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mri2fe

Automated generation of finite element head models from magnetic resonance imaging and elastography data

https://github.com/turnerjennings/mri2fe

Science Score: 44.0%

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Repository

Automated generation of finite element head models from magnetic resonance imaging and elastography data

Basic Info
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  • Stars: 2
  • Watchers: 1
  • Forks: 0
  • Open Issues: 4
  • Releases: 0
Created 10 months ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License Citation

readme.md

MRI2FE

Workflows for automated FE head model generation from MRI/MRE data

Overview

This package provides tools for the generation of patient-specific finite element (FE) models of the head and brain. This package currently supports integration of structural data from magnetic resonance imaging (MRI) as well as material data from magnetic resonance elastography (MRE).

Installation

Package installation is confirmed working for Windows and MacOS. To install the package, download or clone the repository to your local machine. Run the appropriate installation script for your system, which will install all dependencies as well as the package.

```shell git clone https://github.com/turnerjennings/MRI2FE

cd MRI2FE

if on windows

./install_windows.bat

if on mac

./install_mac.sh

if on linux

./install_linux.sh ```

Quick Start

All steps can be completed at once with a short build script:

```python import MRI2FE

define structural MRI paths

labeledgeompath = "path/to/labeledimage.nii" geomroimaskpath = "path/to/roi_mask.nii"

define MRE geometry paths

MREgeometrypaths = ["path/to/30Hzgeom.nii", "path/to/50Hzgeom.nii", "path/to/70Hzgeom.nii"]

MREmaskpath = "/path/to/MRE_mask.nii"

define a list of tuples containing the MRE data

either stiffness/damping ratio or G'/G"

MREpropertiespaths = [ ("path/to/30Hzstiffness.nii","path/to/30Hzdamping.nii"), ("path/to/50Hzstiffness.nii","path/to/50Hzdamping.nii"), ("path/to/70Hzstiffness.nii","path/to/70Hzdamping.nii") ]

model builder workflow: returns model object and writes to output

mdl = ( MRI2FE.FEModelbuilder() .mesh(imgpath = labeledgeompath, imglabels = ["region1","region2","region3"]) .mapmre(targetlabel = 1, MREtype = "stiffnessdamping", MREgeom = MREgeometrypaths, MREmask = MREmaskpath, MREfrequency = [30,50,70], MREtotransform = MREproperties_paths) .write("/output/path/example.k") .build() )

```

Owner

  • Login: turnerjennings
  • Kind: user

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Jennings"
  given-names: "Turner"
  orcid: "https://orcid.org/0009-0003-3536-3645"
- family-names: "Biggs"
  given-names: "Matteo"
- family-names: "Shirude"
  given-names: "Anshul"
title: "MRI2FE"
version: 0.0.1
date-released: 2025-07-01
url: "https://github.com/turnerjennings/MRI2FE"

GitHub Events

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Last Year
  • Issues event: 22
  • Delete event: 8
  • Issue comment event: 25
  • Push event: 77
  • Public event: 1
  • Pull request review comment event: 3
  • Pull request review event: 17
  • Pull request event: 33
  • Create event: 18

Dependencies

requirements.txt pypi
pyproject.toml pypi