Just want to do image and tensor post-processing steps....

[gonzoBlackMamba]

Discussed in https://github.com/muscbridge/PyDesigner/discussions/313

^{Originally posted by RoosvOeveren November 28, 2023} Hi PyDesigner community,

Is it possible to run PyDesigner without any pre-processing at all? I have multi-shell data that has already been preprocessed, from which I would like to obtain DTI and DKI metrics.

I ran PyDesigner on my raw data ('pydesigner -s --verbose -o [output directory] [xxx.nii]'), which resulted in all the expected outcome measures. However, brain distortions in these outcome measures (e.g. in dti_fa maps) are worse than in my own pre-processed data.

I tried simply running PyDesigner with my pre-processed data, without any pre-processing flag ('pydesigner --verbose -o [output directory] [xxx.nii]'). The outputs however are noisy DTI metrics and no DKI at all.

Is there a command line or flag that enables only post-processing?

Thank you in advance, Roos