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Segmentation

Available tools

Several state-of-the-art segmentation algorithms have been wrapped and tested in fetpype.

Algorithm Repository Docker
BOUNTI1 https://github.com/gift-surg/NiftyMIC https://hub.docker.com/r/renbem/niftymic
dHCP2 https://github.com/SVRTK/SVRTK https://hub.docker.com/r/fetalsvrtk/svrtk

Config structure

Here's a typical structure found in the BOUNTI config. 

pipeline: "bounti"
docker: 
  cmd: "docker run --rm <mount>
    fetalsvrtk/segmentation:general_auto_amd 
    bash /home/auto-proc-svrtk/scripts/auto-brain-bounti-segmentation-fetal.sh 
    <input_dir> <output_dir>"
singularity:
  cmd: "singularity exec -u --bind <singularity_mount> --bind /home/gmarti/tmp:/home/tmp_proc --nv
    <singularity_path>/bounti.sif
    bash /home/auto-proc-svrtk/auto-brain-bounti-segmentation-fetal.sh 
    <input_dir> <output_dir>"
path_to_output: "<basename>-mask-brain_bounti-19.nii.gz"

Note

All the container runs use the command above and are passed through the function run_seg_cmd

Tags

There are a limited set of tags that can be used for reconstruction:

Command
 Description Comments
<mount> Where the different folders will be mounted on Docker Docker only
<singularity_mount> Where the different folders will be mounted on Singularity Singularity only
<singularity_path> The base path of the Singularity image Singularity only

| <input_stacks> | The list of inputs stacks will be given as arguments | Mutually exclusive with <input_dir> | | <input_dir> | The folder that contains the input stacks | Mutually exclusive with <output_dir> | | <output_dir> | The output directory | Mutually exclusive with

  1. Alena U Uus and others. BOUNTI: brain volumetry and automated parcellation for 3d fetal mri. bioRxiv, 2023. ↩

  2. Antonios Makropoulos, Emma C Robinson, Andreas Schuh, Robert Wright, Sean Fitzgibbon, Jelena Bozek, Serena J Counsell, Johannes Steinweg, Katy Vecchiato, Jonathan Passerat-Palmbach, and others. The developing human connectome project: a minimal processing pipeline for neonatal cortical surface reconstruction. Neuroimage, 173:88–112, 2018. ↩