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

3

Thank you @Steven .I wonder if reverse transformation will reduce the accuracy of DTI data? I’m calculating DTI-ALPS index,and find that almost all preprocess pipelines transform dwi data into anatomic space or template space after utilizing fsl-ditfit.I attempted to run fsl-ditfit on QSIprep preprocessed dwi data. However,I found that the brain mask provided by QSIprep was mismatched with the FA/V1 images.Additionally, the FA/V1 images appeared more blurred compared to thosed generated by standard DTI-ALPS preprocessing pipeline.