Skip to content

Add abdomen IVIM preprocessing pipeline (SP_IRFMN) - #181

Closed
siria98 wants to merge 9 commits into
OSIPI:mainfrom
siria98:main
Closed

siria98 wants to merge 9 commits into
OSIPI:mainfrom
siria98:main

Conversation

@siria98

@siria98 siria98 commented Oct 12, 2026

Copy link
Copy Markdown
Contributor

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 ringing
    removal, 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

Checklist

  • Self-review of changed code
  • Added automated tests where applicable
  • Update Docs & Guides

@IvanARashid

Copy link
Copy Markdown
Contributor

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 :)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants