Difference between revisions of "Diffusion Pipeline"
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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: | ||
| + | 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 | ||
Latest revision as of 23:22, 30 September 2015
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:
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
