# Volume render with signed 16 bit integer data not working

**URL:** <https://community.mrtrix.org/t/volume-render-with-signed-16-bit-integer-data-not-working/2968>\
**Category:** Development\
**Tags:** error\
**Created:** [October 29, 2019, 11:23am UTC](https://community.mrtrix.org/t/volume-render-with-signed-16-bit-integer-data-not-working/2968 "2019-10-29T11:23:46Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Darius](https://community.mrtrix.org/user_avatar/community.mrtrix.org/darius/32/3187_2.png) [@Darius](https://community.mrtrix.org/u/Darius)\
**Post date:** [October 29, 2019, 11:23am UTC](https://community.mrtrix.org/t/volume-render-with-signed-16-bit-integer-data-not-working/2968/1 "2019-10-29T11:23:46Z")

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Hey,

I tried to open the endings\_segmentations files generated by TractSeg in volume render mode. Opening the file in 2D slices seems to work normally but upon switching to volume render mode the visualization vanishes.

I noticed that after combining begins and ends with `mrcalc *_b.nii.gz *_e.nii.gz -max *.mif` the volume rendering succeeds.

After investigation with mrinfo I noticed that mrcalc implicitly converts the 16 bit signed integer file exported by TractSeg to a 32 bit float datatype (little endian). After converting all the files explicitely using mrconvert I can open all of them in volume render mode now.

As this does not seem to be wanted behaviour I thought I would report it here.

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**Author:** ![jdtournier](https://community.mrtrix.org/user_avatar/community.mrtrix.org/jdtournier/32/2594_2.png) [@jdtournier](https://community.mrtrix.org/u/jdtournier)\
**Post date:** [October 30, 2019, 11:14am UTC](https://community.mrtrix.org/t/volume-render-with-signed-16-bit-integer-data-not-working/2968/2 "2019-10-30T11:14:49Z")

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I’m afraid I can’t reproduce the issue on my system… I don’t have any issues displaying `int16` images in volume render mode. Any chance you could send me the problematic file? And/or post the full output of `mrinfo` on one of them? I’m wondering whether this might relate to the data scaling, or the size of the image.

Also, what system are you running on? Maybe you can post a screenshot of the Help-\>OpenGL dialog box? I’ve noticed funny issues on a colleague’s MacBook Pro recently that might have something to do with this…

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**Author:** ![Darius](https://community.mrtrix.org/user_avatar/community.mrtrix.org/darius/32/3187_2.png) [@Darius](https://community.mrtrix.org/u/Darius)\
**Post date:** [October 30, 2019, 1:45pm UTC](https://community.mrtrix.org/t/volume-render-with-signed-16-bit-integer-data-not-working/2968/3 "2019-10-30T13:45:01Z")

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I’m on a MBP with Mac OS 10.15 Catalina. I will send you the file via mail.

```auto
************************************************
Image: "CC_b.nii"
************************************************
  Dimensions: 145 x 174 x 145
  Voxel size: 1.25 x 1.25 x 1.25
  Data strides: [-1 2 3]
  Format: NIfTI-1.1
  Data type: signed 16 bit integer (little endian)
  Intensity scaling: offset = 0, multiplier = 1
  Transform: 1 0 0 -90
                               -0 1 0 -126
                               -0 0 1 -72

```

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<div class="post-metadata">

**Author:** ![Darius](https://community.mrtrix.org/user_avatar/community.mrtrix.org/darius/32/3187_2.png) [@Darius](https://community.mrtrix.org/u/Darius)\
**Post date:** [October 30, 2019, 2:07pm UTC](https://community.mrtrix.org/t/volume-render-with-signed-16-bit-integer-data-not-working/2968/4 "2019-10-30T14:07:51Z")

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We also always had problems with streamtube visualization of connectome data on Mac.

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<div class="post-metadata">

**Author:** ![jdtournier](https://community.mrtrix.org/user_avatar/community.mrtrix.org/jdtournier/32/2594_2.png) [@jdtournier](https://community.mrtrix.org/u/jdtournier)\
**Post date:** [November 1, 2019, 3:41pm UTC](https://community.mrtrix.org/t/volume-render-with-signed-16-bit-integer-data-not-working/2968/5 "2019-11-01T15:41:54Z")

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OK, I can confirm there is indeed a problem, which comes down as far as I can tell to the weird difference in the way the OpenGL standard maps signed & unsigned integers to the [0 1] range. I’m going to need to mull on that one, and it’ll most likely have to wait until at least after ISMRM – sorry…

In the meantime, you can get around it by adding 0.5 to both intensity values, and both transparency values in the View tool.

> [@Darius](#):
>
> We also always had problems with streamtube visualization of connectome data on Mac.

Can you expand? Might it be related to [this issue](https://github.com/MRtrix3/mrtrix3/pull/1720)?