5ttseg keep original voxel numbers and dimensions



After 5ttseg, the dimensions of the 5ttseg.mif output is different from that of the input, even when using -nocrop option. I’m using the WM output for subsequent steps, so it’s slightly problematic to have to do a rigid registration again to the original T1.
Could you please tell me how to keep all the original information in the segmentation output?

Many thanks


Hi Adriana,

I have some vague recollection of having fixed an issue with 5ttgen changing the output voxel grid despite having been provided with the -nocrop option. This shouldn’t be happening…

  • Are you using an up-to-date MRtrix3 version?
  • Which 5ttgen algorithm are you using?
  • Are you providing any other command-line options?

Assuming the voxel grid is just being cropped and not reoriented in any way, you should be able to use mrtransform with the -interp nearest and -template command-line options to get back to the original voxel grid with no loss of detail. But obviously my own interest is in solving the underlying issue.



Hi Rob,

Thanks for getting back to me.
Yes I am using MRtrix3 and the fsl algorithm.
I am currently using mrtransform following 5ttgen. But since I’m applying this to many images and have to QC after each step, I thought I might be missing something with the 5ttgen command to prevent it from changing the voxel grid.

Thanks again,


Yes I am using MRtrix3 …

Can you provide a more precise version (i.e. output of mrconvert -version)?


The following version, from June 22 2018
== mrconvert 3.0_RC3-51-g52a2540d ==