DOI: 10.6084/m9.figshare.23790120
title: Data set_reliability_analysis_segmentation_DTI

description: Data acquisition: Magnet resonance imaging (MRI) of the right shoulder was performed using a 3 Tesla MRI scanner (Siemens MAGNETOM Prisma Fit, Erlangen, Germany) with a dedicated 16-channel shoulder coil in the head-first supine position. The right shoulder was placed in a neutral position with the arm adducted and the hand supinated. The MR protocol consisted of a 3D coronal T1-weighted (T1w) and a sagittal DTI sequence from distal to proximal. The total scan time was approximately twelve minutes. The T1w sequence was acquired with the following parameters: repetition and echo time TR/TE = 492/20 ms, slice thickness = 0.7 mm, flip angle = 120°, field of view FOV = 180 x 180 mm2, matrix = 256 x 256 mm2. For DTI a commercial Siemens 2D echo planar diffusion image sequence was acquired with the following parameters: repetition and echo time TR/TE = 6100/69 ms, slice thickness = 4 mm, flip angle = 90°, field of view FOV = 240 x 240 mm2, matrix = 122 x 122 mm2, 48 diffusion sampling directions with b = 400 s/mm2. Muscle segmentation Manual segmentation was based on common mDTI methods described previously. Segmentation was performed using Mimics Materialise (v.24.0, Leuven, Belgium). Two independent and operators (SBA 1 and SBA 2) segmented each M. supraspinatus. Segmentation was based on the recorded T1w sequence of each subject. To compare individual differences in segmentation, each operator generated an individual segmentation routine for the whole data set. The first segmentation step was to generate a base mask by setting a threshold on the grey values of the images to separate muscle-tendons from bony structures. Then, both operators split the basic muscle mask to separate the M. supraspinatus from the other surrounding tissues and to proceed with manual segmentation and correction. While SBA 1 preferred manual segmentation, operator two (SBA 2) focused on interpolation using the integrated multi-slice editing function (Figure 1). However, both operators used semi-automatic segmentation functions and differed in time spent on each step. Finally, each surface model was smoothed by a factor of 0.5 and exported as a ROI for fiber tracking. <br> Figure 1. Workflow of methods. Workflow displays different processing steps and each methods duration in minutes (‘). Segmentation-based analysis by operator 1 (SBA 1) included four major segmentation steps, operator 2 (SBA 2) displayed three steps. Model-free analysis (MFA) did not include a segmentation and used the entire field of view as seeding area for deterministic fiber tracking. Within MFA the red cross symbolises the manual exclusion of tracts outside of the highlighted M. supraspinatus (blue color). <br> DTI data processing and fiber tracking DSI Studio (v. 3th of December 2021. http://dsi-studio.labsolver.org) was used for DTI processing, deterministic fiber tracking and tract calculations. To perform tractography for the M. supraspinatus, we registered and resampled the DTI images to the T1w images. The quality of the DTI and FA maps was first visually checked by two experts using DSI Studio. In addition, the DTI images were corrected for motion and eddy current distortion using DSI Studio's integrated FSL eddy current correction. To ensure plausible fiber tracking results, we used the following stopping criteria recommended: maximum angle between tract segments 15°, 20 mm ≤ tract length ≤ 130 mm; step size = 1.5 mm. These settings were oriented to FL results of cadaveric dissectionsand recommendations for deterministic muscle fiber tracking stopping criteria. Fiber tracking was then performed either within a model ROI (SBA methods) or for the entire DTI images without using a segmented model (MFA). After a reconstruction of ~10.000 tracts for the M. supraspinatus region, tractography was terminated and duplicates were deleted. Since MFA used the entire DTI image as a seeding area for tractography we removed all tracts outside the M. supraspinatus. Next, clearly implausible tracts and tracts crossing the muscle boundary within the SBA and MFA were reviewed and removed by two experts. Finally, DTI tensor parameters (FA, AD, MD and RD) and muscle parameters (MV, FL and FV) were calculated based on a deterministic fiber tracking algorithm and specific tracking strategies using DSI Studio. Since MFA did not include a muscle segmentation step, it took approximately 30 minutes. In contrast, SBA 1 and SBA 2, including segmentation, took approximately 90 and 60 minutes respectively. <br> Abbreviations dataset: SBA 1 Segmentation-based analysis by operator 1 SBA 2 Segmentation-based analysis by operator 2 MFA model-free analysis FL Fascicle length (mm) Fiber volume, FV (mm^3) MV (mm^3) muscle model volume FA (10^-3 mm/s) Fractional Anisotropy MD Mean Diffusivity RD Radial Diffusivity AD Axial Diffusivity