# Tensor visualisation

**URL:** <https://community.mrtrix.org/t/tensor-visualisation/1847>\
**Category:** Uncategorized\
**Created:** [August 17, 2018, 7:54am UTC](https://community.mrtrix.org/t/tensor-visualisation/1847 "2018-08-17T07:54:23Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![judominguez](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/j/cc9497/32.png) [@judominguez](https://community.mrtrix.org/u/judominguez)\
**Post date:** [August 17, 2018, 7:54am UTC](https://community.mrtrix.org/t/tensor-visualisation/1847/1 "2018-08-17T07:54:23Z")

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Hello,

I am trying to visualise tensors after running

> dwi2tensor dwi.mif dt.mif

but upon loading in mrview this is what I am seeing:

> mrview dt.mif

 ![fig1](https://community.mrtrix.org/uploads/default/original/2X/2/256229a2f0ca28248e2be99c61bf4cbf7609acac.jpg)

> mrview dt.mif -odf.load\_tensor dt.mif

 ![fig2](https://community.mrtrix.org/uploads/default/original/2X/9/9e951de7f90dd2061d4747abab2f54facb5b7808.jpg)

I have tried dwi2tensor on a MacBook, an iMac and a cluster running ubuntu (all with mrtrix/3.0\_rc3) and images from three different datasets at b1000/30dir and b3000/60dir (and the images were converted from DICOM with mrconvert).

However, the following command works fine:

> dwi2tensor dwi\_biascorr.mif - | tensor2metric - -fa - | mrcalc - mask.mif -mult fa.mif

I also tried running _dwi2tensor dwi.mif dt.mif_ with mrtrix/3.0\_RC1, but the command simply gets stuck at dwi2tensor: [100%] computing tensors (it never finishes).

Any help is much appreciated.

Juan

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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:** [August 17, 2018, 3:36pm UTC](https://community.mrtrix.org/t/tensor-visualisation/1847/2 "2018-08-17T15:36:42Z")

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This sounds to me like the same issue as in [this recent thread](https://community.mrtrix.org/t/tensor2metric-rd-adc-ad-not-giving-good-values/1839). The problem is probably simply that you’re getting totally wild ADC values (i.e. values for the tensor elements) in non-brain regions. You try simply masking the data at the `dwi2tensor` stage, i.e.:

```auto
dwi2tensor dwi.mif -mask mask.mif dt.mif

```

That ought to get rid of _most_ of the problem – but probably not all of it, there’s likely to be a few remaining non-brain regions included in the mask that still cause trouble…

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<div class="post-metadata">

**Author:** ![judominguez](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/j/cc9497/32.png) [@judominguez](https://community.mrtrix.org/u/judominguez)\
**Post date:** [August 21, 2018, 12:44am UTC](https://community.mrtrix.org/t/tensor-visualisation/1847/3 "2018-08-21T00:44:26Z")

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That was exactly the issue. Many thanks.