Citation
Cieslak, Matthew, Philip A Cook, Xiaosong He, Fang-Cheng Yeh, Thijs Dhollander, Azeez Adebimpe, Geoffrey K Aguirre, et al. 2021. “QSIPrep: An Integrative Platform for Preprocessing and Reconstructing Diffusion Mri Data.” Nature Methods 18 (7). Nature Publishing Group US New York: 775–78. https://doi.org/10.1038/s41592-021-01185-5.
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Preprocessed diffusion data (QSIPrep outputs) were further analyzed using QSIRecon, which executes reconstruction workflows defined in a recon-spec YAML file. This file specifies reconstruction steps, parameter settings, post-processing tools, and software dependencies. We used two recon-spec files: one for AutoTrack bundle reconstruction and bundle-wise statistics (Bundle Stats), and another for whole-brain connectivity matrices (Inter-regional tractography).

Bundle Stats

Diffusion tensors were estimated with TORTOISE, and diffusion orientation distribution functions (ODFs) were reconstructed using two approaches: generalized q-sampling imaging (GQI) in DSI Studio and single-shell three-tissue constrained spherical deconvolution (SS3T-CSD) in MRtrix3. AutoTrack tractography was applied to both GQI and SS3T reconstructions to delineate major white matter tracks. For each method, bundle-wise mean values were computed for GQI and tensor scalars.

Inter-regional tractography

Streamlines were generated using Anatomically-Constrained Tractography (ACT) with Hybrid Surface/Volume Segmentation (HSVS), and connectivity matrices were computed with tck2connectome.

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