BrainMaker

BrainMaker converts reconstructed surfaces into a printable 3D models.

Description

BrainMaker will take a single participant's reconstructed surfaces and create .stl files (one for each hemisphere and one of both hemispheres combined). It will then slice the .stl file of both hemispheres into a printable file.

By default, BrainMaker will use Freesurfer to convert left and right hemisphere surfaces into a .stl files. These will be loaded into Blender to position, combine, and export a complete model of the brain via a default python script. The right hemisphere is moved slightly closer to the left hemisphere to ensure that a printable file is produced. The complete model is sliced using Slic3r using a default configuration file at 0.2 scale. The configuration is built for a Prusa i3 MK2S printer. The Python script for Blender and the .ini file for Slic3r can be replaced for advanced controls of those components of the process.

Documentation

A Freesurfer license is necessary, it should be placed in the volume mounted to /configs.

It is expected that there are reconstructed surfaces available to convert into .stl files. Freesurfer's recon-all must be run before this Docker. The recon-all outputs are, by default, expected to be placed inside a subject specific BIDS directory: {bids_dir}/derivatives/freesurfer/sbj_{ID}/surf/. The level of analysis will always be at the participant level, therefore, the participant label name-value argument is required.

The default configuration for Blender and Slic3r files can be overwritten by placing the file in the volume mounted to /configs with the corresponding name-value argument. The default configuration prints within two hours with the Prusa i3 MK2S printer.

The Blender python script imports .stl files for manipulation and output using the bpy and bmesh modules. These modules are built into Blender and do not require further dependencies. However, these modules do not function independently from Blender and therefore must be tested using Blender. A custom Blender python script must accept and output a similar format of .stl files. For more information on these modules, refer to the documentation.

The Slic3r configuration file controls the parameters that create the print instructions. It should be noted that Slic3r only generates G-Code files and some printers require other formats. The automated slicing can be disabled in this case. As the default configuration file was built with the Prusa i3 MK2S printer in mind, the generated G-Code may not be usable for some printers. Slic3r is highly configurable for many printers, using its GUI to generate a customized configuration file is recommended. For more information on Slic3r, refer to the manual.

Usage

BrainMaker has the following command line arguments:

usage: BrainMaker.sh [-h] bids_dir output_dir participant  
                     --participant_label PARTICIPANT_LABEL  
                     [--freesurfer_output_loc FREESURFER_OUTPUT_DIR]  
                     [--blender_config BLENDER_CONFIG] [--slicer_config SLICER_CONFIG]  
                     [--gcode_scale SCALE] [--skip_slice]  

Entry point shell script to generate printable 3D models from reconstructed surface.  

positional arguments:  
 bids_dir                    The directory with the input dataset formatted  
                             according to the BIDS standard.  
 output_dir                  The directory where the output files should be stored.  
 participant                 BrainMaker only allows for participant level analysis.  

required arguments:  
 --participant_label PARTICIPANT_LABEL  
                             The label for the participant's data to be used to create
                             printable files.  

optional arguments:  
 -h, --help                  Show this help message and exit.  
 --freesurfer_output_loc FREESURFER_OUTPUT_DIR  
                             The subdirectory within the BIDS directory where the  
                             participant's reconstructed surfaces are located.  
 --blender_config BLENDER_CONFIG  
                             The python script to run with Blender.  
 --slicer_config SLICER_CONFIG  
                             The configuration .ini file to generate G-Code with.  
 --gcode_scale SCALE         A value between 0-1 to scale the model in the G-Code.  
 --skip_slice                Skips the slicing step of the pipeline.  

Basic usage:

docker run --rm -it \
  -v /data/BrainMakerTest/bids:/data:ro \
  -v /data/BrainMakerTest/bids/derivatives/BrainMaker:/outputs \
  -v /data/BrainMakerTest/bids/code:/configs:ro \
  macklabuoft/brainmaker:latest /data /outputs participant \
  --participant_label 001

An example usage of using BrainMaker with all possible arguments:

docker run --rm -it \
  -v /data/BrainMakerTest/bids:/data:ro \
  -v /data/BrainMakerTest/bids/derivatives/BrainMaker:/outputs \
  -v /data/BrainMakerTest/bids/code:/configs:ro \
  macklabuoft/brainmaker:latest /data /outputs participant \
  --participant_label 001 \
  --freesurfer_output_loc derivatives/freesurfer \
  --blender_config blender.py \
  --slicer_config slicer.ini \
  --skip_slice \
  --gcode_scale 0.1

Acknowledgement

Please mention this Docker specifically by name with a link to our GitHub repository.