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Hi! We still have the epi distortion phantom in the history here which is an issue. Start a new branch from main and move the relevant files there and try again :) |
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Describe the changes you have made in this PR
Adds a full preprocessing pipeline for abdomen IVIM diffusion-weighted MRI data
under
src/original/preprocessing/SP_IRFMN/, consisting of:abdomen_preproc.py— a 5-step pipeline (MP-PCA denoising, Gibbs ringingremoval, motion correction, susceptibility distortion correction via topup,
and N4 bias field correction) designed for abdominal organs (kidneys, liver)
where respiratory motion and RF inhomogeneity are the main artefact sources.
README.md— documents requirements, usage, parameters, and outputs.Two motion correction backends are available: dipy (pure Python, default) and
MIRTK (two-stage intra-shell + iterative template registration).
Link this PR to an issue [optional]
Fixes #ISSUE-NUMBER
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