# 5ttgen fsl ERROR

**URL:** https://community.mrtrix.org/t/5ttgen-fsl-error/1379
**Category:** Uncategorized
**Created:** [December 18, 2017, 3:11pm UTC](https://community.mrtrix.org/t/5ttgen-fsl-error/1379 "2017-12-18T15:11:20Z")
**Posts on this page:** 1
**Showing post:** 2

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### Author: ![rsmith](https://community.mrtrix.org/user_avatar/community.mrtrix.org/rsmith/32/2672_2.png) [@rsmith](https://community.mrtrix.org/u/rsmith)
#### Post date: [December 19, 2017, 3:58am UTC](https://community.mrtrix.org/t/5ttgen-fsl-error/1379/2 "2017-12-19T03:58:50Z")

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Hi Jan,

FSL’s FIRST tool is genuinely failing for some of your subjects. Unfortunately `5ttgen fsl` is producing an intermediate error regarding one of the internal library functions, rather than providing the error it was intended to (see code [here](https://github.com/MRtrix3/mrtrix3/blob/master/lib/mrtrix3/_5ttgen/fsl.py#L177-L180)); however fundamentally the issue is that the `run_first_all` script is failing, and hence `5ttgen fsl` cannot proceed.

While I have implemented improvements to the Python library regarding how the outcomes of the `run_first_all` script are assessed & reported to users, and hope to push this to users, I cannot provide support on the underlying operation of FSL commands themselves. Unless by chance your failure is being caused by [unnecessary image down-sampling](https://community.mrtrix.org/t/5ttgen-waiitng-for-creation-of-new-file/1044/3?u=rsmith).

Cheers  
Rob

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