Generating 5tt image for HCP data


I tried to generate a 5tt image for HCP 3T data. I tested it with the T1w_acpc_dc.nii.gz and with the T1w_acpc_dc_restore_brain.nii.gz file and the -premasked option.

Unfortunately the command ends with a warning: “[WARNING] Generated image does not perfectly conform to 5TT format:”

The _restore_brain run looks a lot better but I’m still wondering whether I should use the result or if I can tweak the generation somehow.

This is a slice of 5ttvis.mif from the _restore_brain input:

Hi Darius,

I’ve experienced this with HCP data. chances are that below (or above) that warning there will be a line saying how many voxels are affected (it is usually something tiny (between 1-5). You can also check which voxels are affected by running:

5ttcheck -mask prefix 5tt.mif

The voxels affected aren’t usually brain voxels.

I believe there was some other post about this at some point - if my memory serves the issue seems to stem from the way FSL operates…


that command resulted in a messasge telling me that the file is a correct 5tt image. Which is a bit odd because the generation produced the stated warning. Thanks for your help I will just use this image now.