How can I get preprocessed dwi data in native dwi space

Software Support
1

Hello,Neurostars
How can I run QSIPrep to perform the standard preprocessing pipeline (MP-PCA, Gibbs, susceptibility, and motion correction) but skip the T1w registration step? I need the final output to remain in the native dwi space, not resampled to the anatomical ACPC space

2

Hi @mazh357, and welcome to neurostars!

There is no option to do this in qsiprep, but the transform between native and ACPC is supplied in the outputs, which you can apply to your outputs. Keep in mind you will also have to rotate the gradient table if you realign your DWI.

Best,
Steven