cernymichal / mri3d

DICOM volume processor with GUI

MRI3D

is and application for processing DICOM volume images into more standard 3D formats for further usage. Currently implemented are:

• TIFF - volume is saved as stack of images into a single file
• MagicaVoxel VOX - the volume should be normalized first, so that voxels represent actual cubes

The loaded volume can also be munipulated with:

• Rotation around axis by 90 degrees
• Upsampling twice
• Downsampling twice
• Resampling along one axis to normalize physical voxel size

Interpolation is done trilinearly

*All of these operations can take some time, especially resampling, even though it's multithreaded and compiled.

Installation

• Python 3.9.13

Preferably use a virtual environment

python -m venv .venv
./.venv/Scripts/activate

Install dependencies

pip install -r requirements.txt --use-pep517

Running

py mri3d

samples contains some demo datasets

Testing

pytest

Fixing DICOM files

Convert potentially non-standard files to complient ones (../fixed/)

find . -type d -exec mkdir -p -- ../fixed/{}
find -type f | xargs -L 1 -d '\n' -P 12 -I '{}' dcmconv --replace-wrong-delim --ignore-parse-errors "{}" "../fixed/{}"

Generate DICOMDIR file for images in DICOM

dcmmkdir --recurse -Pdv --invent DICOM/