dti toolbox  (MathWorks Inc)

Journal: bioRxiv

Article Title: Detection of Region-specific Fiber Damage within Injured Spinal Cord Using Advanced Diffusion MRI

doi: 10.1101/2025.07.02.662840

Figure Lengend Snippet: Comparison of diffusion parametric maps of the center slice from one representative subject. (A) Pre-lesion. (B) Post-lesion. MTC, magnetization transfer contrast. Measures from spherical mean technique: D ax , intrinsic axonal diffusivity; D ex , extra axonal transverse diffusivity; V ax , apparent axonal volume fraction. Measures from diffusion tensor imaging: MD, mean diffusivity; AD, axial diffusivity; RD, radial diffusivity; FA, fractional anisotropy. Red cross indicates the column lesion on one side of dorsal pathway (DP). V, ventral; D, dorsal; C, non-lesion contralateral side, L, lesion side. The segment directly underwent unilateral dorsal column lesion is shown.

Article Snippet: Conventional DTI parameters, including FA, AD, RD, and MD, were quantified using the DTI Toolbox in MATLAB based on diffusion data from the b = 1000 s/mm shell.

Techniques: Comparison, Diffusion-based Assay, Imaging

Journal: bioRxiv

Article Title: Detection of Region-specific Fiber Damage within Injured Spinal Cord Using Advanced Diffusion MRI

doi: 10.1101/2025.07.02.662840

Figure Lengend Snippet: Comparison of diffusion parametric maps and corresponding histological maps in one representative spinal cord with a unilateral dorsal column lesion across five axial slices from caudal to rostral along the cord. (A) DTI-derived parameter maps. (B) SMT-derived parameter map. (C) Silver staining of corresponding spinal cord tissue. V: ventral; D: dorsal; C: non-lesion contralateral side; L: lesion side. FA, fractional anisotropy; AD, axial diffusivity; RD, radial diffusivity; MD, mean diffusivity. V ax , apparent axonal volume fraction; D ax , intrinsic axonal diffusivity; D ex , extra axonal transverse diffusivity. The red cross indicates the lesion site. The red asterisks indicate the increase of AD and D ax at the lesion site while the white asterisks indicate unilateral decrease in slice distal to the lesion on the rostral side. Fonts are too small.

Article Snippet: Conventional DTI parameters, including FA, AD, RD, and MD, were quantified using the DTI Toolbox in MATLAB based on diffusion data from the b = 1000 s/mm shell.

Techniques: Comparison, Diffusion-based Assay, Derivative Assay, Silver Staining

Journal: bioRxiv

Article Title: Detection of Region-specific Fiber Damage within Injured Spinal Cord Using Advanced Diffusion MRI

doi: 10.1101/2025.07.02.662840

Figure Lengend Snippet: Regional comparison of DTI-derived diffusion measures in five ROIs across slices of injured spinal cords with those from healthy cords. Boxplots of DTI-derived FA, RD, AD, and MD metrics show the differences for the selected ROIs from the healthy spinal cords without injury, non-lesioned contralateral side of the lesioned segment (slice 3 as indicated in ), and different segments on the lesion side from caudal to rostral (slices 1-5 as indicated in ) of the injured spinal cord. Middle lines indicate medians and markers indicate mean values. * p < 0.05, ** p < 0.01, *** p < 5x10 - , **** p < 10 - , ***** p < 5x10 - , and ****** p < 2x10 - vs. the corresponding regional values for the healthy spinal cords (Wilcoxon rank sum test). Three white matter ROIs (VP: ventral pathway, LP: lateral pathway, DP: dorsal pathway) and two gray matter ROIs (VH: ventral horn, DH: dorsal horn) are as defined in . MD, mean diffusivity; AD, axial diffusivity; RD, radial diffusivity; FA, fractional anisotropy.

Article Snippet: Conventional DTI parameters, including FA, AD, RD, and MD, were quantified using the DTI Toolbox in MATLAB based on diffusion data from the b = 1000 s/mm shell.

Techniques: Comparison, Derivative Assay, Diffusion-based Assay

Journal: bioRxiv

Article Title: Detection of Region-specific Fiber Damage within Injured Spinal Cord Using Advanced Diffusion MRI

doi: 10.1101/2025.07.02.662840

Figure Lengend Snippet: Regional correlations between diffusion and histological measures. (A) Matrix plot of correlation coefficients ( r values) between different SMT- and DTI-derived metrics and histological inD ex (HI) of fiber density. ‘x’ indicates correlation that is not significant ( p > 0.05). Diffusion measures: V ax , apparent axonal volume fraction; D ax , intrinsic axonal diffusivity; D ex , extra axonal transverse diffusivity; FA, fractional anisotropy; MD, mean diffusivity; AD, axial diffusivity; RD, radial diffusivity. Number of entries per injured subject is 50 (10 ROIs on both control and lesion sides for each of the 5 slices). Total 300 entries for each metrics (number of subjects = 6) were included in correlation analysis. (B) Linear regression curve showing the relationship between histological inD ex and V ax . The regression statistics including adjusted R and root mean squared error (RMSE) from modeling are included to show the goodness of predication for histological inD ex . The cysts were indicated by + symbols (Histological inD ex < 50).

Article Snippet: Conventional DTI parameters, including FA, AD, RD, and MD, were quantified using the DTI Toolbox in MATLAB based on diffusion data from the b = 1000 s/mm shell.

Techniques: Diffusion-based Assay, Derivative Assay, Control

Journal: bioRxiv

Article Title: Detection of Region-specific Fiber Damage within Injured Spinal Cord Using Advanced Diffusion MRI

doi: 10.1101/2025.07.02.662840

Figure Lengend Snippet: Regional correlations between normalized differences of diffusion and histological measures across all the regions within the injured spinal cord. (A) Matrix plot of correlation coefficients ( r values) between normalized regional differences of different SMT- and DTI-derived metrics and that of histological inD ex (ΔHI) of the injured spinal cords. The symbol ‘x’ indicates correlation that is not significant ( p > 0.05). Normalized regional difference of axonal volume fraction between respective regions on the lesion and non-lesioned contralateral sides: ΔV ax = (lesion-side V ax – contralateral V ax )/contralateral V ax . The normalized regional differences of other diffusion metrics and histological measures were calculated similarly. ΔD ax , ΔD ex , ΔFA, ΔMD, ΔAD, and ΔRD are normalized regional differences of intrinsic axonal diffusivity, extra axonal transverse diffusivity, fractional anisotropy, mean diffusivity, axial diffusivity, and radial diffusivity, respectively. ΔHI, normalized difference of histological inD ex . Number of entries per injured subject is 25 (5 entries for each of the 5 slices). Total 150 entries for each metrics (number of subjects = 6) were included in correlation analysis. (B) Linear regression curve showing the relationship between ΔHistological InD ex and ΔV ax . The regression statistics including adjusted R and root mean squared error (RMSE) from modeling are included to show the goodness of predication for Δhistological inD ex . The cysts were indicated by + symbols (Histological inD ex < 50).

Article Snippet: Conventional DTI parameters, including FA, AD, RD, and MD, were quantified using the DTI Toolbox in MATLAB based on diffusion data from the b = 1000 s/mm shell.

Techniques: Diffusion-based Assay, Derivative Assay

Journal: Tomography

Article Title: Magnetic Resonance Imaging Biomarkers of Muscle

doi: 10.3390/tomography10090106

Figure Lengend Snippet: Representative images of three athletes showing coronal fat-suppressed T2-weighted images of the hamstring injury depicted by the red oval (first column) together with axial spin-echo EPI images ( b -value = 0 s/mm 2 ) (second column), reconstructed mean diffusivity (MD) maps (third column), and reconstructed qT2 maps (fourth column) at the three time points (time point 1: within 1 week postinjury; time point 2: 2 weeks after visit 1; and time point 3: at clinical return to play). DTI, diffusion tensor imaging; qT2, quantitative T2. Reproduced with permission from the authors in Ref. .

Article Snippet: Recently, a DTI Matlab toolbox was released that allows users to perform tractography as well as to obtain muscle architectural parameters including fiber length, pennation angle, and curvature [ ]. is an example of fiber tracking in the medial gastrocnemius using this toolbox customized to the acquisition in the authors’ lab.

Techniques: Diffusion-based Assay, Imaging