# 5ttgen stuck at first-L\_accu\_first.vtk

**URL:** https://community.mrtrix.org/t/5ttgen-stuck-at-first-l-accu-first-vtk/941
**Category:** Uncategorized
**Created:** [June 4, 2017, 5:07pm UTC](https://community.mrtrix.org/t/5ttgen-stuck-at-first-l-accu-first-vtk/941 "2017-06-04T17:07:43Z")
**Posts on this page:** 1
**Showing post:** 4

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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: [June 5, 2017, 1:02am UTC](https://community.mrtrix.org/t/5ttgen-stuck-at-first-l-accu-first-vtk/941/4 "2017-06-05T01:02:24Z")

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> All other first.vtks like Thal, Put, etc are built.

OK, that’s interesting; I was under the impression that it was most typically the registration steps in `run_first_all` that failed, in which case none of the segmentations would be produced.

Firstly, I would confirm that you are able to reproduce the fault by manually executing `run_first_all` on the relevant T1 image. It may seem like a pointless exercise, but from a software support perspective it makes a very big difference whether _MRtrix3_ is doing something that is causing an FSL tool to fail, or whether the FSL tool is failing for your data independently of _MRtrix3_.

The second thing you could try is executing the `fsl_anat` script. I mentioned [here](http://community.mrtrix.org/t/5ttgen/133/29) that `5ttgen fsl` could conceivably be modified to make use of this FSL-maintained script; it’s possible that some of the extra steps in that script are making the process more robust. (Or maybe I could just duplicate those extra steps)

> Interestingly it’s running smoothly on native T1 image. I think the registration was problematic. But a further problem arises: Is it possible to register after 5ttgen?

`5ttgen` does not incorporate any multi-modal registration, nor does it depend on DWI data in any way.

> Update: 5ttgen has finished with this error:

OK, an up-to-date _MRtrix3_ `5ttgen` shouldn’t be producing that error. If you run `5ttcheck` manually, you should be able to get a more specific error message, and optionally a mask of image voxels where an error was detected.

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_[View the full topic](https://community.mrtrix.org/t/5ttgen-stuck-at-first-l-accu-first-vtk/941)._