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 ✂️

Usage 💻

To get your first brain.stl just run

from brain_stl import run_brain_stl

run_brain_stl()  # 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

from brain_stl import run_brain_stl

run_brain_stl('/path/to/scan.nii.gz')  # or '/path/to/dicom_folder'

The main arguments of run_brain_stl are

• scan_filepath: Path to the input scan (if None, use scan from url). Default: None
• output_folder: Folder to save the .stl file and other outputs. Default: '.'
• stl_name: Name of the example .stl file (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

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 🤗