# Fiber tract visualised on a glass brain

**URL:** <https://community.mrtrix.org/t/fiber-tract-visualised-on-a-glass-brain/4932>\
**Category:** Uncategorized\
**Tags:** tractography\
**Created:** [May 28, 2021, 8:44am UTC](https://community.mrtrix.org/t/fiber-tract-visualised-on-a-glass-brain/4932 "2021-05-28T08:44:37Z")\
**Posts on this page:** 1\
**Showing post:** 2

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**Author:** ![bjeurissen](https://community.mrtrix.org/user_avatar/community.mrtrix.org/bjeurissen/32/28_2.png) [@bjeurissen](https://community.mrtrix.org/u/bjeurissen)\
**Post date:** [May 28, 2021, 9:24am UTC](https://community.mrtrix.org/t/fiber-tract-visualised-on-a-glass-brain/4932/2 "2021-05-28T09:24:33Z")

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You can follow the steps described by Matteo Mancini in [Making a glass brain // NeuroSnippets](https://neurosnippets.com/posts/glass-brain/) :

1. upsample the mask
2. use a Gaussian filter to smooth the upsampled mask
3. use a threshold to obtain a neat black-and-white result
4. dilate the previous volume
5. subtract the volume obtained in point 4 from the dilated volume

```auto
mrresize mask.mif -scale 5 mask_up.mif
mrfilter mask_up.mif smooth -stdev 2 mask_smooth.mif
mrthreshold mask_smooth.mif -abs 0.5 mask_thres.mif
maskfilter mask_thres.mif dilate -npass 2 mask_dilated.mif
mrcalc mask_dilated.mif mask_thres.mif -subtract glass_brain.mif

```

Then open `glass_brain.mif` with `mrview` and switch to volume renderer view and play with the alpha settings untill you get the desired effect.

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