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https://github.com/codingfisch/brain-stl

Turn your brain MRI into a printable 3D model in seconds 🧠➡️🖨️

https://github.com/codingfisch/brain-stl

Science Score: 13.0%

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Repository

Turn your brain MRI into a printable 3D model in seconds 🧠➡️🖨️

Basic Info
  • Host: GitHub
  • Owner: codingfisch
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 115 KB
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  • Stars: 8
  • Watchers: 1
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  • Open Issues: 0
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Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

brain-stl 🧠

The easiest and fastest way to turn brain MRI scans into 3D printable models 🖨️ powered by deepmriprep ✨

Use the Colab demo or install it locally via pip install brain_stl 💨

By default, the model is saved as brain.stl, but you can customize the filename along with other options like - Threshold: Pick a value between 0 and 3 for different tissue types (see GIF left, 2.5: white matter only) 🧠 - Hollowness: Adjust how hollow the brain is (enables faster printing) 💨 - Text: Add personalized text that works as a support structure 🔤 - Smoothing: Achieve a polished surface via iterative Laplacian smoothing ✨ - Mesh Reduction: Simplify the mesh to reduce the size of brain.stl ✂️

gif

Usage 💻

To get your first brain.stl just run ```python from brainstl import runbrain_stl

runbrainstl() # per default output_folder='.' (current folder) ``` and a publicly available brain MRI scan (from OpenNeuro) will be used 🌐

Scan files can be inputted in NifTi (.nii or .nii.gz) or DICOM (.dcm or folder) format ```python from brainstl import runbrain_stl

runbrainstl('/path/to/scan.nii.gz') # or '/path/to/dicomfolder' `` The main arguments ofrunbrainstlare - **scanfilepath**: Path to the input scan (ifNone, use scan fromurl). Default:None - **outputfolder**: Folder to save the.stlfile and other outputs. Default:'.' - **stlname**: Name of the example.stlfile (without extension). Default:'brain'`

Click here, to see all remaining arguments 📑 - **`nifti_name`**: If DICOM produces multiple NifTis, this NifTi filename is used to proceed. Default: `None` - **`url`**: URL to download a brain scan if no `scan_filepath` is provided. Default: `OPENNEURO_URL` - **`use_cache`**: If `True`, reuses intermediate outputs (e.g., tissue data). Default: `False` - **`threshold`**: Threshold tissue value (`0.5`: fluid, `1.5`: gray matter, `2.5`: white matter). Default: `1.5` - **`hollow`**: How hollow the brain is (0 to 1). Default: `0` - **`in_template_space`**: If `True`, the 3D model is in standardized (template) orientation. Default: `False` - **`mesh_reduction`**: Fraction of mesh reduction (0 to 1) for smaller `.stl` file size. Default: `0` (no reduction) - **`smooth_iter`**: Number of iterations for Laplacian smoothing. Default: `0` (none) - **`smooth_lamb`**: Strength of each Laplacian smoothing step. Default: `0.2` - **`text`**: Custom text used as structural support. Default: `None` - **`text2`**: Second line of text. Default: `None` - **`textsize`**: Size (height) of the text. Default: `120` - **`textback`**: Coronal (depth) position of the back of the text. Default: `300` - **`textfront`**: Coronal (depth) position of the front of the text. Default: `330` - **`textlinelength`**: Length of line below the text. Default: `10`

Command-Line Interface 🖥️

Process your first brain scan from the terminal by just running bash brain-stl Without providing any arguments, it downloads a publicly available scan and creates a brain.stl of it 🧠

Run brain-stl --help (+copy&paste into ChatGPT) to understand the usage of custom settings 💡

Share Your Brains 🧠🌐

Use create_gif.py to get a GIF of your model and share it on social media with the hashtag #brain-stl 🤗

Owner

  • Login: codingfisch
  • Kind: user

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Dependencies

pyproject.toml pypi
  • PyMCubes *
  • dcm2niix *
  • deepmriprep *
  • fast_simplification 0.1.7
  • niftiview *
  • python ^3.9
  • trimesh *