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muscbridge / PyDesigner

A hands-free DTI, DKI, FBI and FBWM preprocessing pipeline. Information on algorithms and preprocessing steps are available at https://www.biorxiv.org/content/10.1101/2021.10.20.465189v1 A video tutorial on PyDesigner and its usage is now available at https://www.youtube.com/watch?v=mChQFuQqX3k
https://pydesigner.readthedocs.io/en/latest/
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Just want to do image and tensor post-processing steps.... #315

Open gonzoBlackMamba opened 10 months ago

gonzoBlackMamba commented 10 months ago

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