VeinSeg
Physics-informed deep learning for cerebral vein segmentation from QSM.
Overview
VeinSeg segments cerebral veins from Quantitative Susceptibility Mapping (QSM). It supports multi-site, multi-field-strength data (3T and 7T) across five QSM reconstruction methods (TGV, MEDI, L1, STAR, iLSQR) and R2* maps using a physics-informed training objective.
Installation
Install PyTorch first (pytorch.org), then:
pip install veinseg
Download the model weights (~290 MB, once only):
veinseg-install /path/to/models/dir
On shared HPC clusters, set:
export VEINSEG_CHECKPOINT=/shared/models/veinseg/checkpoint.pth
Usage
veinseg -i qsm.nii.gz -r tgv -f 7t -o mask.nii.gz -p prob.nii.gz
Required arguments
| Flag | Description |
|---|---|
-i |
QSM susceptibility map (.nii / .nii.gz, ppm), or R2* map with -r r2star |
-r |
Reconstruction method: tgv | medi | l1 | star | ilsqr | r2star |
-f |
MRI field strength: 7t | 3t |
-o |
Output binary vein mask |
-p |
Output vein probability map |
Optional arguments
| Flag | Default | Description |
|---|---|---|
--local-field PATH |
— | Measured background-removed local field (skips dipole computation) |
--local-field-units |
auto |
hz | ppm | auto |
--b0 X Y Z |
0 0 1 |
B0 direction in world/scanner axes |
--frangi-erode-mm |
5 |
Zero the Frangi prior within this distance (mm) of the brain edge |
--threshold |
0.5 |
Probability threshold for binary mask |
--step-size |
0.5 |
Sliding window overlap as fraction of patch |
--no-tta |
off | Disable test-time augmentation |
--device |
auto |
auto | cpu | cuda |
--out-field PATH |
— | Save local field channel used (ppm) |
--out-frangi PATH |
— | Save Frangi vesselness channel |
Examples
# Dipole field computed automatically from QSM
veinseg -i qsm.nii.gz -r tgv -f 7t -o mask.nii.gz -p prob.nii.gz
# With measured local field (Romeo output in Hz — auto-detected)
veinseg -i qsm.nii.gz -r medi -f 7t -o mask.nii.gz -p prob.nii.gz \
--local-field bgrm_field.nii.gz
# Inspect intermediate channels
veinseg -i qsm.nii.gz -r tgv -f 7t -o mask.nii.gz -p prob.nii.gz \
--out-field dipole_field.nii.gz --out-frangi frangi.nii.gz
License
Apache 2.0
1 maintainer
Metadata
1 maintainer
Release files for veinseg-qsm 1.1.0
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| File | Size | Uploaded | Provenance | Actions |
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| veinseg_qsm-1.1.0-py3-none-any.whl | Python 3 | none | any | Details for veinseg_qsm-1.1.0-py3-none-any.whl |
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Release files / veinseg_qsm-1.1.0.tar.gz
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