Image "5TT.mif" contains 1 brain voxels with non-unity sum of partial volume fractions

On preprocessed HCP data 100307, I am executing the command 5ttgen (5ttgen fsl T1w_acpc_dc_restore_brain.nii.gz 5TT.mif -premasked)and receiving a warning

5ttgen: [WARNING] Command failed: 5ttcheck result.mif
5ttgen: [WARNING] Generated image does not perfectly conform to 5TT format

I did 5ttcheck on 5TT.mif image and received below error

5ttcheck: [WARNING] Image "5TT.mif" contains 1 brain voxels with non-unity sum of partial volume fractions
5ttcheck: [ERROR] Input image does not conform to 5TT format

I have performed this step on this data before and executed without error but now its giving this error.
Please advise.
Many thanks.

Hi @Sarbani,

The same issue was reported and discussed here. I might need to reduce the implied severity of the reporting of that issue so that people don’t panic about it; as I said in the other thread, having one solitary voxel where the tissues don’t perfectly sum to 1 is unlikely to have any effect whatsoever.

Nevertheless, it would be handy to know exactly what’s happening in that voxel through the script that’s resulting in a residual error:

5ttgen fsl T1w_acpc_dc_restore_brain.nii.gz 5TT.mif -premasked -nocleanup
5ttcheck 5TT.mif -masks 5TTerr_
maskdump 5TTerr_5TT.mif # Print out the voxel location
# The following access image intensities just in that one voxel
for i in `seq 0 2`: do
  mrdump 5ttgen-tmp-*/T1_masked_pve_${i}.nii* -mask 5TTerr_5TT.mif
done
mrdump 5ttgen-tmp-*/all_sgms.mif -mask 5TTerr_5TT.mif

(or something like that)

I have performed this step on this data before and executed without error but now its giving this error.

If it was prior to version 3.0_RC1, this check was simply not performed. Alternatively, one of the commands used by the script may not be perfectly deterministic.

Rob

Thanks @rob for clarifying the issue.
Glad to know that this is not a severe error and can continuing with further steps.
Also thanks for clarifying that the issue may be was before but check was not performed that time.

Sarbani