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Pipeline publication

[…] ue = 1,000, directions = 32, slice thickness = 3 mm, acquisition time = 9 min 7 sec. A high-resolution 3D TFE sequence was acquired with the following parameters: TR = 7.7 ms, TE = 3.6 ms, matrix = 228 × 228, FOV = 250 mm × 250 mm, 230 axial slices, acquisition time = 6 min 53 sec. In addition, axial T2-weighted MR images were acquired with the parameters: TR = 2,500 ms, TE = 80 ms, matrix = 332 × 225, FOV = 250 mm × 220 mm, slice thickness = 6 mm, 18 axial slices, acquisition time = 55 sec. The anatomical MR images were re-evaluated for any structural abnormalities and were reported as normal in all subjects., In this study, DTI data preprocessing and brain network were performed using the PANDA toolbox () which was an integration analysis toolbox comprising the Diffusion Toolkit (), FMRIB Software Library (), MRIcron (), and Pipeline System for Octave and Matlab (PSOM) (). And the whole process had been described in detail previously ()., Briefly, the preprocessing procedure included skull-stripping, eddy-current, and head-motion correction, FA calculation and whole-brain deterministic DTI fiber tractography (). First, the non-brain tissues of the images were deleted by employing the brain extraction tool (). Second, the head motion and eddy current distortions were corrected through registering the DW images to the b0 image with an affine transformation (). After correction, six elements of the diffusion tensor were then estimated from which FA was calculated. Then, Whole-brain fiber tractography was subsequently reconstructed by seeding at every voxel in the brain and using fiber assignment by continuous tracking algorithm (). This algorithm computes fiber trajectories starting from the deep WM regions and terminating at a voxel with a turning angle greater than 45° or reached a voxel with FA less than 0.15., As the construction of the structural network requires the f […]

Pipeline specifications

Software tools PANDA, FSL, MRIcron, BET