Computational protocol: A Symmetry-Based Method to Infer Structural Brain Networks from Probabilistic Tractography Data

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Protocol publication

[…] We utilize the publicly available FiberCup dataset (Poupon et al., , ; Fillard et al., ) as one of the benchmarks to evaluate MANIA's accuracy. We use a FiberCup acquisition in which the b-value is 1500. FiberCup resembles a human brain coronal section with 18 ROIs and seven fiber bundles—see Figure 2 of Neher et al. (). These fiber bundles are constructed to include sharp turns as well as crossing, kissing and branching points, making it a challenging benchmark for any tractography algorithm. Due to the practical difficulties of generating a realistic phantom, FiberCup does not contain any complex 3D fiber structures.We apply probtrackx and MANIA on the FiberCup phantom to infer the network of the seven underlying connections. The FDT probabilistic tractography parameters are set to their default values (number of streamlines = 5000, maximum number of steps = 2000, loop check: set, curvature threshold = 0.2, step length = 0.5 mm, no distance bias correction). Probtrackx is seeded at the WGB of the ROIs that are connected to fiber terminals. [...] We also apply MANIA in Diffusion Tensor Imaging (DTI) data collected by an earlier study: “Brain aging in humans, chimpanzees (Pan troglodytes), and rhesus macaques (Macaca mulatta): magnetic resonance imaging studies of macro- and microstructural changes” (Chen et al., ). All subjects gave written informed consent, and the study was approved by the Emory University Institutional Review Board. We analyzed the data for 28 of those subjects mostly based on handedness (right-handed females, without a history of psychiatric disorder). Diffusion-weighted images were acquired using a Siemens 3T with a 12-channel parallel imaging phase-array coil. Foam cushions were used to minimize head motion. Diffusion MRI data were collected with a diffusion weighted SE-EPI sequence (Generalized Autocalibrating Partially Parallel Acquisitions [GRAPPA] factor of 2). A dual spin-echo technique combined with bipolar gradients was used to minimize eddy-current effects. The parameters used for diffusion data acquisition were as follows: diffusion-weighting gradients applied in 60 directions with a b-value of 1000 s/mm2; TR/TE of 8500/95 ms; FOV of 216 × 256 mm2; matrix size of 108 × 128; resolution of 2 × 2 × 2 mm3; and 64 slices with no gap, covering the whole brain. Averages of 2 sets of diffusion-weighted images with phase-encoding directions of opposite polarity (left–right) were acquired to correct for susceptibility distortion. For each average of diffusion-weighted images, 4 images without diffusion weighting (b = 0 s/mm2) were also acquired with matching imaging parameters. The total diffusion MRI scan time was approximately 20 min. T1-weighted images were acquired with a 3D MPRAGE sequence (GRAPPA factor of 2) for all participants. The scan protocol, optimized at 3T, used a TR/TI/TE of 2600/900/3.02 ms, flip angle of 8°, volume of view of 224 × 256 × 176 mm3, matrix of 224 × 256 × 176, and resolution of 1 × 1 × 1 mm3. Total T1 scan time was approximately 4 min.The resulting DTI data were processed using the FMRIB's Diffusion Toolbox (FDT) provided by FSL (FMRIB 4 Software Library) (Behrens et al., ). The FDT probabilistic tractography parameters were set to their default values (number of streamlines = 5000, maximum number of steps = 2000, loop check: set, curvature threshold = 0.2, step length = 0.5 mm, no distance bias correction).We applied MANIA on 18 corticolimbic ROIs. All ROIs are in the left hemisphere and localized in Montreal Neurological Institute (MNI) standard space using the Automated Anatomical Labeling (AAL) (Jenkinson and Smith, ) of the WFU PickAtlas toolbox (Lancaster et al., ). The ROI acronym as well as the number of voxels in each ROI are shown in Table . The shape of these ROIs are not dilated and we adhere to the standard masks provided in the WFU PickAtlas toolbox. We chose these ROIs because they are known to play a significant role in various psychiatric disorders such as MDD, PTSD, OCD, anxiety and addiction (Mayberg, ; Seminowicz et al., ; Craddock et al., ; James et al., ). This sample of ROIs includes cortical, subcortical and limbic regions. Specifically, the cortical ROIs are BA6, BA9, BA10, BA40, BA46, BA47, the limbic are BA24, Th, BS, and the sub-cortical are BA11, BA25, BA32, Acb, Amg, Hp, Ht, Ins, Pc. […]

Pipeline specifications

Software tools Probtrackx, MANIA, AAL
Applications Magnetic resonance imaging, Diffusion magnetic resonance imaging analysis
Organisms Homo sapiens