# Limiting DTI computation to a masked region, axis re-oreintaton

**URL:** <https://discourse.slicer.org/t/limiting-dti-computation-to-a-masked-region-axis-re-oreintaton/26040>\
**Category:** Support\
**Created:** [November 2, 2022, 4:47pm UTC](https://discourse.slicer.org/t/limiting-dti-computation-to-a-masked-region-axis-re-oreintaton/26040 "2022-11-02T16:47:30Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![Ron](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ron/32/10835_2.png) [@Ron](https://discourse.slicer.org/u/Ron)\
**Post date:** [November 2, 2022, 4:47pm UTC](https://discourse.slicer.org/t/limiting-dti-computation-to-a-masked-region-axis-re-oreintaton/26040/1 "2022-11-02T16:47:30Z")

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To all,

1. I am trying to limit the computation of the DTI data to a masked region (created using the segment editor) within the volume (in this case a human disc). For reference, I am trying to remove the green regions around the disc.  
 ![Master Scene View](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/b/fb169f0e83b32e1ac94e0000aeec740a409797de.jpeg)
2. How would re-Oriente the imaging planes ( green and yellow) windows to better match the disc anatomical axes  
 ![Imaging axes](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/e/b/eb21d27d3f6779ac6e5b339a8a519a7131e1214d.jpeg)  
Thank you, Ron

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**Author:** ![Ron](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ron/32/10835_2.png) [@Ron](https://discourse.slicer.org/u/Ron)\
**Post date:** [November 3, 2022, 5:36pm UTC](https://discourse.slicer.org/t/limiting-dti-computation-to-a-masked-region-axis-re-oreintaton/26040/2 "2022-11-03T17:36:12Z")

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@lassoan  
Andras hi, could ask for your help with the first issue? I hope to present next week, and it would be very helpful to be able to segment out all the data outside the disc segmentation. I think there used to be an option to use the segment label to restrict the region of DTI reconstruction. However, I cannot find a way to do so (only option is brain label?). Happy to share the slicer file. R

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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:** [November 3, 2022, 5:42pm UTC](https://discourse.slicer.org/t/limiting-dti-computation-to-a-masked-region-axis-re-oreintaton/26040/3 "2022-11-03T17:42:11Z")

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> [@Ron](#):
>
> I am trying to limit the computation of the DTI data to a masked region

You can use “Mask volume” effect in Segment Editor to blank out voxels of a volume outside the current segment. Would that be sufficient for you?

> [@Ron](#):
>
> How would re-Oriente the imaging planes ( green and yellow) windows to better match the disc anatomical axes

You can use Crop volume module for this. You can enable rotation for the region of interest (by right-clicking on any of its control point and in check “Interaction options” → “Rotate”.

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**Author:** ![Ron](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ron/32/10835_2.png) [@Ron](https://discourse.slicer.org/u/Ron)\
**Post date:** [November 3, 2022, 5:43pm UTC](https://discourse.slicer.org/t/limiting-dti-computation-to-a-masked-region-axis-re-oreintaton/26040/4 "2022-11-03T17:43:41Z")

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I hope so, I will try this now. Steve is also looking into this.

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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:** [November 3, 2022, 5:59pm UTC](https://discourse.slicer.org/t/limiting-dti-computation-to-a-masked-region-axis-re-oreintaton/26040/5 "2022-11-03T17:59:05Z")

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Trying to mask a DTI volume with the segment editor led to a crash (maybe not a surprise but still not good).

This method works after exporting the segmentation to a label:

```auto
>>> d = array("Output DTI*e")
>>> m = array("11-9001-pre_load-Segmentation-label")
>>> d[numpy.where(m != 1)] = numpy.zeros([3,3])

```

I’ll make new nrrd dti files for you Ron.

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/2/426e655f1e7b2c37ff703611a286c76c0823fcd1.jpeg)

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**Author:** ![Ron](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ron/32/10835_2.png) [@Ron](https://discourse.slicer.org/u/Ron)\
**Post date:** [November 3, 2022, 6:02pm UTC](https://discourse.slicer.org/t/limiting-dti-computation-to-a-masked-region-axis-re-oreintaton/26040/6 "2022-11-03T18:02:55Z")

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Steve Thanks!!!

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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:** [November 3, 2022, 6:38pm UTC](https://discourse.slicer.org/t/limiting-dti-computation-to-a-masked-region-axis-re-oreintaton/26040/7 "2022-11-03T18:38:40Z")

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Thanks for your help with this @lassoan. I showed @Ron how to do the numpy approach so he’s set now.

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<div class="post-metadata">

**Author:** ![Ron](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ron/32/10835_2.png) [@Ron](https://discourse.slicer.org/u/Ron)\
**Post date:** [November 3, 2022, 7:11pm UTC](https://discourse.slicer.org/t/limiting-dti-computation-to-a-masked-region-axis-re-oreintaton/26040/8 "2022-11-03T19:11:30Z")

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![Full spine hi-res-oreintation map](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/5/7/57ef0c39043f20087191876c8ab50c0c1d6a6c87.jpeg)  
:)!