Questions about the input of the raw data.

[Silflame]

Hi, I want to ask if I'm using --raw_diffusion_input and --preprocess, is it necessary to do eddy_correct for the raw data before taking the data as input? In other words, I am concerned about whether this pipeline will automatically perform eddy_correct with the this commd: TractSeg -i /dti/data.nii.gz -o /output/ --bvals /dti/bvals --bvecs /dti/bvecs --raw_diffusion_input --preprocess --single_output_file. And when using this command, what preprocessing operations will it contain ? Thank you.

[wasserth]

This command will not run eddy_correct for you. You will have to do that yourself before feeding the data to the script.

• --preprocess will only move the Diffusion image + bvecs to MNI space (rigid registration) and move the results of TractSeg back to subject space in the end
• --raw_diffusion_input will only run Mrtrix CSD and extract the peaks

Everything else you have to do on your own.