dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
Originally posted by **GalBenZvi** November 22, 2021
Hi all,
I've been using **mrtrix3** to process my diffusion data for the past few months and it seems to provide good results.
I was wondering if it might be beneficial to provide a mrtrix3-based pipeline in dMRIPrep?
I know that several functions of **mrtrix3** actually serve as wrappers for **FSL** functions (like dwifslpreproc), but some preprocessing tools that are available in **mrtrix3** aren't in **FSL** (like MP-PCA denoising, Gibbs de-ringing, etc.).
Would love your input on this matter!
Over the past few months, I've learned that mrtrix has an internal procedure for handling the rotation of b-vectors when applying such rotations and transformations to the DWI images (as part of many processes during preprocessing).
Additionally, I've implemented a pre-processing pipeline that is suitable for handling sophisticated fieldmap schemes (DWI+EPI) as this is the scheme we're using in my lab.
It is currently located in my fork of dMRIPrep but I would love to merge it into nipreps's original tool.
As mentioned, my pipeline utilizes mrtrix, but if this poses a problem in terms of integration with nipreps, I would be happy to explore alternatives.
Discussed in https://github.com/nipreps/dmriprep/discussions/186
Over the past few months, I've learned that mrtrix has an internal procedure for handling the rotation of b-vectors when applying such rotations and transformations to the DWI images (as part of many processes during preprocessing).
Additionally, I've implemented a pre-processing pipeline that is suitable for handling sophisticated fieldmap schemes (DWI+EPI) as this is the scheme we're using in my lab. It is currently located in my fork of dMRIPrep but I would love to merge it into nipreps's original tool. As mentioned, my pipeline utilizes mrtrix, but if this poses a problem in terms of integration with nipreps, I would be happy to explore alternatives.
Looking forward to your thoughts! (: