/habenula_segmentation_lawson

Geometry based human habitual segmentation from anatomical MRI

Primary LanguagePythonMIT LicenseMIT

Improved implementation1 of Lawson's geometric habenula segmentation2

Depencency

with Docker
  • Docker
  • X11 server
    • linux: Most desktop linux distributions contain X11 server. If not, install Xorg and/or openbox.
    • macOS: XQuartz
    • Windows: VcXsrv, Xming, MobaXterm, ... but it has not been tested.
without Docker
  • python 2.7
  • numpy
  • nibabel
  • pyside

Input

  • T1w_acpc_dc.nii.gz (AC-PC-aligned T1-weighted image)

Installation and usage

with Docker

  • Make sure you are in docker group. If not, run sudo usermod -aG docker $USER and logout/login.

  • macOS users should check "Allow connection from network clients" option in the Security tab in Xquartz Preferences.

  • Build docker: in src directory, run docker build -t hb_lawson .

  • src/run_hb_lawson_docker.sh seg T1w_acpc_dc.nii.gz my_habenula_segmentation_name : open segmentation program

  • src/run_hb_lawson_docker.sh to_nifti T1w_acpc_dc.nii.gz my_habenula_segmentation_name_lawson_hb.csv : convert csv file to nifti file

  • It is convenient to copy src/run_hb_lawson_docker.sh file to one of your PATH environment directory.

  • macOS user note: if detected IP address is wrong, modify src/run_hb_lawson_docker.sh file:line 10.

  • Windows user note: this has not been tested on Windows.

without Docker
  • python hb_segmentation_lawson.py T1w_acpc_dc.nii.gz my_habenula_segmentation_name : open segmentation program
  • python hb_lawson_to_nifti.py T1w_acpc_dc.nii.gz my_habenula_segmentation_name_lawson_hb.csv : convert csv file to nifti file

Reference

[1] Kim et al., Reproducibility of myelin content‐based human habenula segmentation at 3 Tesla. Human Brain Mapping. 2018; 39: 3058-3071 https://doi.org/10.1002/hbm.24060

[2] Lawson et al., Defining the habenula in human neuroimaging studies. Neuroimage. 2013; 64: 722–727 https://doi.org/10.1016/j.neuroimage.2012.08.076