CLI Reference
imatools installs eight command-line entry points. Each is a subcommand group —
run imatools-<tool> --help, or imatools-<tool> <subcommand> --help, for the
authoritative flags.
Operations on segmentation label maps.
add · cc-extract · cc-identify · cc-regionprops · chain · combine ·
compare · extract-label · fill · gaps · inr · largest · mask ·
merge-labels · morph-label · op · resample · sharp-regions · show ·
show-voxels · split-label · swap
imatools-segmentation extract-label -in image.nii -l 1 -out label1.nii
imatools-segmentation mask -in image.nii -mask mask.nii
| Subcommand |
What it does |
export |
Export a VTK polydata file to another mesh format |
flip-xy |
Flip X/Y coordinates of a VTK polydata mesh |
from-dotmesh |
Convert a .mesh (dotmesh) file to CARP .pts/.elem |
points-to-image |
Paint image voxels near a point-cloud with a label |
project-scalars |
Project scalar arrays onto a mesh |
map |
Build a mapping between two meshes |
map-stats |
Report statistics from a mapping directory |
fibrosis-overlap |
Compare fibrosis overlap between two meshes |
imatools-mesh export input.vtk -o output.vtp
imatools-mesh from-dotmesh input.mesh -o output
imatools-mesh map -in1 left.vtk -in2 right.vtk -map elem
| Subcommand |
What it does |
mesh-props |
Print surface area and volume of a VTK mesh |
label-volumes |
Print or save volumes of labels in a segmentation image |
imatools-volume mesh-props /path/to/mesh.vtk
imatools-volume label-volumes -in seg.nii
| Subcommand |
What it does |
coords-to-index |
Convert world coordinates to image indices |
gen-circle |
Generate a circle/sphere test image |
gen-cube |
Generate a cube test image |
imatools-image coords-to-index -im image.nii -xyz points.mps -o indices.txt
imatools-image gen-circle -out circle.nii -r 80 -c 150 150 50
| Subcommand |
What it does |
patient-table |
Build a patient metadata table from DICOM (folder or single) |
stack-slices |
Stack individual DICOM slices into a volume |
imatools-dicom patient-table folder -in /data/dicom -out table.csv
imatools-dicom stack-slices -d /data -i slices -o volume.nii.gz
| Subcommand |
What it does |
lge |
Create synthetic LGE test image (prism) |
surf |
Create segmentation surface mesh with MIRTK |
scar-opts |
Write CEMRG scar-options JSON file |
scar |
Run CEMRG MitkCemrgScarProjectionOptions |
mask |
Apply a mask with a threshold file |
vscar-pipeline |
Full ventricular-scar projection pipeline |
vscar-scale |
Scale a mesh (e.g. µm → mm) |
vscar-deform |
Deform a mesh onto the LGE image with MIRTK |
vscar-cog |
Compute cell centres of gravity |
vscar-project |
Project scar onto the mesh from a reference image |
enhance |
Enhance/debug a scar corridor image (--jobs N for parallel) |
check |
Check a scar corridor CSV |
score |
Report the scar score for a mesh from custom blood-pool stats |
# Scar score from custom blood-pool statistics (no stats file needed)
imatools-scar score --mesh mesh.vtk --mean-bp 120 --stdev-bp 15 \
--method iir --value 0.97 1.2 1.32
score prints a value / threshold / score table — one row per --value. Use
--field to select a named cell array (otherwise the active scalars are used) and
--scalar-type {cell,point} to choose the array association.
Both subcommands read a manifest CSV with columns
comparison_dir,case_left,case_right.
| Subcommand |
What it does |
map-fibres |
Build fibre mappings across the cohort |
compare |
Compare fields across the mapped cohort |
imatools-comparisons map-fibres --manifest manifest.csv -n in -map pts
imatools-comparisons compare --manifest manifest.csv -n lat -f 1
| Subcommand |
What it does |
report |
Create a report with images for mesh quality assessment |
render-single |
Render a folder of VTK files into a single grid PNG |
render-multi |
Render a folder of VTK files into individual PNGs |
imatools-report report --sims-folder /data/case1 --report-name report.pdf --print-all
imatools-report render-single --base-dir /data/vtks --output grid.png