# \[Slicer\] Wrong threshold when opening NifTi file

**URL:** <https://discourse.slicer.org/t/slicer-wrong-threshold-when-opening-nifti-file/198>\
**Category:** Support\
**Created:** [April 26, 2017, 6:56pm UTC](https://discourse.slicer.org/t/slicer-wrong-threshold-when-opening-nifti-file/198 "2017-04-26T18:56:05Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Guido\_Buezas](https://avatars.discourse-cdn.com/v4/letter/g/ed8c4c/32.png) [@Guido\_Buezas](https://discourse.slicer.org/u/Guido_Buezas)\
**Post date:** [April 26, 2017, 6:56pm UTC](https://discourse.slicer.org/t/slicer-wrong-threshold-when-opening-nifti-file/198/1 "2017-04-26T18:56:05Z")

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Hi everyone

I made a NifTi file from a stack of Tiff slices (8-bit gray scale) in ImageJ. After i save the .nii file, i check it in ImageJ and it’s OK.

When i load .nii file into Slicer, the threshold levels are wrong, with a narrower interval than the original files, so a big number of gray pixels cant be seen. This problem is only with Slicer, with ImageJ i can see it as the original Tiff files. Is it normal? What should i do?

Best regards

Guido

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [April 26, 2017, 7:32pm UTC](https://discourse.slicer.org/t/slicer-wrong-threshold-when-opening-nifti-file/198/2 "2017-04-26T19:32:28Z")

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Left-click and drag up/down, left/right in image slice viewers to adjust the default brightness/contrast.

If you work with volumetric images then use a file format that can store image slice spacing. For example, you can use NIFTI (ImageJ: File / Save as / Analyze 7.5).

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**Author:** ![Guido\_Buezas](https://avatars.discourse-cdn.com/v4/letter/g/ed8c4c/32.png) [@Guido\_Buezas](https://discourse.slicer.org/u/Guido_Buezas)\
**Post date:** [April 28, 2017, 2:44pm UTC](https://discourse.slicer.org/t/slicer-wrong-threshold-when-opening-nifti-file/198/3 "2017-04-28T14:44:41Z")

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Well, that was a silly question. Anyway, i tried directly with threshold effect and (as i remember) the lower limit was at the lowest level possible. So, i thougth it can’t be lowered anymore. Additionally, i tried actions with the mouse but is evident that i didn’t use left-click + drag.

Thank you very much!!