# Applying Transform Changes number of stacks on the file

**URL:** <https://discourse.slicer.org/t/applying-transform-changes-number-of-stacks-on-the-file/44478>\
**Category:** Support\
**Tags:** registration\
**Created:** [September 15, 2025, 9:44am UTC](https://discourse.slicer.org/t/applying-transform-changes-number-of-stacks-on-the-file/44478 "2025-09-15T09:44:34Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![ylcnkzy](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ylcnkzy/32/12189_2.png) [@ylcnkzy](https://discourse.slicer.org/u/ylcnkzy)\
**Post date:** [September 15, 2025, 9:44am UTC](https://discourse.slicer.org/t/applying-transform-changes-number-of-stacks-on-the-file/44478/1 "2025-09-15T09:44:34Z")

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**Dear Colleagues,**

I am registering the _Fixed.tiff_ image to the _Moving.tiff_ image using the Elastix module within 3D Slicer. Both images are 512 × 512 × 381. The registration works well, and after I apply the transform, everything looks perfect in Slicer — I can see the high-precision alignment.

However, when I export and save the transformed moving image as a .tiff file, the number of slices in the Z-dimension increases to 384, and it no longer aligns with the fixed image in ImageJ.

Does anyone have any idea how to fix this problem?

Best regards,

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [September 15, 2025, 3:14pm UTC](https://discourse.slicer.org/t/applying-transform-changes-number-of-stacks-on-the-file/44478/2 "2025-09-15T15:14:55Z")

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You probably need to resample the Moving volume in the space of the Fixed (use the Resample module)

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**Author:** ![ylcnkzy](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ylcnkzy/32/12189_2.png) [@ylcnkzy](https://discourse.slicer.org/u/ylcnkzy)\
**Post date:** [September 24, 2025, 12:37pm UTC](https://discourse.slicer.org/t/applying-transform-changes-number-of-stacks-on-the-file/44478/3 "2025-09-24T12:37:08Z")

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Hi Steve,

I have managed it via **Resample Scalar/Vector/DWI Volume** option within the Slicer.

Thanks for the info.