# badly loaded ct scans

**URL:** <https://discourse.slicer.org/t/badly-loaded-ct-scans/27358>\
**Category:** Support\
**Created:** [January 19, 2023, 6:01pm UTC](https://discourse.slicer.org/t/badly-loaded-ct-scans/27358 "2023-01-19T18:01:20Z")\
**Posts on this page:** 9\
**Page:** 1

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**Author:** ![pawel](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@pawel](https://discourse.slicer.org/u/pawel)\
**Post date:** [January 19, 2023, 6:01pm UTC](https://discourse.slicer.org/t/badly-loaded-ct-scans/27358/1 "2023-01-19T18:01:20Z")

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Hello  
I have a problem with loaded ct scans. In te red window ct scany are properly visible but in green an yellow view ct scan are stretched or narrowed. I send screen with my problem.

 ![Ct scan problem](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/8/6/86543d1e9c61defa26de86201016b4511e8445a1.png)

Best,

Pawel

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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:** [January 19, 2023, 6:52pm UTC](https://discourse.slicer.org/t/badly-loaded-ct-scans/27358/2 "2023-01-19T18:52:50Z")

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Please post what kind of files these are and how you loaded them (e.g. dicom, tiff, etc).

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**Author:** ![pawel](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@pawel](https://discourse.slicer.org/u/pawel)\
**Post date:** [January 19, 2023, 8:07pm UTC](https://discourse.slicer.org/t/badly-loaded-ct-scans/27358/3 "2023-01-19T20:07:11Z")

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This Ct scans are tiff and I loaded them as tiff.

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<div class="post-metadata">

**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:** [January 19, 2023, 8:38pm UTC](https://discourse.slicer.org/t/badly-loaded-ct-scans/27358/4 "2023-01-19T20:38:10Z")

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That explains a lot. Tiff files don’t track the spacing so you need to add it manually. In the Volumes → Volume Information you can add the spacing manually for the pixel and slice spacing. Or you may find SlicerMorph’s [ImageStacks module](https://github.com/SlicerMorph/Tutorials/tree/main/ImageStacks) useful.

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<div class="post-metadata">

**Author:** ![pawel](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@pawel](https://discourse.slicer.org/u/pawel)\
**Post date:** [January 19, 2023, 9:17pm UTC](https://discourse.slicer.org/t/badly-loaded-ct-scans/27358/5 "2023-01-19T21:17:10Z")

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Thank you:) I have different ct scans for several skulls and only one ct scan loaded good although these ct scan also are Tiff files.  
I add the spacing manually and I think that is all good. Do I have to add in the Image spacing same value (e.g 30 mm) to all ct scan in windows (red , yellow and green) have this same proportion?  
Best,

 ![Ct scan problem 1](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/6/b/6baa468b5631eb56bae22d092da5efbfb2a844c5.png)

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [January 19, 2023, 9:23pm UTC](https://discourse.slicer.org/t/badly-loaded-ct-scans/27358/6 "2023-01-19T21:23:36Z")

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> [@pawel](#):
>
> Do I have to add in the Image spacing same value (e.g 30 mm) to all ct scan in windows (red , yellow and green) have this same proportion?

You have to check that with whoever provided you with the dataset. Often microCT scans are isotropic (same spacing along all axes), but not guaranteed to be that way.

Also spacing units are mm. I don’t think you have 30mm spacing in your scan. 30 micrometers perhaps? (=0.030mm). Again check this with whoever gave you the data.

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<div class="post-metadata">

**Author:** ![pawel](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@pawel](https://discourse.slicer.org/u/pawel)\
**Post date:** [January 19, 2023, 10:23pm UTC](https://discourse.slicer.org/t/badly-loaded-ct-scans/27358/7 "2023-01-19T22:23:41Z")

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Thank you for your help.

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<div class="post-metadata">

**Author:** ![pawel](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@pawel](https://discourse.slicer.org/u/pawel)\
**Post date:** [January 20, 2023, 10:51am UTC](https://discourse.slicer.org/t/badly-loaded-ct-scans/27358/8 "2023-01-20T10:51:09Z")

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Do I understand correctly that the introduced good values in the Image spacing will cause that measurements made on ct scans will be correct? For example, I know that the skull is 40 mm lenght.  
Correct data in the Image spacing will cause that measurements made on ct scans skull is also 40 mm length.

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<div class="post-metadata">

**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:** [January 20, 2023, 1:10pm UTC](https://discourse.slicer.org/t/badly-loaded-ct-scans/27358/9 "2023-01-20T13:10:39Z")

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Yes, if the spacing is correct the measurements should be correct. But using a format such as tiff where you need to enter values manually there’s always room for human error. Better would be to work on the acquisition process to use a format where the spacing is automatically encoded (perhaps dicom) and do some test runs with calibration phantoms to be sure it’s working as expected.