Dear all,
When I am trying to use ’ tck2connectome ’ to generate the connectome with the .tck file on the AAL116 template, some nodes do not have any streamlines assigned. This only happens when I use the DTI method to do the fibertracking. When I use the CSD method, although still don’t know if I do it correctly or not, at least all nodes have streamlines assigned.
I used the command bellow:
(DTI method):
tckgen eddy_denoise.mif track.tck -algorithm fact -cutoff 0.1 -angle 45 -mask dti_mask.mif -select 200k -seed_image dti_mask.mif -force
tck2connectome -zero_diagonal dti_mask.mif track.tck aal_diff.nii.gz connectome_FN.csv
The ’ eddy_denoised.mif ’ is the diffusion image after dwidenoise(use mrtrix3) and eddy_correct(use FSL), ’ dti_mask.mif ’ is the mask generated by the ’ eddy_denoised.mif '. The ’ aal_diff.nii.gz ’ is the AAL116 template which is registered to the b0 image(I use ’ bet ’ command offered by FSL to remove the skull bones) eddy_denoise.mif, and I think the registration is not that bad:
Here is the warning:
tck2connectome: [WARNING] The following nodes do not have any streamlines assigned:
tck2connectome: [WARNING] 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 71, 72, 73, 74, 75, 76, 77, 78, 95, 96, 98, 709, 111, 114, 115, 116
[WARNING] (This may indicate a poor registration)
Any help would be appreciated.
Best,
Liu