Computational protocol: 3D interactive tractography informed resting state fMRI connectivity

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Protocol publication

[…] Non-local means (NLM) denoising was applied to the T1-weigthed image prior to using the brain extraction tool (BET) of FSL (Smith, ). This facilitated the registration procedure to the upsampled (1 mm isotropic resolution) b = 0 diffusion image using ANTS (Avants et al., ). [...] Images were first motion and slice-time corrected using the efficient implementation publicly available in AFNI (Cox, ). Next, the data were spatially smoothed using NLM denoising (Coupe et al., ; Bernier et al., ) implemented in Dipy (Garyfallidis et al., ) using default parameters, and band-pass filtered (0.008–0.08 Hz). The global signal at each voxel was not regressed to avoid the introduction of anti-correlated regions (Saad et al., ). […]

Pipeline specifications

Software tools BET, AFNI, Dipy
Applications Magnetic resonance imaging, Functional magnetic resonance imaging
Organisms Homo sapiens
Diseases Neoplasms, Nervous System Diseases