Legacy Segmentation Tool (fetal_brain_seg)

Using the legacy segmentation tool in NiftyMIC

NiftyMIC releases before v0.8 relied on fetal_brain_seg as automated fetal brain segmentation tool. If required, this can still be used instead of the default monaifbs segmentation tool.

Requirements and Dependencies

• Installation of NiftyMIC
• Installation of fetal_brain_seg for automatic fetal brain segmentations
• The use of a Python virtual environment is recommended

Installation

1. Install NiftyMIC and all its dependencies

2. Check fetal_brain_seg installation:

   • add export FETAL_BRAIN_SEG="absolute-path-to-fetal_brain_seg to your .bashrc (or equivalent)
   • run python -m nose tests/installation_test_fetal_brain_seg.py and verify the fetal_brain_seg tool is used.

Using fetal_brain_seg

The NiftyMIC command needed to generate the automated brain masks with fetal_brain_seg is:

niftymic_segment_fetal_brains \
--filenames \
nifti/name-of-stack-1.nii.gz \
nifti/name-of-stack-2.nii.gz \
nifti/name-of-stack-N.nii.gz \
--filenames-masks \
seg/name-of-stack-1.nii.gz \
seg/name-of-stack-2.nii.gz \
seg/name-of-stack-N.nii.gz \
--neuroimage-legacy-seg 1

The subsequent reconstruction pipeline command is unchanged (more information here).