diffusion
====== Differences ====== This shows you the differences between two versions of the page.
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diffusion [2016/08/17 19:31] bdelab created |
diffusion [2016/08/17 19:33] (current) bdelab |
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| ====Preprocess diffusion data==== | ====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: | + | 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> | <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 | This function is also wrapped within another utility to run this whole pipeline (steps a-e) on a subject | ||
| <code>bde_preprocessdiffusion</code> | <code>bde_preprocessdiffusion</code> | ||
diffusion.1471462312.txt.gz · Last modified: 2016/08/17 19:31 by bdelab
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