# 5tt file, mouse brain, tracts detected only in the subcortical gray matter

**URL:** <https://community.mrtrix.org/t/5tt-file-mouse-brain-tracts-detected-only-in-the-subcortical-gray-matter/372>\
**Category:** Uncategorized\
**Created:** [August 1, 2016, 2:03pm UTC](https://community.mrtrix.org/t/5tt-file-mouse-brain-tracts-detected-only-in-the-subcortical-gray-matter/372 "2016-08-01T14:03:13Z")\
**Posts on this page:** 1\
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**Author:** ![trang229](https://community.mrtrix.org/user_avatar/community.mrtrix.org/trang229/32/1293_2.png) [@trang229](https://community.mrtrix.org/u/trang229)\
**Post date:** [May 30, 2018, 3:08pm UTC](https://community.mrtrix.org/t/5tt-file-mouse-brain-tracts-detected-only-in-the-subcortical-gray-matter/372/6 "2018-05-30T15:08:39Z")

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Dear Francesca,  
I am currently trying manually segmentation for mouse brain to create 5tt file. However I got problem with identify WM, GM, sub-cortical GM. How did you deal with that?  
I based on a atlas and a segmentation results retrieved from internet, but that’s not enough for accurately segmentation.  
And Could you describe more about how to create 4D 5TT file?

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