# Resample volume to specific voxel spacing - SimpleITK
**URL:** https://discourse.itk.org/t/resample-volume-to-specific-voxel-spacing-simpleitk/3531
**Category:** Beginner Questions
**Tags:** simpleitk
**Created:** [October 14, 2020, 1:05pm UTC](https://discourse.itk.org/t/resample-volume-to-specific-voxel-spacing-simpleitk/3531 "2020-10-14T13:05:13Z")
**Posts on this page:** 8
**Page:** 1
### Author:  [@Tommaso\_Di\_Noto](https://discourse.itk.org/u/Tommaso_Di_Noto)
#### Post date: [October 14, 2020, 1:05pm UTC](https://discourse.itk.org/t/resample-volume-to-specific-voxel-spacing-simpleitk/3531/1 "2020-10-14T13:05:13Z")
Hi everyone!
I have a series of 3D, MR volumes acquired from different scanners. I would like to resample all volumes to their median voxel size [0.39, 0.39, 0.55] mm. Moreover, for each volume, I also have a binary mask (same size or MR) that delineates a ROI.
By looking at similar topics, I came up with a solution that seems to work. However, when I load the newly created volume with itksnap, this is not centered and I can only see part of it.
Can someone please tell me what is wrong? 🙂 Thanks a lot!
Here’s my code:
```
import numpy as np
import SimpleITK as sitk
def resample_volume(volume_path, mask=False):
volume = sitk.ReadImage(volume_path)
volume = sitk.Cast(volume, sitk.sitkFloat32) # cast to float32
resample_vol = sitk.ResampleImageFilter() # create resampler object
if mask: # if mask is True
resample_vol.SetInterpolator = sitk.sitkNearestNeighbor # set interpolator for mask (it does not create new masks)
else:
resample_vol.SetInterpolator = sitk.sitkLinear # set interpolator for volume
resample_vol.SetOutputDirection = volume.GetDirection() # set output volume direction equal to input volume direction
resample_vol.SetOutputOrigin = volume.GetOrigin() # set output volume origin equal to input volume origin
new_spacing = [0.39, 0.39, 0.55]
resample_vol.SetOutputSpacing(new_spacing)
orig_size = np.array(volume.GetSize(), dtype=np.int)
orig_spacing = volume.GetSpacing()
new_size = orig_size * (np.divide(orig_spacing, new_spacing))
new_size = np.ceil(new_size).astype(np.int) # volume dimensions are in integers
new_size = [int(s) for s in new_size] # convert from np.array to list
resample_vol.SetSize(new_size)
resampled_volume = resample_vol.Execute(volume)
return resampled_volume
path_to_MR_volume = "/home/newuser/.../mr.nii.gz"
path_to_mask = "/home/newuser/.../mask.nii.gz"
resampled_MR = resample_volume(path_to_MR_volume) # resample volume
resampled_mask = resample_volume(path_to_mask, mask=True) # resample mask
```
---
### Author:  [@zivy](https://discourse.itk.org/u/zivy)
#### Post date: [October 14, 2020, 1:56pm UTC](https://discourse.itk.org/t/resample-volume-to-specific-voxel-spacing-simpleitk/3531/2 "2020-10-14T13:56:44Z")
Hello @Tommaso_Di_Noto,
Didn’t look too deeply into the code as it is rather long for the task. Please find below a shorter version that will resample volumes. As the only difference between resampling a mask and a scalar volume is in the interpolator that is a required parameter and not a boolean flag. Also, not sure why the volumes are converted to `sitkFloat32` after reading, but I assume you have your reasons, so combined it with the reading:
```auto
def resample_volume(volume_path, interpolator = sitk.sitkLinear, new_spacing = [0.39, 0.39, 0.55]):
volume = sitk.ReadImage(volume_path, sitk.sitkFloat32) # read and cast to float32
original_spacing = volume.GetSpacing()
original_size = volume.GetSize()
new_size = [int(round(osz*ospc/nspc)) for osz,ospc,nspc in zip(original_size, original_spacing, new_spacing)]
return sitk.Resample(volume, new_size, sitk.Transform(), interpolator,
volume.GetOrigin(), new_spacing, volume.GetDirection(), 0,
volume.GetPixelID())
```
If this code doesn’t do what you wanted, please provide additional details and we’ll get you there.
---
### Author:  [@Tommaso\_Di\_Noto](https://discourse.itk.org/u/Tommaso_Di_Noto)
#### Post date: [October 14, 2020, 2:42pm UTC](https://discourse.itk.org/t/resample-volume-to-specific-voxel-spacing-simpleitk/3531/3 "2020-10-14T14:42:12Z")
Dear @zivy,
It works! Thank you very much! 😃
Just a question: what are the last two arguments for in sitk.Resample (namely, 0 and volume.GetPixelID())?
---
### Author:  [@zivy](https://discourse.itk.org/u/zivy)
#### Post date: [October 14, 2020, 2:51pm UTC](https://discourse.itk.org/t/resample-volume-to-specific-voxel-spacing-simpleitk/3531/4 "2020-10-14T14:51:13Z")
Hi @Tommaso_Di_Noto,
Happy to hear.
Please see the documentation for [Resample](https://simpleitk.org/doxygen/latest/html/namespaceitk_1_1simple.html#a785a433b01484e8390f1f2723807cf65) and [ResampleImageFilter](https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1ResampleImageFilter.html). I always have the documentation pages open, there’s just too much to remember.
---
### Author:  [@Tommaso\_Di\_Noto](https://discourse.itk.org/u/Tommaso_Di_Noto)
#### Post date: [October 19, 2020, 4:39pm UTC](https://discourse.itk.org/t/resample-volume-to-specific-voxel-spacing-simpleitk/3531/5 "2020-10-19T16:39:24Z")
Dear @zivy,
What if I now have to transform (i.e. get the coordinates of) a set of points from original to resampled space?
E.g. [i,j,k] = [120, 150, 90] is an important landmark and I’d like to know its [i,j,k] after resampling.
Thanks a lot again! 🙂
---
### Author:  [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [October 19, 2020, 4:46pm UTC](https://discourse.itk.org/t/resample-volume-to-specific-voxel-spacing-simpleitk/3531/6 "2020-10-19T16:46:34Z")
It should be something like this:
```python
oldInd=[120, 150, 90]
p=oldImage.TransformIndexToPhysicalPoint(oldInd)
newInd=newImage.TransformPhysicalPointToIndex(p)
print(newInd)
```
---
### Author:  [@zivy](https://discourse.itk.org/u/zivy)
#### Post date: [October 19, 2020, 5:00pm UTC](https://discourse.itk.org/t/resample-volume-to-specific-voxel-spacing-simpleitk/3531/7 "2020-10-19T17:00:17Z")
Hello @Tommaso_Di_Noto,
To expand upon @dzenanz’s answer, the philosophy of ITK/SimpleITK is that we work in the physical world. That is, there is a physical point associated with the indexes into the image and you move between indexes and physical points using methods from the [Image](https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1Image.html) class. The relevant methods are `TransformContinuousIndexToPhysicalPoint, TransformIndexToPhysicalPoint, TransformPhysicalPointToContinuousIndex,` and `TransformPhysicalPointToIndex`.
---
### Author:  [@Tommaso\_Di\_Noto](https://discourse.itk.org/u/Tommaso_Di_Noto)
#### Post date: [October 20, 2020, 7:22am UTC](https://discourse.itk.org/t/resample-volume-to-specific-voxel-spacing-simpleitk/3531/8 "2020-10-20T07:22:49Z")
Dear @dzenanz, @zivy,
Thank you both for your answers! Of course, it makes sense to leverage the physical space to link points 😃