# BRAINSFit python environment

**URL:** <https://discourse.slicer.org/t/brainsfit-python-environment/35902>\
**Category:** Support\
**Created:** [May 3, 2024, 9:29pm UTC](https://discourse.slicer.org/t/brainsfit-python-environment/35902 "2024-05-03T21:29:59Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![zoey](https://avatars.discourse-cdn.com/v4/letter/z/b4bc9f/32.png) [@zoey](https://discourse.slicer.org/u/zoey)\
**Post date:** [May 3, 2024, 9:29pm UTC](https://discourse.slicer.org/t/brainsfit-python-environment/35902/1 "2024-05-03T21:29:59Z")

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Hi all,

I am trying to perform registration of two MRI modalities of the same subject using BRAINSfit in a non-slicer python environment. I try to use the method described in this link https://www.slicer.org/w/index.php/Documentation/4.1/Modules/BRAINSFit. However, when I access the folder of ‘Slicer-5.6.2-linux-amd64/lib/Slicer-5.6/cli-modules’ and try to run ‘BRAINSFit’, it has the error of

> ‘BRAINSFit: command not found’  
> Does anyone know how to run the BRAINSFit properly in terminal?

Thanks!

Best,  
Zoey

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<div class="post-metadata">

**Author:** ![zoey](https://avatars.discourse-cdn.com/v4/letter/z/b4bc9f/32.png) [@zoey](https://discourse.slicer.org/u/zoey)\
**Post date:** [May 6, 2024, 3:09pm UTC](https://discourse.slicer.org/t/brainsfit-python-environment/35902/2 "2024-05-06T15:09:59Z")

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Update: the problem solved by adding whatever paths that are missing using ‘export’ command.