Registration problem


Hello, MRtrix experts
I followed ISMRM protocol, and
I am struggling with registration problem and cannot figure out solution.

The error message I got is
tck2connectome: [WARNING] The following nodes do not have any streamlines assigned:
tck2connectome: [WARNING] 5, 11, 13, 18, 25, 31, 32, 35, 39, 41, 42, 48, 49, 50, 54, 55, 57, 62, 63, 67, 74, 78, 80, 81, 84
tck2connectome: [WARNING] (This may indicate a poor registration)

So, I overlayed
nodes_fixSGM.mif with meanb0.mif

and they are not well - registered

I overlayed
meanb0.mif and tissueRGB.mif

they look well-registered

finally I overlayed
nodes_fixSGM.mif and RF_voxels.mif

and they look well registered to each other.

I think the problem is that nodes_fixSGM.mif and meanb0.mif are poorly registered.

But when I tried with another subject, with same protocol,

It does not seem perfect, but the registration process ran okay.
I do not get error message of ‘tck2connectome: [WARNING] (This may indicate a poor registration)’
from this subject.

How can I find a solution to this poor registration problem?

Best wishes,

In generating connectome, I provided input structure images from products of freesurfer ‘recon-all’

The commands used are
mri_convert brain.mgz T1_brain.nii.gz
mri_convert aparc+aseg.mgz aparc+aseg.nii.gz


I could avoid this problem by registering
aparc+aseg.nii.gz and T1_brain.nii.gz to DTI B0 image using ANTs,
But I am not sure this is appropriate way.


Dear @MCKim,

I think that the best way to register DWI to FreeSurfer data is to use bbregister. See this thread:

or this:



Thank you Antonin
So I think registration process is nessasary…