Registration problem

[MCKim]

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,
Minchul

P.S.
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

[MCKim]

addendum
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.

[Antonin_Skoch]

Dear @MCKim,

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

Dilating of brain mask and some other general queries

Dear @Michiko, I am working with HCP pipelines, but I cannot give answer specific to HCP data since I am not working with them (probably the dwi and structural HCP data are already in register?). But generally, you have to assure that the structural and diffusion data are in register. This, however, does not mean that their voxel size has to be identical. Registering and regridding (reslicing) are two distinct things. You can bring the data to common coordinate systems without reslicing by adj…

or this:

Beginner: Connectome pipeline (Updated)

Dear Elijah, I was reading the post and I found it very interesting. I have a small doubt: In the third step of the structural processing, when you use tkregister to register T1 to DTI, how do you conserve the resolution? I mean if the DTI is 2x2x2 (for example) and the T1 1x1x1, the registered T1 should be also 2x2x2, am I correct? or there is something that I am missing… Regards, Manuel

Antonin

[MCKim]

Thank you Antonin
So I think registration process is nessasary…

Minchul