# Model To Model Distance running as CLI

**URL:** <https://discourse.slicer.org/t/model-to-model-distance-running-as-cli/46971>\
**Category:** Support\
**Tags:** extensions-manager, 3d-model\
**Created:** [May 8, 2026, 1:09pm UTC](https://discourse.slicer.org/t/model-to-model-distance-running-as-cli/46971 "2026-05-08T13:09:28Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![Mrdlev](https://avatars.discourse-cdn.com/v4/letter/m/7ab992/32.png) [@Mrdlev](https://discourse.slicer.org/u/Mrdlev)\
**Post date:** [May 8, 2026, 1:09pm UTC](https://discourse.slicer.org/t/model-to-model-distance-running-as-cli/46971/1 "2026-05-08T13:09:28Z")

</div>

Hi everyone,

I’m trying to use the **Model-to-Model Distance** extension in 3D Slicer to quantify the **average displacement between two structures** (one with deformation and one without).

However, I’ve run into an issue:

- I’ve installed the extension multiple times and restarted Slicer each time

- The module does not appear to function correctly in the GUI

- The only way I can access it is via the CLI

The problem is that running it through the CLI does not provide the specific output I need, particularly the **average displacement metric** between the models.

Has anyone encountered a similar issue or knows:

1. How to properly enable/use the extension through the GUI?

2. How to retrieve average displacement (or equivalent statistics) using this tool or an alternative workflow?

Any guidance would be greatly appreciated.

Thanks in advance!

---

<div class="post-metadata">

**Author:** ![ebrahim](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ebrahim/32/13403_2.png) [@ebrahim](https://discourse.slicer.org/u/ebrahim)\
**Post date:** [May 11, 2026, 1:27pm UTC](https://discourse.slicer.org/t/model-to-model-distance-running-as-cli/46971/2 "2026-05-11T13:27:52Z")

</div>

> [@Mrdlev](#):
>
> The module does not appear to function correctly in the GUI

Can you elaborate? In what way does it not function correctly?

I hope the below AI generated response is helpful; I have verified the snippets work.

> 🤖 This post contains AI-generated content.

ModelToModelDistance is a **CLI module** , so it does not have a custom GUI. In Slicer, its “GUI” is the automatically generated CLI module panel. After installing the extension and restarting Slicer, search for:

`Model To Model Distance`

or look under the **Quantification** category.

The module does not print an average distance as a CLI return value. Instead, it writes distance arrays into the **output model’s point data**. You can then compute the average from those arrays in the Python console.

First, inspect the available arrays:

```python
modelNode = slicer.util.getNode("VTK Output File") # use your output model name

pointData = modelNode.GetPolyData().GetPointData()
for i in range(pointData.GetNumberOfArrays()):
    print(i, pointData.GetArrayName(i))

```

The array name depends on the selected distance mode.

For `corresponding_point_to_point`, use:

```python
import numpy as np

distances = slicer.util.arrayFromModelPointData(
    modelNode, "AbsolutePointToPointDistance"
)

print("mean displacement:", np.mean(distances))
print("std:", np.std(distances))
print("min:", np.min(distances))
print("max:", np.max(distances))
print("median:", np.median(distances))
print("95th percentile:", np.percentile(distances, 95))

```

Or compute the magnitude from the displacement vectors:

```python
import numpy as np

vectors = slicer.util.arrayFromModelPointData(modelNode, "PointToPointVector")
magnitudes = np.linalg.norm(vectors, axis=1)

print("mean displacement:", np.mean(magnitudes))

```

For `absolute_closest_point`, use:

```python
import numpy as np

distances = slicer.util.arrayFromModelPointData(modelNode, "Absolute")
print("mean closest-point distance:", np.mean(distances))

```

For `signed_closest_point`, use:

```python
import numpy as np

distances = slicer.util.arrayFromModelPointData(modelNode, "Signed")
print("mean signed closest-point distance:", np.mean(distances))

```

One caveat: if the option **Save target name in distance fields** / `--targetInFields` is enabled, the array name gets a suffix based on the target filename, for example:

```python
Absolute_to_targetModelName
Signed_to_targetModelName

```

That is why it is best to print the point-data array names first.

Also, be careful about the interpretation. If the two models have matching point order, `corresponding_point_to_point` gives a true pointwise displacement. If they do not have corresponding points, use closest-point distance, but that is a surface-to-surface distance, not necessarily a physical displacement vector.