Data Analysis
Data Acquisition
Human Connectome Project
Lab Admin
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- Lab Handbook
Useful Resources
Data Analysis
Data Acquisition
Human Connectome Project
Lab Admin
Useful Resources
If diffusion data was acquired on the subject we want to (a) correct for EPI distortions in the data using FSL's topup tool; (b) correct for subject motion and eddy currents; (c) fit a tensor model and create a dt6.mat file; (d) fit the CSD model with mrtrix; (e) run AFQ to segment the fibers into all the major fiber groups. Jason Yeatman has written a helpful utility to run FSL's topup and eddy functions:
fsl_preprocess(dwi_files, bvecs_file, bvals_file, pe_dir, outdir)
This function is also wrapped within another utility to run this whole pipeline (steps a-e) on a subject
bde_preprocessdiffusion