# Extracting Exact Metric Value in SimpleITK Python
**URL:** https://discourse.itk.org/t/extracting-exact-metric-value-in-simpleitk-python/2423
**Category:** Beginner Questions
**Tags:** python, simpleitk
**Created:** [November 19, 2019, 3:43pm UTC](https://discourse.itk.org/t/extracting-exact-metric-value-in-simpleitk-python/2423 "2019-11-19T15:43:19Z")
**Posts on this page:** 7
**Page:** 1
### Author:  [@jhess](https://discourse.itk.org/u/jhess)
#### Post date: [November 19, 2019, 3:43pm UTC](https://discourse.itk.org/t/extracting-exact-metric-value-in-simpleitk-python/2423/1 "2019-11-19T15:43:19Z")
Hi there,
I am using Elastix in command line to register images using Mattes mutual information metric, and at the end of the registration process, I am recording the exact metric value between the fixed and moving image, a functionality introduced in Elastix 4.9.0. I am attempting to compute the same value with simpleITK in python, and I am not able to reproduce the result that I am getting through elastix. I would appreciate any help on the topic.
Here is my python code and attached is the transform parameter file used in Elastix:
import simpleitk as sitk
pixelType = sitk.sitkFloat64
fixedImage = sitk.ReadImage(’/path/fixed\_image.nii’, pixelType)
movingImage = sitk.ReadImage(’/path/moving\_image.nii’, pixelType)
Reg = sitk.ImageRegistrationMethod()
Reg.SetOptimizerAsGradientDescentLineSearch(learningRate=1.0,numberOfIterations=1,convergenceMinimumValue=1e-5,convergenceWindowSize=5)
Reg.SetMetricSamplingPercentage(100.0)
Reg.SetInitialTransform(sitk.Transform(2,sitk.sitkIdentity))
Reg.SetMetricAsMattesMutualInformation(numberOfHistogramBins = 32)
Reg.MetricEvaluate(fixedImage,movingImage)
[Affine\_Double.txt](https://discourse.itk.org/uploads/short-url/ucy8fVjmUQTfeNzcn7PhbFtYpht.txt) (1.8 KB)
Josh
---
### Author:  [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [November 19, 2019, 3:54pm UTC](https://discourse.itk.org/t/extracting-exact-metric-value-in-simpleitk-python/2423/2 "2019-11-19T15:54:04Z")
`NumberOfSpatialSamples 8000` is a far cry from 100% sampling. There are a lot of other parameters in that file, and you are explicitly setting only a subset. And how is the metric value different?
@Niels_Dekker might have more advice.
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### Author:  [@jhess](https://discourse.itk.org/u/jhess)
#### Post date: [November 19, 2019, 4:01pm UTC](https://discourse.itk.org/t/extracting-exact-metric-value-in-simpleitk-python/2423/3 "2019-11-19T16:01:28Z")
Thank you for the quick response. The exact metric value recorded in the resulting elastix.log is -0.595666 between the fused moving image and fixed image, and the computed value is -0.59268 in python. Those are close, but not quite the same, and I am afraid to move forward without being able to recapitulate the elastix results. 8000 spatial samples is certainly different than 100% sampling, but I was under the impression that computing the exact metric in elastix was performed by sampling all locations, which is why I chose 100% with simpleITK.
Thanks for the help!
---
### Author:  [@zivy](https://discourse.itk.org/u/zivy)
#### Post date: [November 19, 2019, 4:13pm UTC](https://discourse.itk.org/t/extracting-exact-metric-value-in-simpleitk-python/2423/4 "2019-11-19T16:13:13Z")
Hi @jhess,
Some additional things to be aware of:
1. Setting the random sampling to 100% doesn’t sample all voxels. This is just a way to specify the number of samples (repeated samples will occur).
2. The random sampling in ITK does not take the actual voxel center, there is a jitter factor inside each voxel, so each time the sample value from the same voxel will be slightly different.
3. To use the actual voxel values for 100% of the voxels don’t sample
```auto
Reg.SetMetricSamplingStrategy(Reg.NONE)
```
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### Author:  [@jhess](https://discourse.itk.org/u/jhess)
#### Post date: [November 19, 2019, 4:41pm UTC](https://discourse.itk.org/t/extracting-exact-metric-value-in-simpleitk-python/2423/5 "2019-11-19T16:41:21Z")
Hi @zivy and @dzenanz,
Using the advice given (setting Reg.SetMetricSamplingStrategy(Reg.NONE)), I am still receiving a metric value of -0.59268. Happy to hear any other suggestions on how to reproduce the elastix exact metric.
Thanks again.
Josh
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### Author:  [@blowekamp](https://discourse.itk.org/u/blowekamp)
#### Post date: [November 19, 2019, 4:52pm UTC](https://discourse.itk.org/t/extracting-exact-metric-value-in-simpleitk-python/2423/6 "2019-11-19T16:52:23Z")
Perhaps there is Gaussian smoothing going on in Elastix?
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### Author:  [@jhess](https://discourse.itk.org/u/jhess)
#### Post date: [November 19, 2019, 5:57pm UTC](https://discourse.itk.org/t/extracting-exact-metric-value-in-simpleitk-python/2423/7 "2019-11-19T17:57:47Z")
Hi @blowekamp,
I think you may be correct. In elastix the default smoothing schedule for the multi-resolution registration approach was used, and it seems that the default sigma value for the final resolution is 1. It would and need to be 0 for a fair comparison to the simpleITK implementation.
Josh