5ttgen warning poor registration

Dear community:
I have run the code below,
5ttgen fsl anat.mif 5tt_nocoreg.mif -mask mask.mif -force

and it gavem me this warning

5ttgen: [WARNING] Generated image does not perfectly conform to 5TT format:
5ttgen: [WARNING] 5ttcheck: [WARNING] Image “result.mif” contains 44 brain voxels with non-unity sum of partial volume fractions
5ttgen: [WARNING] 5ttcheck: [WARNING] Input image does not perfectly conform to 5TT format, but may still be applicable (suggest re-running using the -masks option to see voxels where tissue fractions do not sum to 1.0)

if i continue the processing towards the structural connectome

tck2connectome: [WARNING] The following nodes do not have any streamlines assigned:
tck2connectome: [WARNING] 1, 3, 7, 8, 10, 14, 17, 18, 19, 21, 23, 26, 29, 30, 31, 33, 36, 37, 38, 39, 40, 42, 43, 44, 46, 80
tck2connectome: [WARNING] (This may indicate a poor registration)

Hey there - a few questions/suggestions for troubleshooting:

  1. Did you inspect the 5tt_nocoreg.mif image after you generated it? Does the segmentation into gray matter, white matter, etc. make sense? If you’re using the gmwm boundary, overlay that on the image as a sanity check.
  2. Did anything funky happen when you generated whole-brain streamlines? Do you find streamlines across the whole-brain when you overlay the tractography on the diffusion image? (Warning: don’t overlay the main streamline output, but a tck file with a smaller number of streamlines to avoid crashing your computer.)
  3. What about QAing the atlas-related outputs in the steps between 5ttgen and tck2connectome? The tck2connectome suggestion about poor registration means you should probably make sure that nothing went wrong for: atlas parcellation of your T1 anat image, the transformation from T1-space to diffusion space?

Good luck!

5tt_nocoreg.mif makes no sense. It seems everything is condensed in one image. I don’t know how to explain just that you don’t have all the views normally but just one square with all brain views superimposed. Anyways thats the issue. I don’t know if just omit this subject from the study or there is any fix.

Is there any fix? sorry if I wasn’t explicit enough in the question.


Just to be sure about this, are you using adult human data right?

If 5tt_nocoreg.mif makes no sense, could you post an image of the anat.mif and the mask.mif?

Best regards,


yes adult human data!!

anat.mif and mask.mif files?


Yes, the ones you use for the 5ttgen command:

Best regards,


I don’t have them with me when I do I’ll post them.

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here are the files requested Transfer - Dropbox

I understand a lot of time has passed since this post originally was posted. Anyways I decided to discard this subject.