	6	36	1	Between-subject	Linear regression	FA: r = .856, p < .0001	not reported	+	BS Pearson
24	Kelm, N. D., West, K. L., Carson, R. P., Gochberg, D. F., Ess, K. C., & Does, M. D. (2016). Evaluation of diffusion kurtosis imaging in ex vivo hypomyelinated mouse brains. NeuroImage, 124, 612–626.	Kelm2016	Mouse	TSC / Rictor	Whole brain	NA	CC midbody, CC genu, CC splenium (SCC), AC, EC, IC	manual	DWI	FA, MD, RD, MK, AK, RK	15.2	0.15 x 0.15 x 0.15 mm	perfusion fixed	17 ± 0.5 °C	ultrasectioning	70 nm	EM	-	+	staining fraction	ROI to ROI	No coregistration	4 TSC, 3 Rictor, 5 Controls	12	6	Mixed (not modelled)	not reported	FA: not significant; MD: R2 = .35; RD: R2 =.37; MK: R2 = .48; AK: not significant; RK: r = .49	NA	-	- (statistical design)
24	Kelm, N. D., West, K. L., Carson, R. P., Gochberg, D. F., Ess, K. C., & Does, M. D. (2016). Evaluation of diffusion kurtosis imaging in ex vivo hypomyelinated mouse brains. NeuroImage, 124, 612–626.	Kelm2016	Mouse	TSC / Rictor	Whole brain	NA	CC midbody, CC genu, CC splenium (SCC), AC, EC, IC	manual	Relaxometry	MWF	15.2	0.15 x 0.15 x 0.15 mm	perfusion fixed	17 ± 0.5 °C	ultrasectioning	70 nm	EM	-	+	staining fraction	ROI to ROI	No coregistration	4 TSC, 3 Rictor, 5 Controls	12	6	Mixed (not modelled)	not reported	not reported	NA	-	- (statistical design)
24	Kelm, N. D., West, K. L., Carson, R. P., Gochberg, D. F., Ess, K. C., & Does, M. D. (2016). Evaluation of diffusion kurtosis imaging in ex vivo hypomyelinated mouse brains. NeuroImage, 124, 612–626.	Kelm2016	Mouse	TSC / Rictor	Whole brain	NA	CC midbody, CC genu, CC splenium (SCC), AC, EC, IC	manual	MT	MP ('PSR')	15.2	0.15 x 0.15 x 0.15 mm	perfusion fixed	17 ± 0.5 °C	ultrasectioning	70 nm	EM	-	+	staining fraction	ROI to ROI	No coregistration	4 TSC, 3 Rictor, 5 Controls	12	6	Mixed (not modelled)	not reported	not reported	NA	-	- (statistical design)
25	Khodanovich, M. Y., Sorokina, I. V., Glazacheva, V. Y., Akulov, A. E., Nemirovich-Danchenko, N. M., Romashchenko, A. V., … Yarnykh, V. L. (2017). Histological validation of fast macromolecular proton fraction mapping as a quantitative myelin imaging method in the cuprizone demyelination model. Scientific Reports, 7(March), 46686.	Khodanovich2017	Mouse	Cuprizone (D+R) and Controls	Whole brain	NA	GM and WM	manual	MT	MP ('MPF')	11.7	0.1 x 0.1 x 0.5 mm	fixed	body temperature	cryosectioning	10 µm	LFB	-	-	staining intensity	ROI to ROI	No coregistration	7 cuprizone, 7 controls	14	6	Within-subject (mixed, modelled)	Pearson; linear regression	MP: R2 = .897, p < .001 (all); r = .870, p = .007 (control); r = .927, p = 0.002 (Cuprizone)	MP = 0.124 * myelin + 6.278	+	WS Pearson
26	Khodanovich, M., Pishchelko, A., Glazacheva, V., Pan, E., Akulov, A., Svetlik, M., … Anan, T. (2019). Quantitative imaging of white and gray matter remyelination in the cuprizone demyelination model using the macromolecular proton Fraction. Cells, 8(1204).	Khodanovich2019	Mouse	Cuprizone (D+R) and Controls	Whole brain	NA	ROIs across the brain, including WM and GM	manual	MT	MP ('MPF')	11.7	0.1 x 0.1 x 0.5 mm	fixed	body temperature	cryosectioning	10 µm	MBP	-	-	staining fraction	ROI to ROI	No coregistration	4 demyelination, 5 remyelination, 4 controls	13	1	Between-subject	Pearson; linear regression	MP: r = .90, p < .001 (CC); r = .83, p < .001 (Caudate/putamen); r = .80, p < .001 (Hippocampus); r = .88, p < .001 (CT)	MP = 0.4-0.6 * myelin + 6.2-7.84 (slope and intercept vary depending on anatomical area)	-	BS Pearson
27	Kozlowski, P., Raj, D., Liu, J. I. E., Lam, C., Yung, A. C., & Tetzlaff, W. (2008). Characterizing white matter damage in rat spinal cord with quantitative histology and histology. Journal of Neurotrauma, 25, 653–676.	Kozlowski2008	Rat	SCI and Controls	Spinal cord	NA	Fasciculus gracilis, fasciculus cuneatus, and CST	manual	DWI	FA, AD, MD, RD	7	1 x 1 x 1 mm	perfusion fixed	not reported	cryosectioning	20 µm	LFB, MBP	-	+	staining intensity (MBP), inverse staining intensity (LFB)	ROI to ROI	No coregistration	6 at 3 weeks post injury, 4 at 8 weeks post injury, 6 controls (controls not used in correlation)	6 and 4 depending on the analysis	3	Mixed (not modelled)	Pearson	AD: r = -.27, p = .07) for LFB at 3 weeks, r = .24 (p = .16) for LFB at 8 weeks, r = -.35 (p = .02) for MBP at 3 weeks, r = .03 (p =.88) for MBP at 8 weeks; FA: r= .33 (p = .02) for LFB at 3 weeks, r = .72 (p < .001) for LFB at 8 weeks, r = -.66 (p < .0001) for MBP at 3 weeks, r = .22 (p =.19) for MBP at 8 weeks; MD: r = -.60 (p < .001) for LFB at 3 weeks, r= -.57 (p < .001) for LFB at 8 weeks, r = .26 (p = .08) for MBP at 3 weeks, r = -.19 (p = .26) for MBP at 8 weeks; RD: r = -.49 (p < .001) for LFB at 3 weeks, r = -.71 (p < .001) for LFB at 8 weeks, r = .51 (p < .001) for MBP at 3 weeks, r = -.21 (p = .22) for MBP at 8 weeks	NA	-	- (statistical design)
27	Kozlowski, P., Raj, D., Liu, J. I. E., Lam, C., Yung, A. C., & Tetzlaff, W. (2008). Characterizing white matter damage in rat spinal cord with quantitative histology and histology. Journal of Neurotrauma, 25, 653–676.	Kozlowski2008	Rat	SCI and Controls	Spinal cord	NA	Fasciculus gracilis, fasciculus cuneatus, and CST	manual	Relaxometry	MWF	7	0.078 x 0.078 x 1 mm	perfusion fixed	not reported	cryosectioning	20 µm	LFB, MBP	-	+	staining intensity (MBP), inverse staining intensity (LFB)	ROI to ROI	No coregistration	6 at 3 weeks post injury, 4 at 8 weeks post injury, 6 controls (controls not used in correlation)	6 and 4 depending on the analysis	3	Mixed (not modelled)	Pearson	MWF: r = .64 (p < .001) for LFB at 3 weeks, r = .88 (p < .001) for LFB at 8 weeks, r= -.28 (p = .07) for MBP at 3 weeks, r = .15 (p = .40) for MBP at 8 weeks	NA	-	- (statistical design)
28	Kozlowski, P., Rosicka, P., Liu, J., Yung, A. C., & Tetzlaff, W. (2014). In vivo longitudinal myelin water imaging in rat spinal cord following dorsal column transection injury. Magnetic Resonance Imaging, 32(3), 250–258.	Kozlowski2014	Rats	SCI	Spinal cord	NA	Dorsal column	manual	DWI	FA	7	1 x 1 x 1 mm (only ex vivo)	in vivo (relaxometry) and fixed (DWI)	body temperature / not reported	cryosectioning	20 µm	MBP, Eriochrome–cyanine	-	+	normalised staining intensity	ROI to ROI	No coregistration	8	16	1	Between-subject	Pearson	not reported	NA	-	- (no result)
28	Kozlowski, P., Rosicka, P., Liu, J., Yung, A. C., & Tetzlaff, W. (2014). In vivo longitudinal myelin water imaging in rat spinal cord following dorsal column transection injury. Magnetic Resonance Imaging, 32(3), 250–258.	Kozlowski2014	Rats	SCI	Spinal cord	NA	Dorsal column	manual	Relaxometry	MWF	7	0.117 x 0.117 x 1 mm (ex vivo) 1 x 1 x 1.5 mm (in vivo)	in vivo (relaxometry) and fixed (DWI)	body temperature / not reported	cryosectioning	20 µm	MBP, Eriochrome–cyanine	-	+	normalised staining intensity	ROI to ROI	No coregistration	8	16	1	Between-subject	Pearson	MWF: r = .63, p = .0047 (EC, in vivo), r = .74, p = .0001 (EC, ex vivo), r = .64, p = .05 (MBP, in vivo), r = .63, p = .038 (MBP, ex vivo)	NA	-	BS Pearson
29	Laule, C., Kozlowski, P., Leung, E., Li, D. K. B., MacKay, A. L., & Moore, G. R. W. (2008). Myelin water imaging of multiple sclerosis at 7T: Correlations with histopathology. NeuroImage, 40, 1575–1580.	Laule2008	Human	MS	1 cm brain sections	not reported	WM, GM and lesions	manual	Relaxometry	MWF	7	0.234 x 0.234 x 1 mm	fixed	not reported	paraffin embedding	10 µm	LFB	-	-	staining intensity	ROI to ROI	Landmark-based linear registration	3 MS patients, 10 samples	3	22-30 per sample	Within-subject	Not reported (likely linear regression)	MWF: R2 between .56 and .95 (mean: .78), all p < .0001; R2 between 0 and .79 (mean R2 = .43, p < .0001) just in WM ROIs	NA	-	- (N = 3)
30	Laule, C., Leung, E., Li, D. K. B., Traboulsee, A. L., Paty, D. W., Mackay, A. L., & Moore, G. R. W. (2006). Myelin water imaging in multiple sclerosis: quantitative correlations with histopathology. Multiple Sclerosis, 12, 747–753.	Laule2006	Human	MS	1 cm brain sections	not reported	WM, GM and lesions	manual	Relaxometry	MWF	1.5	in plane resolution not reported, 3mm thick slices	fixed	20°C	paraffin embedding	10 µm	LFB	-	-	staining intensity	ROI to ROI	Landmark-based linear registration	13	13	23-45 per slice	Within-subject	Not reported (likely linear regression)	MWF: R2 between .45 and .92 (mean .67), all p < .0001; mean R2 = .29 (p < .0001) just in WM ROIs	NA	-	WS Pearson
31	Laule, C., Vavasour, I. M., Leung, E., Li, D. K. B., Kozlowski, P., Traboulsee, A. L., … Moore, G. R. W. (2011). Pathological basis of diffusely abnormal white matter: insights from magnetic resonance imaging and histology. Multiple Sclerosis Journal, 17(2), 144–150.	Laule2011	Human	MS	1 cm brain sections	not reported	DAWM and NAWM	manual	Relaxometry	MWF	1.5 and 7	0.586 x 0.586 x 3 mm (1.5T), 0.234 x 0.234 x 1mm (7T)	fixed	not reported	paraffin embedding	10 µm	LFB, MBP	-	+	normalised staining intensity	ROI to ROI	Landmark-based linear registration	9 MS patients, 23 samples	9	Not reported	Within-subject	Not reported (likely linear regression)	MWF and LFB: R2 between .48 and .95 (mean: .74); MWF and MBP: R2 between .15 and .47 (mean: .31)	NA	-	WS Pearson
32	Lehto, L. J., Albors, A. A., Sierra, A., Tolppanen, L., Eberly, L. E., Mangia, S., … Gröhn, O. (2017). Lysophosphatidyl choline induced demyelination in rat probed by relaxation along a fictitious field in high rank rotating frame. Frontiers in Neuroscience, 11, 1–14.	Lehto2017	Rat	Controls	Whole brain	NA	Contralateral and ipsilateral CC and DTT	manual	Relaxometry	RAFF4	7	0.125 x 0.125 x 0.5 mm	in vivo	body temperature	cryosectioning	30 µm	Gold chloride	-	-	staining intensity	ROI to ROI	No coregistration	21	21	12 and 2 depending on the analysis	Mixed (not modelled)	Pearson	RAFF4: r = -.742, p < .0001 (CC), r = -.745, p = .001 (DTT)	NA	-	- (statistical design)
32	Lehto, L. J., Albors, A. A., Sierra, A., Tolppanen, L., Eberly, L. E., Mangia, S., … Gröhn, O. (2017). Lysophosphatidyl choline induced demyelination in rat probed by relaxation along a fictitious field in high rank rotating frame. Frontiers in Neuroscience, 11, 1–14.	Lehto2017	Rat	Controls	Whole brain	NA	Contralateral and ipsilateral CC and DTT	manual	MT	T1sat, MTR	7	0.125 x 0.125 x 0.5 mm	in vivo	body temperature	cryosectioning	30 µm	Gold chloride	-	-	staining intensity	ROI to ROI	No coregistration	21	21	13 and 2 depending on the analysis	Mixed (not modelled)	Pearson	MTR: r = .741, p < .001 (CC), r = .719, p = .001 (DTT); T1sat: r = -.741, p < .001 (CC), r = -.705, p = .001 (DTT)	NA	-	- (statistical design)
32	Lehto, L. J., Albors, A. A., Sierra, A., Tolppanen, L., Eberly, L. E., Mangia, S., … Gröhn, O. (2017). Lysophosphatidyl choline induced demyelination in rat probed by relaxation along a fictitious field in high rank rotating frame. Frontiers in Neuroscience, 11, 1–14.	Lehto2017	Rat	Controls	Whole brain	NA	Contralateral and ipsilateral CC and DTT	manual	DWI	AD, FA, MD, RD	7	0.125 x 0.125 x 0.5 mm	in vivo	body temperature	cryosectioning	30 µm	Gold chloride	-	-	staining intensity	ROI to ROI	No coregistration	21	21	14 and 2 depending on the analysis	Mixed (not modelled)	Pearson	AD: r = .714, p < .001 (CC), r = .279, p = .223 (DTT); FA: r = .662, p < .001 (C), r = .438, p = .053 (DTT); MD: r = .708, p < .001 (CC), r = .112, p = .610 (DTT); RD: r = .257, p = .048 (CC), r = -.079, p = .739 (DTT)	NA	-	- (statistical design)
33	Lodygensky, G. A., Marques, J. P., Maddage, R., Perroud, E., Sizonenko, S. V, Hüppi, P. S., & Gruetter, R. (2012). In vivo assessment of myelination by phase imaging at high magnetic field. NeuroImage, 59(3), 1979–1987.	Lodygensky2012	Rat	Controls	Whole brain	NA	AC, CC	manual	QSM	Susceptibility	9.4	slice thickness of 0.5 mm, in-plane resolution between 0.0625 mm isotropic and 0.105 mm isotropic	in vivo	body temperature	perfusion fixation, cryosectioning	50 µm	Black Gold II	+	-	staining intensity	ROI to ROI	Not reported	13 (across different ages)	13	2	Between-subject	Linear regression; Spearman mentioned but not reported	Susceptibility: R2 = .673, p < .0003 (AC); R2 = .76, p < .0001 (CC)	Susceptibility = - 0.0107 * myelin - 0.0017 (AC); Susceptbility = - 0.015 * myelin + 0.004 (CC)	+	BS Pearson
34	Martirosyan, N. L., Turner, G. H., Kaufman, J., Patel, A. A., Belykh, E., Kalani, M. Y. S., … Preul, M. C. (2016). Manganese-enhanced MRI offers correlation with severity of spinal cord injury in experimental models. The Open NeuroImaging Journal, 10, 139–147.	Martirosyan2016	Rat	SCI	Spinal cord (T9)	NA	Epicenter of injury	manual	DWI	FA	7	0.195 x 0.195 x 10 mm	perfusion fixed	not reported	paraffin embedding	15 µm	LFB	-	-	staining intensity, percentage difference between injury epicenter to control animals	ROI to ROI	No coregistration	15 from different types of SCI, 3 controls	18	1	Between-subject	Pearson	FA: r = -.94 (p = .0001)	NA	+	BS Pearson
35	Moll, N. M., Rietsch, A. M., Thomas, S., Ransohoff, A. J., Lee, J., Fox, R., … Fisher, E. (2011). Multiple sclerosis normal-appearing white matter: pathology – imaging correlations. Ann Neurol, 70, 764–773. https://doi.org/10.1002/ana.22522	Moll2011	Human	MS	Whole brain	5.8±1 hours	WM, considering distance from lesion	manual	DWI	AD, FA, MD, RD	1.5	1.9 × 1.9 × 3 mm	in situ / fixed	body temperature	cryosectioning	30 µm	MBP	-	+	staining intensity	ROI to ROI	No coregistration	4	4	12 (in total across subjects)	Mixed (not modelled)	Spearman	AD: r = -.41 (p = .004); FA: r = .38 (p = .008); MD: r = -.58 (p < .0001), RD: r = -.52 (p = .0002)	NA	-	- (statistical design)
35	Moll, N. M., Rietsch, A. M., Thomas, S., Ransohoff, A. J., Lee, J., Fox, R., … Fisher, E. (2011). Multiple sclerosis normal-appearing white matter: pathology – imaging correlations. Ann Neurol, 70, 764–773. https://doi.org/10.1002/ana.22522	Moll2011	Human	MS	Whole brain	5.8±1 hours	WM, considering distance from lesion	manual	MT	MTR	1.5	0.9 × 0.9 × 3 mm	in situ / fixed	body temperature	cryosectioning	30 µm	MBP	-	+	staining intensity	ROI to ROI	No coregistration	4	4	12 (in total across subjects)	Mixed (not modelled)	Spearman	MTR: r = 0.63 (p < .0001)	NA	-	- (statistical design)
36	Mollink, J., Hiemstra, M., Miller, K. L., Huszar, I. N., Jenkinson, M., Raaphorst, J., … van Cappellen van Walsum, A. M. (2019). White matter changes in the perforant path area in patients with amyotrophic lateral sclerosis. Neuropathology and Applied Neurobiology, 45(6), 570–585.	Mollink2019	Human	ALS and controls	Brain tissue blocks including hippocampus	range: 0.5-5 days	Perforant path	tractography / manual	DWI	FA, MD, RD, AD	11.7	0.4 x 0.4 x 0.4 mm resolution.	fixed	not reported	paraffin embedding	6 µm	PLP	-	+	staining fraction	ROI to ROI	No coregistration	14 ALS and 5 Controls	19	1	Between-subject	Pearson	FA: r = .52, p = .03	NA	+	BS Pearson
37	Mottershead, J. P., Schmierer, K., Clemence, M., Thornton, J. S., Scaravilli, F., Barker, G. J., … Miller, D. H. (2003). High field MRI correlates of myelin content and axonal density in multiple sclerosis: A post-mortem study of the spinal cord. J Neurol, 250, 1293–1301.	Mottershead2003	Human	MS and Controls	Spinal cord, 2 cm pieces	72±39.2	MS lesions, diffuse damage, NAMW	manual	Relaxometry	PD, T1, T2	7	Single 1.5 mm slices, in plane resolution between 0.055 and 0.068 mm	fresh	29-38°C	fixation, paraffin embedding	10 µm	LFB	-	+	staining fraction	ROI to ROI	No coregistration	4 MS patients, 1 control	5	108 (in total across subjects)	Mixed (not modelled)	Spearman	PD: r = -.72 (p < .001); T1: r = -.78 (p < .001); T2: r = -.75 (p < .001)	NA	-	- (statistical design)
37	Mottershead, J. P., Schmierer, K., Clemence, M., Thornton, J. S., Scaravilli, F., Barker, G. J., … Miller, D. H. (2003). High field MRI correlates of myelin content and axonal density in multiple sclerosis: A post-mortem study of the spinal cord. J Neurol, 250, 1293–1301.	Mottershead2003	Human	MS and Controls	Spinal cord, 2 cm pieces	72±39.2	MS lesions, diffuse damage, NAMW	manual	DWI	ADC, SDI	7	Single 1.5 mm slices, in plane resolution between 0.055 and 0.068 mm	fresh	29-38°C	fixation, paraffin embedding	10 µm	LFB	-	+	staining fraction	ROI to ROI	No coregistration	4 MS patients, 1 control	5	108 (in total across subjects)	Mixed (not modelled)	Spearman	ADC: r = -.45 (p = .001); SDI: r = .51 (p < .001)	NA	-	- (statistical design)
37	Mottershead, J. P., Schmierer, K., Clemence, M., Thornton, J. S., Scaravilli, F., Barker, G. J., … Miller, D. H. (2003). High field MRI correlates of myelin content and axonal density in multiple sclerosis: A post-mortem study of the spinal cord. J Neurol, 250, 1293–1301.	Mottershead2003	Human	MS and Controls	Spinal cord, 2 cm pieces	72±39.2	MS lesions, diffuse damage, NAMW	manual	MT	MTR	7	Single 1.5 mm slices, in plane resolution between 0.055 and 0.068 mm	fresh	29-38°C	fixation, paraffin embedding	10 µm	LFB	-	+	staining fraction	ROI to ROI	No coregistration	4 MS patients, 1 control	5	108 (in total across subjects)	Mixed (not modelled)	Spearman	MTR: r = -.29 (p = .075)	NA	-	- (statistical design)
38	Oakden, W., Kwiecien, J. M., Reilly, M. A. O., Dabrowski, W., Whyne, C., Finkelstein, J., … Stanisz, G. J. (2015). Quantitative MRI in a non-surgical model of cervical spinal cord injury. NMR in Biomedicine, 28, 925–936.	Oakden2015	Rat	SCI	Caudal end of the C2 vertebra	NA	WM	manual	DWI	AD, RD	1.5	0.2 × 0.2 x 1 mm	in vivo / fixed	body temperature	paraffin embedding	10 µm	LFB	-	-	visual classification of severity of pathology	ROI to ROI	Manual coregistration	8 for acute group, 8 for chronic group	16	Variable and only specified for significant correlations	Mixed (not modelled)	Pearson	AD: r = .39; RD: r = .57	NA	-	- (statistical design)
38	Oakden, W., Kwiecien, J. M., Reilly, M. A. O., Dabrowski, W., Whyne, C., Finkelstein, J., … Stanisz, G. J. (2015). Quantitative MRI in a non-surgical model of cervical spinal cord injury. NMR in Biomedicine, 28, 925–936.	Oakden2015	Rat	SCI	Caudal end of the C2 vertebra	NA	WM	manual	Relaxometry	MWF	1.5	0.2 × 0.2 x 1 mm	in vivo / fixed	body temperature	paraffin embedding	10 µm	LFB	-	-	visual classification of severity of pathology	ROI to ROI	Manual coregistration	8 for acute group, 8 for chronic group	16	Variable and only specified for significant correlations	Mixed (not modelled)	Pearson	MWF: r = -.06	NA	-	- (statistical design)
39	Odrobina, E. E., Lam, T. Y. J., Pun, T., Midha, R., & Stanisz, G. J. (2005). MR properties of excised neural tissue following experimentally induced demyelination. NMR in Biomedicine, 18(5), 277–284.	Odrobina2005	Rat	Tellerium diet and Controls	Sciatic nerves	NA	Distal and proximal portion of nerve	not reported	Relaxometry	MWF, T1, T2	1.5	not reported	fixed	room temperature (20°C)	epon-araldite embedding	1 µm	Toluidine blue	-	-	staining fraction	unclear (likely ROI to ROI)	No coregistration	Not reported	Not reported	Not reported (likely 2)	Unclear (likely mixed, not modelled)	Not reported	MWF: r = .71 ± .16 (p < .001); T1: r = -.88 ± 12 (p < .0001); T2: r = -.91 ± .08 (p < .0001)	NA	-	- (statistical design)
39	Odrobina, E. E., Lam, T. Y. J., Pun, T., Midha, R., & Stanisz, G. J. (2005). MR properties of excised neural tissue following experimentally induced demyelination. NMR in Biomedicine, 18(5), 277–284.	Odrobina2005	Rat	Tellerium diet and Controls	Sciatic nerves	NA	Distal and proximal portion of nerve	not reported	MT	MTR, MP('M0b')	1.5	not reported	fixed	room temperature (20°C)	epon-araldite embedding	1 µm	Toluidine blue	-	-	staining fraction	unclear (likely ROI to ROI)	No coregistration	Not reported	Not reported	Not reported (likely 2)	Unclear (likely mixed, not modelled)	Not reported	MTR: r = .56 ± .22 (p < .0005); MP: r = .77 ± .15 (p < .0001)	NA	-	- (statistical design)
40	Peters, J. M., Struyven, R. R., Prohl, A. K., Vasung, L., Stajduhar, A., Taquet, M., … Warfield, S. K. (2019). White matter mean diffusivity correlates with myelination in tuberous sclerosis complex. Annals of Clinical and Translational Neurology, 6(7), 1178–1190.	Peters2019	Human	Tuberculosis	Whole brain	NA	Surgically removed tissue blocks	NA	DWI	FA, MD	3	1.72 x 1.72 x 2.2 mm	in vivo	body temperature	fixation and sectioning	13 µm	LFB	-	-	staining intensity	voxel-wise	3D registration	3	3 (1 reported)	not reported	Within-subject	Spearman	FA: r = .10 (CT), r = .09 (Tuber), r = .45 (Perituber), r = .19 (WM), r = .70 (All); MD: r = .04 (CT), r = .07 (Tuber), r = -.63 (Perituber), r = -.60 (WM), r = -.85 (All)	NA	-	- (N = 1)
41	Pol, S., Sveinsson, M., Sudyn, M., Babek, N., Siebert, D., Bertolino, N., … Zivadinov, R. (2019). Teriflunomide’s effect on glia in experimental demyelinating disease: A neuroimaging and histologic study. Journal of Neuroimaging, 29(1), 52–61.	Pol2019	Mouse	Teliflunomide and Controls	Whole brain	NA	CC (caudal medial, rostral lateral, rostral medial)	manual	DWI	FA, MD	9.4	0.078 × 0.078 × 0.250 mm	in vivo	body temperature	perfusion fixation and cryosectioning	16 µm	Solochrome	-	-	staining intensity	ROI to ROI	No coregistration	13 Teliflunomide, 12 controls	25	3	Between-subject	Pearson	FA: r = -.240, p = .675 (caudal medial, controls), r = -.130, p = .802 (rostral lateral, controls), r = -.147, p = .785 (rostral medial, controls), r = -.122, p = .825 (caudal medial, Teliflunomide), r = -.265, p = .643 (rostral lateral, Teliflunomide), r = .017, p = .981 (rostral medial, Teliflunomide); MD: r = .592, p = .202 (caudal medial, controls), r = .377, p = . 438 (rostral lateral, controls), r = .221, p = .675 (rostral medial, controls), r = -.083, p = .896 (caudal medial, Teliflunomide), r = -.237, p = . 667 (rostral lateral, Teliflunomide), r = .069, p = .903 (rostral medial, Teliflunomide);	NA	+	BS Pearson
41	Pol, S., Sveinsson, M., Sudyn, M., Babek, N., Siebert, D., Bertolino, N., … Zivadinov, R. (2019). Teriflunomide’s effect on glia in experimental demyelinating disease: A neuroimaging and histologic study. Journal of Neuroimaging, 29(1), 52–61.	Pol2019	Mouse	Teliflunomide and Controls	Whole brain	NA	CC (caudal medial, rostral lateral, rostral medial)	manual	QSM	Susceptibility	9.4	not reported	in vivo	body temperature	perfusion fixation and cryosectioning	16 µm	Solochrome	-	-	staining intensity	ROI to ROI	No coregistration	13 Teliflunomide, 12 controls	25	3	Between-subject	Pearson	Susceptibility: r = -.190, p = .723 (caudal medial, controls), r = -.214, p = .675 (rostral lateral, controls), r = .005, p = .987 (rostral medial, controls), r = .601, p = .141 (caudal medial, Teliflunomide), r = .243, p = .658 (rostral lateral, Teliflunomide), r = .211, p = .695 (rostral medial, Teliflunomide)	NA	+	BS Pearson
42	Praet, J., Manyakov, N. V, Muchene, L., Mai, Z., Terzopoulos, V., Backer, S. De, … Verhoye, M. (2018). Diffusion kurtosis imaging allows the early detection and longitudinal follow-up of amyloid- β -induced pathology. Alzheimer’s Research & Therapy, 10(1).	Praet2018	Mouse	APP/PS1 and controls	Whole brain	NA	Motor cortex	manual on study based atlas	DWI	AD, AK, DT, DK, FA, MD, MK, RD, RK	7	0.000214 x 0.000214 x 0.2 mm	in vivo	body temperature (37-37.3°C)	fixation, paraffin embedding	5 µm	MBP	-	-	staining intensity	ROI to ROI and voxelwise	3D stacking of histology, non-linear registration	48 Alzheimer's model, 32 wild type	80	1	Between-subject	Pearson (Bonferroni corrected for multiple comparisons); Bayesian multivariate linear regression	AD: r = -.479, p = .0362; AK: r = .376 (p = .4851); FA: r = -.560 (p = .0025); MD: r = -.175, p = 1; MK: r = .504 (p = .0173); RD: r = .272, p = 1; RK: r = .518 (p = .0110); Voxelwise statistics: DT: r = .5545, DK: r = .4509, DT/DK: .6374	Not reported	+	BS Pearson
43	Pun, T. W. C., Odrobina, E., Xu, Q. G., Lam, T. Y. J., Munro, C. A., Midha, R., & Stanisz, G. J. (2005). Histological and magnetic resonance analysis of sciatic nerves in the tellurium model of neuropathy. Journal of the Peripheral Nervous System, 10(1), 38–46.	Pun2005	Rat	Tellerium and Controls	2 cm pieces of sciatic nerves	NA	Nerves	unclear	Relaxometry	T1, MWF	1.5	not reported	fresh	20 °C	fixation, ultrasectioning	1 µm	Toluidine blue	-	+	staining fraction	unclear	Unclear	62 Tellerium, 34 controls	96	1	Between-subject	not reported	MWF: r = .77, T1: r = .88	NA	-	- (statistical measure)
44	Reeves, C., Tachrount, M., Thomas, D., Michalak, Z., Liu, J., Ellis, M., … Thom, M. (2015). Combined ex vivo 9.4T MRI and quantitative histopathological study in normal and pathological neocortical resections in focal epilepsy. Brain Pathology, 26, 319–333.	Reeves2015	Human	Epilepsy and Control	5 mm thick piece of cortex and underlying WM	0 (samples obtained during surgery)	Normal and pathological GM and WM	manual	Relaxometry	T1, T2, T2*	9.4	0.136 x 0.136 x 0.5 mm	fixed	not reported	not reported	7 µm	MBP	-	+	staining intensity	ROI to ROI	Manual coregistration	12 epilepsy, 1 control	13	3-4 (43 in total across subjects)	Mixed (not modelled)	Spearman; linear regression	T1: R2 = .270 (p < .005); T2: R2 = .235 (p < .005); T2*: p < .05	Not reported	-	- (statistical design)
44	Reeves, C., Tachrount, M., Thomas, D., Michalak, Z., Liu, J., Ellis, M., … Thom, M. (2015). Combined ex vivo 9.4T MRI and quantitative histopathological study in normal and pathological neocortical resections in focal epilepsy. Brain Pathology, 26, 319–333.	Reeves2015	Human	Epilepsy and Control	5 mm thick piece of cortex and underlying WM	0 (samples obtained during surgery)	Normal and pathological GM and WM	manual	MT	MTR	9.4	0.136 x 0.136 x 0.500 mm	fixed	not reported	not reported	7 µm	MBP	-	+	staining intensity	ROI to ROI	Manual coregistration	12 epilepsy, 1 control	13	3-4 (43 in total across subjects)	Mixed (not modelled)	Spearman; linear regression	MTR: p < .005	Not reported	-	- (statistical design)
45	Righart, R., Biberacher, V., Jonkman, L. E., Klaver, R., Schmidt, P., Buck, D., … Zimmer, C. (2017). Cortical pathology in multiple sclerosis detected by the T1/T2-weighted ratio from routine magnetic resonance imaging. Ann Neurol, 82, 519–529.	Righart2017	Human	MS	Whole brain	≤ 7 hours	Left inferior frontal gyrus, superior frontal gyrus, anterior cingulate gyrus, inferior parietal gyrus, and superior temporal gyrus	atlas (Freesurfer aparc)	Other	T1w/T2w	1.5	1 x 1 x 1.5 mm	in situ	not reported	paraffin embedding	10 µm	PLP	-	+	staining intensity	ROI to ROI	No coregistration	9	9	5 per patient; 36 in total across subjects	Mixed (not modelled)	Generalized estimating equations	NA	Not reported	-	- (statistical design)
46	Schmierer, K., Parkes, H. G., So, P., An, S. F., Brandner, S., Ordidge, R. J., … Miller, D. H. (2010). High field (9.4 Tesla) magnetic resonance imaging of cortical grey matter lesions in multiple sclerosis. Brain, 133, 858–867.	Schmierer2010	Human	MS	1 cm coronal brain slices	42±32 hours	Cortical GM lesions and nonlesional CT	manual	Relaxometry	T1	9.4	0.117 x 0.156 x 1 mm	fixed	not reported	paraffin embedding	5 µm	MBP	-	+	inverse staining intensity	ROI to ROI	Manual coregistration	21	2	2	Mixed (not modelled)	Linear regression	T1: not reported	Not reported	-	- (statistical design)
46	Schmierer, K., Parkes, H. G., So, P., An, S. F., Brandner, S., Ordidge, R. J., … Miller, D. H. (2010). High field (9.4 Tesla) magnetic resonance imaging of cortical grey matter lesions in multiple sclerosis. Brain, 133, 858–867.	Schmierer2010	Human	MS	1 cm coronal brain slices	42±32 hours	Cortical GM lesions and nonlesional CT	manual	MT	MTR	9.4	not reported	fixed	not reported	paraffin embedding	5 µm	MBP	-	+	inverse staining intensity	ROI to ROI	Manual coregistration	21	2	2	Mixed (not modelled)	Linear regression	MTR: r = .52, p = .02	Not reported	-	- (statistical design)
47	Schmierer, K., Scaravilli, F., Altmann, D. R., Barker, G. J., & Miller, D. H. (2004). Magnetization transfer ratio and myelin in postmortem multiple sclerosis brain. Ann Neurol, 56, 407–415.	Schmierer2004	Human	MS	1 cm coronal brain slices	14.2±8.5 hours	WM-Ls and NAWM	manual	Relaxometry	T1	1.5	0.938 x 0.938 x 5 mm	fresh	mean 25.0°C (SD: 2.9°C)	paraffin embedding	not reported	LFB	-	+	inverse staining intensity	ROI to ROI	Manual coregistration	19	20	68 (in total across subjects)	Within-subject (mixed, modelled)	Pearson	T1: r = .70, p < .001	NA	+	WS Pearson
47	Schmierer, K., Scaravilli, F., Altmann, D. R., Barker, G. J., & Miller, D. H. (2004). Magnetization transfer ratio and myelin in postmortem multiple sclerosis brain. Ann Neurol, 56, 407–415.	Schmierer2004	Human	MS	1 cm coronal brain slices	14.2±8.5 hours	WM-Ls and NAWM	manual	MT	MTR	1.5	0.938 x 0.938 x 5 mm	fresh	mean 25.0°C (SD: 2.9°C)	paraffin embedding	not reported	LFB	-	+	inverse staining intensity	ROI to ROI	Manual coregistration	20	20	72 (in total across subjects)	Within-subject (mixed, modelled)	Pearson	MTR: r = -.84, p < .001	NA	+	WS Pearson
48	Schmierer, K., Tozer, D. J., Scaravilli, F., Altmann, D. R., Barker, G. J., Tofts, P. S., & Miller, D. H. (2007). Quantitative magnetization transfer imaging in postmortem multiple sclerosis brain. Journal of Magnetic Resonance Imaging, 51, 41–51.	Schmierer2007a	Human	MS	Coronal brain slices	15±8 (range: 4.5-43) hours, scanning: 43±22 (range 10-107) hours	WM-Ls and NAWM	manual	Relaxometry	T1	1.5	0.938 x 0.938 x 5 mm	fresh	room temperature	fixation, paraffin embedding	not reported	LFB	-	+	inverse staining intensity	ROI to ROI	Manual coregistration	35	35	129 (in total across subjects)	Within-subject (mixed, modelled)	Pearson	T1: r = .69, p < .001	NA	+	WS Pearson
48	Schmierer, K., Tozer, D. J., Scaravilli, F., Altmann, D. R., Barker, G. J., Tofts, P. S., & Miller, D. H. (2007). Quantitative magnetization transfer imaging in postmortem multiple sclerosis brain. Journal of Magnetic Resonance Imaging, 51, 41–51.	Schmierer2007a	Human	MS	Coronal brain slices	15±8 (range: 4.5-43) hours, scanning: 43±22 (range 10-107) hours	WM-Ls and NAWM	manual	MT	MTR, MP('fb')	1.5	0.938 x 0.938 x 5 mm	fresh	room temperature	fixation, paraffin embedding	not reported	LFB	-	+	inverse staining intensity	ROI to ROI	Manual coregistration	37 for MTR, 20 for MP	20-37	132 for MTR, 78 for MP (in total across subjects)	Within-subject (mixed, modelled)	Pearson	MP: r = -.80, p < .001; MTR: r = -.84, p < .001	NA	+	WS Pearson
49	Schmierer, K., Wheeler-Kingshott, C. A. M., Boulby, P. A., Scaravilli, F., Altmann, D. R., Barker, G. J., … Miller, D. H. (2007). Diffusion tensor imaging of post mortem multiple sclerosis brain. NeuroImage, 35, 467–477.	Schmierer2007b	Human	MS	1 cm coronal brain slices	16±6 (range: 7-28) hours, scanning: 46±25 (range 10-107) hours	WM-Ls and NAWM	manual	DWI	FA, MD	1.5	2.5 x 2.5 x 5 mm	fresh	17.5 - 25.1°C	fixation, paraffin embedding	9.4±3.6 µm	LFB	-	+	inverse staining intensity	ROI to ROI	No coregistration	16	16	44-51 depending on the analysis	Within-subject (mixed, modelled)	Pearson	FA: r = -.79, p < .001; MD: r = .68, p < .001	NA	-	WS Pearson
50	Schmierer, K., Wheeler-Kingshott, C. A. M., Tozer, D. J., Boulby, P. A., Parkes, H. G., Yousry, T. A., … Miller, D. H. (2008). Quantitative magnetic resonance of postmortem multiple sclerosis brain before and after fixation. Magnetic Resonance in Medicine, 277, 268–277.	Schmierer2008	Human	MS	1 cm coronal brain slices	17±6 (range: 7-28) hours, unfixed samples: 51±28 (range: 7-108) hours	WM-Ls and NAWM	manual	MT	MTR, MP('fb')	1.5	0.94 x 0.94 x 5 mm	fresh / fixed	22.5°C	paraffin embedding	5000 µm	LFB	-	+	inverse staining intensity	ROI to ROI	No coregistration	15	15	40-44 (in total across subjects)	Mixed (unclear whether modelled)	Linear regression	MP: r = -.72 (unfixed) and r = -.86 (fixed), all p < .01; MTR: r = -.83 (unfixed) and r = -.68 (fixed)	Not reported	-	- (statistical design)
50	Schmierer, K., Wheeler-Kingshott, C. A. M., Tozer, D. J., Boulby, P. A., Parkes, H. G., Yousry, T. A., … Miller, D. H. (2008). Quantitative magnetic resonance of postmortem multiple sclerosis brain before and after fixation. Magnetic Resonance in Medicine, 277, 268–277.	Schmierer2008	Human	MS	1 cm coronal brain slices	17±6 (range: 7-28) hours, unfixed samples: 51±28 (range: 7-108) hours	WM-Ls and NAWM	manual	Relaxometry	T1, T2	1.5	0.94 x 0.94 x 5 mm	fresh / fixed	22.5°C	paraffin embedding	5000 µm	LFB	-	+	inverse staining intensity	ROI to ROI	No coregistration	15	15	43-66 (total across subjects)	Mixed (unclear whether modelled)	Linear regression	T1: r = .77 (unfixed) and r = .89 (fixed), T2: r = .82 (unfixed) and r = .92 (fixed), all p < .01	Not reported	-	- (statistical design)
50	Schmierer, K., Wheeler-Kingshott, C. A. M., Tozer, D. J., Boulby, P. A., Parkes, H. G., Yousry, T. A., … Miller, D. H. (2008). Quantitative magnetic resonance of postmortem multiple sclerosis brain before and after fixation. Magnetic Resonance in Medicine, 277, 268–277.	Schmierer2008	Human	MS	1 cm coronal brain slices	17±6 (range: 7-28) hours, unfixed samples: 51±28 (range: 7-108) hours	WM-Ls and NAWM	manual	DWI	AD, FA, MD, RD	1.5	0.25 x 0.25 x 5 mm	fresh / fixed	22.5°C	paraffin embedding	5000 µm	LFB	-	+	inverse staining intensity	ROI to ROI	No coregistration	15	15	43-48 (total across subjects)	Mixed (unclear whether modelled)	Linear regression	AD: r = .53 (unfixed) and r =.8 (fixed) ; FA: r = -.78 (unfixed) and r = -.83 (fixed); MD: r = .73 (unfixed) and r = .78 (fixed); RD: r = .74 (unfixed) and .81 (fixed), all p < .01	Not reported	-	- (statistical design)
51	Schwartz, E. D., Cooper, E. T., Fan, Y., Jawad, A. F., Chin, C., Nissanov, J., & Hackney, D. B. (2005). MRI diffusion coefficients in spinal cord correlate with axon morphometry. Brain Imaging, 16(1), 73–76.	Schwartz2005	Rat	Controls	Whole brain	NA	Various WM tracts	manual	DWI	AI, iADC, tADC	9.4	0.039 x 0.039 x 0.5 mm	perfusion fixed	20°C	epon immersion	1 µm	Toluidine blue	-	+	staining fraction (MVF, MST)	ROI to ROI	No coregistration	3	3	6	Mixed (unclear whether modelled)	Pearson; linear regression	AI: r = -.58, p = .0125 (MVF) , r = 0.19, p = 0.4536 (MST); lADC: r = -.48, p = .0437 (MVF), r = .43, p = .0717 (MST); tADC: r = -.74, p = .0004 (MVF), r = .34, p = .1701 (MST)	Not reported	-	- (statistical design)
52	Seehaus, A., Roebroeck, A., Bastiani, M., & Fonseca, L. (2015). Histological validation of high-resolution DTI in human post mortem tissue. Frontiers in Neuroanatomy, 9, 1–12.	Seehaus2015	Human	Control	Whole brain	6 hours	CT and WM	NA	DWI	FA	9.4	0.34 x 0.34 x 0.34 mm	fixed	30 °C	cryosectioning	60 µm	Gallyas	-	-	staining intensity	voxel-wise	3D affine	1	1	voxel-wise (62782)	Within-subject	Pearson	FA: r = .487, MD: r = -.542, RD: r = -.554	NA	-	- (N = 1)
53	Seewann, A., Vrenken, H., Van der Valk, P., Blezer, E., Knol, D., Castelijns, J., … Geurts, J. (2020). Diffusely abnormal white matter in chronic multiple sclerosis. Arch Neurol, 66(5), 601–609.	Seewann2009	Human	MS	1 cm coronal brain slices	mean: 8.5 hours	WM-Ls, DAWM and NAWM	manual	Relaxometry	T1	1.5	1 x 1 x 3 mm	fixed	not reported	paraffin embedding	10 µm	LFB, PAS, PLP	-	+	inverse staining intensity	ROI to ROI	Manual coregistration	10	10	42 (in total across subjects)	Mixed (modelled, but unclear whether result refers to within or between subject variance)	Pearson; Spearman mentioned but not reported	T1 and LFB: r = .68, p < .01; T1 and PLP: r = .41, p < .05	NA	-	- (statistical design)
53	Seewann, A., Vrenken, H., Van der Valk, P., Blezer, E., Knol, D., Castelijns, J., … Geurts, J. (2020). Diffusely abnormal white matter in chronic multiple sclerosis. Arch Neurol, 66(5), 601–609.	Seewann2009	Human	MS	1 cm coronal brain slices	mean: 8.5 hours	WM-Ls, DAWM and NAWM	manual	DWI	FA, ADC	1.5	2 x 2 x 8 mm	fixed	not reported	paraffin embedding	10 µm	LFB, PAS, PLP	-	+	inverse staining intensity	ROI to ROI	Manual coregistration	10	10	42 (in total across subjects)	Mixed (modelled, but unclear whether result refers to within or between subject variance)	Pearson; Spearman mentioned but not reported	ADC and LFB: r = .28; ADC and PLP: r = .16 ; FA and LFB: r = -.63, p < .01; FA and PLP: r = -.35, p < .05	NA	-	- (statistical design)
53	Seewann, A., Vrenken, H., Van der Valk, P., Blezer, E., Knol, D., Castelijns, J., … Geurts, J. (2020). Diffusely abnormal white matter in chronic multiple sclerosis. Arch Neurol, 66(5), 601–609.	Seewann2009	Human	MS	1 cm coronal brain slices	mean: 8.5 hours	WM-Ls, DAWM and NAWM	manual	MT	MTR	1.5	1 x 1 x 5 mm	fixed	not reported	paraffin embedding	10 µm	LFB, PAS, PLP	-	+	inverse staining intensity	ROI to ROI	Manual coregistration	10	10	42 (in total across subjects)	Mixed (modelled, but unclear whether result refers to within or between subject variance)	Pearson; Spearman mentioned but not reported	MTR and LFB: r = -.63, p < .01; MTR and PLP: r = -.27	NA	-	- (statistical design)
54	Soni, N., Vegh, V., To, X. V., Mohamed, A. Z., & Borges, K. (2020). Combined diffusion tensor imaging and quantitative susceptibility mapping discern discrete facets of white matter pathology post-injury in the rodent brain. Frontiers in Neurology, 11, 1–16.	Soni2020	Mouse	TBI and Controls	Whole brain	NA	Middle CC, CC-EC ipsilateral and contralateral to injury	AMBMC mouse atlas / Allen mouse atlas	QSM	Susceptibility	9.4	0.1 x 0.1 x 0.3 mm	in vivo	body temperature (36.5–37°C)	perfusion fixation, paraffin embedding	10 µm	MBP	-	-	manual scoring of immunoreactivity	ROI to ROI	No coregistration	36 TBI, 6 controls; correlation only for TBI group	36	3	Between-subject	Spearman	susceptibility: R2 = .1, p = .02 (only reported for 1 out of 3 ROIs)	NA	-	BS Spearman
55	Soustelle, L., Antal, M. C., Lamy, J., Rousseau, F., Armspach, J.-P., & Loureiro de Sousa, P. (2019). Correlations of quantitative MRI metrics with myelin basic protein (MBP) staining in a murine model of demyelination. NMR in Biomedicine, e4116.	Soustelle2019	Mouse	Cuprizone and Controls	Whole brain	NA	Medial and lateral CC, CT	manual	MT	MP('f')	7	0.1 x 0.1 x 0.750 mm	perfusion fixed	room temperature (20°C)	sectioning	60 µm	MBP	-	-	normalized staining intensity	ROI to ROI	No coregistration	7 cuprizone‐fed, 8 controls	15	3 (1/animal in each correlation)	Between-subject	Spearman	MP: All: r = .87, p < .05 (medial CC), r = .91, p < .05 (lateral CC); r = .89, p < .05 (CT); Controls only: MP: r = .36 (medial CC); r = .55 (lateral CC); r = .86 (CT); Cuprizone only: r = .64 (medial CC); r = .82 (lateral CC); r = .25 (CT);	NA	+	BS Spearman
55	Soustelle, L., Antal, M. C., Lamy, J., Rousseau, F., Armspach, J.-P., & Loureiro de Sousa, P. (2019). Correlations of quantitative MRI metrics with myelin basic protein (MBP) staining in a murine model of demyelination. NMR in Biomedicine, e4116.	Soustelle2019	Mouse	Cuprizone and Controls	Whole brain	NA	Medial and lateral CC, CT	manual	DWI	RD	7	0.1 x 0.1 x 0.750 mm	perfusion fixed	room temperature (20°C)	sectioning	60 µm	MBP	-	-	normalized staining intensity	ROI to ROI	No coregistration	7 cuprizone‐fed, 8 controls	15	3 (1/animal in each correlation)	Between-subject	Spearman	RD: All: r = -.7, p < .05 (medial CC), r = -.63, p > .05 (lateral CC); r = -.21, p > .05 (CT); Controls only: r = .38 (medial CC), r = .40 (lateral CC), r = .45 (CT); Cuprizone only: r = ‐.07 (medial CC), r = .14 (lateral CC), r = .79 (CT);	NA	+	BS Spearman
55	Soustelle, L., Antal, M. C., Lamy, J., Rousseau, F., Armspach, J.-P., & Loureiro de Sousa, P. (2019). Correlations of quantitative MRI metrics with myelin basic protein (MBP) staining in a murine model of demyelination. NMR in Biomedicine, e4116.	Soustelle2019	Mouse	Cuprizone and Controls	Whole brain	NA	Medial and lateral CC, CT	manual	Other	rSPF	7	0.152 x 0.152 x 0.750 mm	perfusion fixed	room temperature (20°C)	sectioning	60 µm	MBP	-	-	normalized staining intensity	ROI to ROI	No coregistration	7 cuprizone‐fed, 8 controls	15	3 (1/animal in each correlation)	Between-subject	Spearman	rSPF: r = .86, p < .05 (medial CC), r = .76, p < .05 (lateral CC), r = .52, p > .05 (CT)	NA	+	BS Spearman
55	Soustelle, L., Antal, M. C., Lamy, J., Rousseau, F., Armspach, J.-P., & Loureiro de Sousa, P. (2019). Correlations of quantitative MRI metrics with myelin basic protein (MBP) staining in a murine model of demyelination. NMR in Biomedicine, e4116.	Soustelle2019	Mouse	Cuprizone and Controls	Whole brain	NA	Medial and lateral CC, Cortex	manual	Relaxometry	MWF	7	0.1 x 0.1 x 0.750 mm	perfusion fixed	room temperature (20°C)	sectioning	60 µm	MBP	-	-	normalized staining intensity	ROI to ROI	No coregistration	7 cuprizone‐fed, 8 controls	15	3 (1/animal in each correlation)	Between-subject	Spearman	MWF: r = .68, p < .05 (medial CC), r = .69, p < .05 (lateral CC), r = .20, p > .05 (CT)	NA	+	BS Spearman
56	Stüber, C., Morawski, M., Schäfer, A., Labadie, C., Wähnert, M., Leuze, C., … Turner, R. (2014). Myelin and iron concentration in the human brain: A quantitative study of MRI contrast. NeuroImage, 93, 95–106.	Stueber2014	Human	Controls	Brain tissue blocks (pre/postcentral gyrus, posterior occipital lobe and subthalamic nucleus)	36 and 28 hours	GM and WM	NA	Relaxometry	R1, R2*	7	R1: 0.1 or 0.2 mm isotropic, R2*: 0.2 mm isotropic	fixed	not reported	cryosectioning	30 µm	PIXE	+	-	model-based estimation of myelin volume fraction	pixel-wise	Landmark-based registration	3	3	pixel-wise	Within-subject	Pearson; linear regression (univariate and multiple)	R1/R2*: p < .001; R2*: r=0.805	R1: slope: 1.066 ± 0.016, intercept: 1.132 ± 0.009; R2*: slope: 38.59 ± 0.50, intercept: 45.86 ± 0.29,	-	- (N = 3)
56	Stüber, C., Morawski, M., Schäfer, A., Labadie, C., Wähnert, M., Leuze, C., … Turner, R. (2014). Myelin and iron concentration in the human brain: A quantitative study of MRI contrast. NeuroImage, 93, 95–106.	Stueber2014	Human	Controls	Brain tissue blocks (pre/postcentral gyrus, posterior occipital lobe and subthalamic nucleus)	36 and 28 hours	GM and WM	NA	QSM	Susceptibility	7	0.070 mm isotropic	fixed	not reported	cryosectioning	30 µm	PIXE	+	-	model-based estimation of myelin volume fraction	pixel-wise	Landmark-based registration	3	3	pixel-wise	Within-subject	Pearson; linear regression (univariate and multiple)	Susceptability: p < .001	Susceptibility: slope: - 0.069 ± 0.002, intercept: - 0.025 ± 0.001	-	- (N = 3)
57	Sundberg, L. M., Herrera, J. J., & Narayana, P. A. (2010). In vivo longitudinal MRI and behavioral studies in experimental spinal cord injury. Journal of Neurotrauma, 27, 1753–1767.	Sundberg2010	Mouse	SCI and Controls	Spinal cord	NA	Area centred on injury	manual	DWI	AD, FA, RD	7	0.2 x 0.2 x 1 mm	in vivo	37°C	perfusion fixation, cryosectioning	35 µm	MAB328	-	+	staining fraction	ROI to ROI	No coregistration	15 injury, 9 control (two groups analysed separately)	15, 9 depending on the analysis	3	Mixed (not modelled)	Pearson	AD: r = .4825, p = .0216 (lateral), r = .4799, p = .0282 (dorsal); FA: r = -.8235, p = .0382 (dorsal column of caudal zone);	NA	-	- (statistical design)
58	Takagi, T., Nakamura, M., Yamada, M., Hikishima, K., Momoshima, S., Fujiyoshi, K., … Okano, H. (2009). Visualization of peripheral nerve degeneration and regeneration: Monitoring with diffusion tensor tractography. NeuroImage, 44(3), 884–892.	Takagi2009	Rat	Injury	Sciatic nerve	NA	Individual nerves	random selection of nerves	DWI	FA	7	0.31 x 0.31 x 0.94 mm	excised	not reported	fixation and sectioning	80 nm	EM	-	+	staining fraction	sample to sample	NA	10	70	1	Unclear	Pearson	FA: r = .2387, p = .4796 (myelin sheath density); r = -.6941, p = .0178 (Myelin sheath thickness)	NA	-	- (statistical design)
59	Thiessen, J. D., Zhang, Y., Zhang, H., Wang, L., Buist, R., Del, M. R., … Martin, M. (2013). Quantitative MRI and ultrastructural examination of the cuprizone mouse model of demyelination. NMR in Biomedicine, 26(11).	Thiessen2013	Mouse	Cuprizone and Controls	Whole brain	NA	CC	manual	DWI	AD, FA, RD	7	0.098 × 0.098 × 0.750 mm	perfusion fixed	room temperature	epon embedding	1 µm	EM	-	+	staining fraction (MA, MSF)	ROI to ROI	No coregistration	5 cuprizone, 5 controls	10	1	Between-subject (both within groups and pooled across groups) and within-group results have n=5 rather than n=10	Spearman	AD: r = -.75, p < .001 (MSF); r = -.89, p < .01 (MA); FA: r = .84, p < .01 (MSF), r = .7, p < .001 (MA); MD: r = .81, p < .01 (MSF); r = .81, p < .01 (MA); RD: r = .87, p < .01 (MSF); r = -.77, p < .001 (MA); for correlation separately for each group see paper	NA	+	BS Spearman
59	Thiessen, J. D., Zhang, Y., Zhang, H., Wang, L., Buist, R., Del, M. R., … Martin, M. (2013). Quantitative MRI and ultrastructural examination of the cuprizone mouse model of demyelination. NMR in Biomedicine, 26(11).	Thiessen2013	Mouse	Cuprizone and Controls	Whole brain	NA	CC	manual	MT	MP('f'), MTR	7	0.098 × 0.098 × 0.750 mm	perfusion fixed	body temperature	epon embedding	1 µm	EM	-	+	staining fraction (MA, MSF)	ROI to ROI	No coregistration	5 cuprizone, 5 controls	10	1	Between-subject (both within groups and pooled across groups) and within-group results have n=5 rather than n=10	Spearman; Pearson only for f	MP: r = .93; p < .001 (MSF); r = .81, p < .01 (MA); MTR: r = .72, p < .001 (MSF); r = .73, p < .001 (MA); for correlation separately for each group see paper; Pearson: r = 0.98	Myelin = 5.37 * MP - 0.25	+	BS Spearman (plus BS Pearson for MP)
59	Thiessen, J. D., Zhang, Y., Zhang, H., Wang, L., Buist, R., Del, M. R., … Martin, M. (2013). Quantitative MRI and ultrastructural examination of the cuprizone mouse model of demyelination. NMR in Biomedicine, 26(11).	Thiessen2013	Mouse	Cuprizone and Controls	Whole brain	NA	CC	manual	Relaxometry	T1	7	0.098 × 0.098 × 0.750 mm	perfusion fixed	room temperature	epon embedding	1 µm	EM	-	+	staining fraction (MA, MSF)	ROI to ROI	No coregistration	5 cuprizone, 5 controls	10	1	Between-subject (both within groups and pooled across groups) and within-group results have n=5 rather than n=10	Spearman	T1: r = -.66, p < .001 (MSF); r = -.73 (MA); for correlation separately for each group see paper	NA	+	BS Spearman
60	Tu, T. W., Williams, R. A., Lescher, J. D., Jikaria, N., Turtzo, L. C., & Frank, J. A. (2016). Radiological-pathological correlation of diffusion tensor and magnetization transfer imaging in a closed head traumatic brain injury model. Annals of Neurology, 79(6), 907–920.	Tu2016	Rat	TBI	Whole brain	NA	AC, CC, CT, CP, EC, PT, ST	manual	DWI	AD, FA, MD, RD, MTR at different ppm	7	DWI: 0.2 x 0.2 x 0.2 mm; MT: 0.2 x 0.2 x 0.5 mm;	in vivo	body temperature	cryosections	10 µm	MBP	-	+	normalised staining intensity	ROI to ROI	No coregistration	5	25	7	Unclear (likely mixed, not modelled)	Pearson	AD: r = -.01; FA: r =.13, MD: r = -.17, RD: r = -.46 (p < .01); MTR-3.5: r = .38 (p < .01), MTR-20: r = .28	NA	-	- (statistical design)
61	Turati, L., Moscatelli, M., Mastropietro, A., Dowell, N. G., Zucca, I., Erbetta, A., … Minati, L. (2015). In vivo quantitative magnetization transfer imaging correlates with histology during de- and remyelination in cuprizone-treated mice. NMR in Biomedicine, 28, 327–337.	Turati2015	Mouse	Cuprizone (D+R) and Controls	Whole brain	NA	CC	manual	MT	MP('f')	7	0.1 x 0.1 x 0.6 mm	in vivo	body temperature	perfusion fixation, cryosectioning	10 µm	Black Gold II, MBP	-	-	staining intensity	ROI to ROI	No coregistration	15 per mouse strain	15 for each analysis	1	Between-subject (pooled across groups)	Spearman	MP: in C57BL/6 mice: r = .743, p = .002 (BGII); r = .589, p = .023 (MBP); in SJL/J mice: r = .586, p = .024 (BGII) and r = .536, p = .042 (MBP)	NA	+	BS Spearman
62	Underhill, H. R., Rostomily, R. C., Mikheev, A. M., Yuan, C., & Yarnykh, V. L. (2011). Fast bound pool fraction imaging of the in vivo rat brain: Association with myelin content and validation in the C6 glioma model. NeuroImage, 54(3), 2052–2065.	Underhill2011	Rat	C6 glioma model and Controls	Whole brain	NA	ROIs across the brain, including WM and GM	manual	MT	MP('BPF'), MTR	3	0.3 × 0.3 × 0.3 mm	in vivo	body temperature	perfusion fixation, paraffin embedding	5 µm	LFB	-	+	normalized staining intensity	ROI to ROI	No coregistration	5 and 4	9	1	Within-subject (mixed, modelled)	Pearson	MP: r = .99 (p < .001), r = .91, p = .03 (just GM), r = .95, p = .0047 (just WM); MTR: r = .96 (p < .001), r = .93, p = .021 (just GM), r = -.21, p = .79 (just WM); for results on four-parameter estimation of MP, see paper	MP = 0.21 * myelin + 3.9	+	WS Pearson
63	van der Voorn, J., Pouwels, P., Powers, J., Kamphorst, W., Martin, J., Troost, D., … van den Knapp, M. (2011). Correlating quantitative MR imaging with histopathology in X-Linked adrenoleukodystrophy. AJNR, 32, 481–489.	Vandervoorn2011	Human	X-ALD and Controls	Coronal brain tissue sections	not reported	Areas with complete or active demyelination and NAWM	manual	DWI	ADC, FA	1.5	2 x 2 x 8 mm	fixed	room temperature (20-22°C)	paraffin embedding	7 µm	LFB	-	+	inverse staining intensity	ROI to ROI	Manual coregistration	15 patients, 5 controls	20	55 (in total across subjects)	Mixed (not modelled)	Pearson, linear regression analysis	ADC: r = - .637 (p < .01); FA: r = .766 (p < .01)	Myelin = -13.7 + 143.9 * FA	-	- (statistical design)
63	van der Voorn, J., Pouwels, P., Powers, J., Kamphorst, W., Martin, J., Troost, D., … van den Knapp, M. (2011). Correlating quantitative MR imaging with histopathology in X-Linked adrenoleukodystrophy. AJNR, 32, 481–489.	Vandervoorn2011	Human	X-ALD and Controls	Coronal brain tissue sections	not reported	Areas with complete or active demyelination and NAWM	manual	MT	MTR	1.5	not reported (3 mm sections)	fixed	room temperature (20-22°C)	paraffin embedding	7 µm	LFB	-	+	inverse staining intensity	ROI to ROI	Manual coregistration	15 patients, 5 controls	20	55 (in total across subjects)	Mixed (not modelled)	Pearson, linear regression analysis	MTR: r = .727 (p < .01)	Not reported	-	- (statistical design)
64	van Tilborg, E., Achterberg, E. J. M., van Kammen, C. M., van der Toorn, A., Groenendaal, F., Dijkhuizen, R. M., … Nijboer, C. H. A. (2018). Combined fetal inflammation and postnatal hypoxia causes myelin deficits and autism-like behavior in a rat model of diffuse white matter injury. Glia, 66(1), 78–93.	VanTilborg2018	Rat	Fetal inflammation and postnatal hypoxia	Whole brain	NA	Motor cortex (M1, M2), sensory cortex	atlas-based	DWI	FA, RD	9.4	0.15 x 0.15 x 0.148 mm	perfusion fixed	not reported	paraffin embedding	8 µm	MBP	-	-	staining fraction	unclear	Unclear	6	12	3	Between-subject	Linear regression	FA: R2 = .341, p = .046 (M1 motor), R2 = .334, p = .049 (M2 motor), R2= .428, p = .021 (sensory)	not reported	+	BS Pearson
65	Wang, S., Wu, E. X., Cai, K., & Lau, H. (2009). Mild hypoxic-ischemic injury in the neonatal rat brain: longitudinal evaluation of white matter. AJNR, 30, 1907–1913.	Wang2009	Rat	MHII	Whole brain	NA	EC (ipsilesional and contralesional)	manual	DWI	AD, FA, RD, "Trace"	7	Varying resolution: 0.250 x 0.250 x 0.5 mm for some scans, 0.313 x 0.313 x 0.7 mm for others	in vivo	body temperature	perfusion fixation, cryosectioning	10 µm	LFB	-	+	staining intensity	ROI to ROI	No coregistration	15 at different ages	15	Unclear (likely 2)	Unclear (likely mixed, not modelled)	Pearson	FA: r = .681, p < .01; RD: r = 0.528, p < .01; AD and Trace showed no significant correlation	NA	-	- (statistical design)
66	Wang, Y., Sun, P., Wang, Q., Trinkaus, K., Schmidt, R. E., Naismith, R. T., … Song, S. (2015). Differentiation and quantification of inflammation, demyelination and axon injury or loss in multiple sclerosis. Brain, 138, 1223–1238.	Wang2015	Human	MS	Section of cervical spinal cord	<10 hours	Voxels with positive histological staining	random selection of voxels	DWI	DBSI-RD	4.7	0.250 x 0.250 x 0.5 mm	fixed	17°C	paraffin embedding	5 µm	LFB	-	+	staining fraction	voxel-wise	Landmark-based linear coregistration (rigid body, based on 13 landmarks)	3	3	80 voxels (subset of total voxels selected for analysis)	Within-subject	Spearman	DBSI-RD: r = - .84 (p < .0001), r = -.42 (p = .039), r = -.82 (p < .0001)	Available for each subject - see paper	-	- (N = 3)
67	Warntjes, J., Persson, A., Berge, J., & Zeche, W. (2017). Myelin detection using rapid quantitative MR imaging correlated to macroscopically registered Luxol Fast Blue – stained brain specimens. AJNR, 1096–1102.	Warntjes2017	Human	Controls	2 cm brain slices (one through caudate nucleus and one through thalamus)	20 hours to 3 days range (during which body was refrigerated)	GM and WM	NA	Relaxometry	MWF, R1	3	0.7 x 0.7 x 4 mm	in situ	mean: 7.8° (SD: 3.1°C)	fixation	4 µm	LFB	-	-	staining intensity	pixel-wise	Manual coregistration by rotation, translation, and scaling	12	12	voxel-wise	Within-subject (mixed, modelled)	Spearman; linear regression	R1: r = .63 ± .12; MWF: r =0.74 ± 0.11	R1: slope: 0.065 ± 0.009; intercept: 1.19 ± 0.10	-	WS Spearman
68	Webb, S., Munro, C. A., Midha, R., & Stanisz, G. J. (2003). Is multicomponent T2 a good measure of myelin content in peripheral nerve? Magnetic Resonance in Medicine, 49(4), 638–645. https://doi.org/10.1002/mrm.10411	Webb2003	Rat	Nerve injury and Controls	Sciatic nerve	NA	Sections of individual nerves	manual	Relaxometry	MWF	1.5	unclear	fresh	20°C	fixation, crosssectioning	1 µm	Toluidine blue	-	+	staining fraction	ROI to ROI	Manual coregistration	6	18	2	Mixed (not modelled)	Linear regression	MWF: r = .59, p < .001 (all fibres); r = .75, p < .0001 (healthy fibres)	MWF: slope = 0.4 ± 0.1 (all fibres), slope = 0.7 ± 0.1 (healthy fibres)		- (statistical design)
69	Wei, P. T., Leong, D., Calabrese, E., White, L., Pierce, T., Platt, S., & Provenzale, J. (2013). Diffusion tensor imaging of neural tissue organization: correlations between radiologic and histologic parameters. The Neuroradiology Journal, 26, 501–510.	Wei2013	Dog	Controls	Whole brain	NA	ROIs across the brain, including WM and GM	manual	DWI	FA, RD	7	0.1 mm isotropic	perfusion fixed	not reported	cryosectioning	50000 µm	Gold chloride	-	-	inverse staining intensity	ROI to ROI	3D stacking of histological images and linear coregistration	1	1	20	Within-subject	Pearson; linear regression	FA: r = .12, p = .68 (WM), r = .61, p = .32 (GM). RD: r = .55, p = .15 (WM), r = .594, p = .28 (GM)	Not reported	-	- (N = 1)
70	West, K. L., Kelm, N. D., Carson, R. P., Gochberg, D. F., Ess, K. C., & Does, M. D. (2018). Myelin volume fraction imaging with MRI. NeuroImage, 182(2016), 511–521.	West2018	Mouse	Genetic model for hyper-/hypomyelination	Whole brain	NA	CC, AC, CT	manual	Relaxometry	MWF	15.2	.150 x .150 x .150 mm	perfusion fixed	not reported	ultrasectioning	0.07 µm	EM	-	+	staining fraction	unclear	NA	3 per group, 6 controls	15	unclear (likely 4)	Mixed (not modelled)	Linear regression	MWF: R2 = .66	MWF = .056 * myelin – 0.014	-	- (statistical design)
70	West, K. L., Kelm, N. D., Carson, R. P., Gochberg, D. F., Ess, K. C., & Does, M. D. (2018). Myelin volume fraction imaging with MRI. NeuroImage, 182(2016), 511–521.	West2018	Mouse	Genetic model for hyper-/hypomyelination	Whole brain	NA	CC, AC, CT	manual	MT	MP (‘BPF')	15.2	.150 x .150 x .150 mm	perfusion fixed	not reported	ultrasectioning	0.07 µm	EM	-	+	staining fraction	unclear	NA	3 per group, 6 controls	15	unclear (likely 4)	Mixed (not modelled)	Linear regression	MWF: R2 = .70	MWF = .056 * myelin– 0.014	-	- (statistical design)
71	Yano, R., Hata, J., Abe, Y., Seki, F., Yoshida, K., Komaki, Y., … Tanaka, K. F. (2018). Quantitative temporal changes in DTI values coupled with histological properties in cuprizone-induced demyelination and remyelination. Neurochemistry International, 119, 151–158.	Yano2018	Mouse	Cuprizone (D+R) and Controls	Whole brain	NA	CC	manual	DWI	FA, MD, RD	7	0.125 × 0.125 × 0.125 mm	perfusion fixed	not reported	cryosectioning	25 µm	PLP	-	-	staining fraction	ROI to ROI	No coregistration	18 cuprizone treated, 3 controls	21	1	Between-subject	Pearson	FA: r = .87, p = 3.89 x 10E-7; MD: r = -.73, p = 1.54 x 10E-4; RD: r = -.91, p = 1.04 x 10E-8	NA	+	BS Pearson