Yeatman Lab Wiki

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====Preprocess diffusion data==== 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: <code>fsl_preprocess(dwi_files, bvecs_file, bvals_file, pe_dir, outdir)</code> This function is also wrapped within another utility to run this whole pipeline (steps a-e) on a subject <code>bde_preprocessdiffusion</code>