3D-printable brain model from a T1w MR image using Docker

You want to 3D print your or another ones brain? Here's a step by step guide on how to end up with a 3D-printable brain model. It's as easy as running two command lines. This is an adaptation and extension of skjerns/3dprintedbrain_docker and miykael/3dprintyourbrain with more options, ease of use and enhanced anatomical accuracy.

What you need

• Structural brain image (T1-weighted) in NIfTI-format
• FreeSurfer license (it's free; see Instructions)
• Installation of 'Docker Desktop' (see Instructions)

Features

• Simple installation and usage — just two commands to get started.
• Compatible with pre-existing FreeSurfer [7.3+] output.
• Enhanced anatomical accuracy by leveraging both FreeSurfer's recon-all and segment_subregions pipelines, and by integrating ventricles.
• Generates print-ready STL files for subcortical structures, cortical regions, and the whole brain.
• Option to create a separate STL file for each hemisphere.
• [BETA] Option to generate STL files for parcels of the Desikan-Killiany Atlas and brain lobes.
• [BETA] Option to generate STL file for cerebral white matter.
• Smaller Docker image (20.46 GB)
• Technical feature: No longer requires FSL as a dependency (saving 10 GB of space).
• Technical feature: Runs entirely from a single Python file

Instructions

1. Get a Freesurfer license (it's free)

Register on the Harvard FreeSurferWiki with your email and get a free Freesurfer 'license.txt' file.

2. Install 'Docker Desktop'

Download and install Docker Desktop. It is free of charge and availabe for Mac, Windows and Linux.

3. Pull the Docker image

Option A: via Terminal

Open the terminal and run: docker image pull lbutry/nii2stl:latest

Option B: via Docker Desktop app

1. Open 'Docker Desktop'
2. Navigate to the search bar at the top and type 'lbutry/nii2stl'.
3. Click on 'Pull' to download the image.

Option C: Build manually from this repository

1. Clone this repository
2. Open the repository folder with the terminal
3. Run docker build -t nii2stl .

4. Run the Docker image

1. Create a new folder (e.g.: home)
2. Copy your FreeSurfer 'license.txt' file and your brain T1w image (.nii or .nii.gz) into the folder
3. Navigate inside the terminal to the folder: cd /path/to/folder
4. Run the command below

Usage: docker run -t -v ./:/app/share <image name> <options>

Example for default use

• Mac/Linux: docker run -t -v ./:/app/share lbutry/nii2stl -t1w brain.nii.gz
• Windows: docker run -t -v .\/:/app/share lbutry/nii2stl -t1w brain.nii.gz

The default run will take several hours to complete.

Example for advanced use

This code is required if you want to e.g. skip FreeSurfer, use custom brainstem smoothing and obtain an STL file for each hemisphere:

• Mac/Linux: docker run -t -v ./:/app/share lbutry/nii2stl -fs_skip -smoothing 0 -hemi
• Windows: docker run -t -v .\/:/app/share lbutry/nii2stl -fs_skip -smoothing 0 -hemi

Arguments and options

Mandatory for default use

• -t1w <file name> Name of the T1w-image (.nii or .nii.gz) inside the home directory.

Freesurfer options

• -fs_skip Skip FreeSurfer's 'recon-all' pipeline. Checks if 'segment_subregion brainstem' needs to be run. Requires FreeSurfer output to be located in home directory.
• -fs_dir <folder name> Name of FreeSurfer output directory. [Default = freesurfer]"
• -fs_flags <flags> Parse more flags to 'recon-all'.

Mesh processing options

• -smooth <int> Number of smoothing steps for subcortical model. Use '0' to disable. [Default = 150]
• -decimate <float> Target number of faces. Use '0' to disable. [Default = 150000]

Optional modules

• -hemi Create STL-file for each hemisphere. Including brainstem, cerebellum and corpus callosum.
  • -planeoffset Indicate where the subcotical model is cut in half on the x-axis. Only applicable when -hemi is set.
  • -rev_overlap_correction Swap subtraction terms in hemi overlap correction. Only applicable when -hemi is set.
• -parcels [BETA] Create STL-file for each parcel of the Desikan-Killiany Atlas and for each brain lobe.
• -wm [BETA] Create STL-file for cerebral white matter.

General options

• -work Keep work directory.
• -tag <tag> Tag for the FreeSurfer and output folder. [Defaut: None]

Output

All outputs are saved in the home directory. If -tag is set, _<tag> is appended to the output and FreeSurfer folder.

• home/freesurfer/... Segmentation output of FreeSurfer.
• home/output/brain_final.stl 3D-printable STL model of the whole brain.
• home/output/cortical_final.stl 3D-printable STL model of the cerebrum.
• home/output/subcortical_final.stl 3D-printable model of the brainstem and cerebellum.
• home/output/hemi/... 3D-printable STL model for both hemispheres.
• home/output/lobes/... 3D-printable STL model for each brain lobe.
• home/output/parcels/... 3D-printable STL model for each parcel of the Desikan-Killiany Atlas.

Q & A

Q1: My MR images are in DICOM format and not in .nii or nii.gz.

• You can convert DICOM to NIfTI using dcm2niix.

Q2: I already have the output of FreeSurfer 'recon-all'. How can I use it?

• Copy the output to the home directory
• Now you have two options: (1) Rename it to 'freesurfer' or 'freesurfer_' when using the -tag option. (2) Use the -fs_dir flag to specify the name of your FreeSurfer output directory.
• Use the -fs_skip option to skip the 'recon-all' pipeline.

Q3: I already have the output of FreeSurfer 'recon-all' but not of 'segment_subregion brainstem'.

• Copy the output to the home directory and rename it to 'freesurfer'. You should now use the '-fs_only_brainstem' flag.