Again i am facing the the problem
I tried applying this transform first to the labels
mrconvert –datatype uint32 hcpmmp1.mgz hcpmmp1.nii.gz
flirt -in hcpmmp1.nii.gz -ref norm_2_t1w.nii.gz -applyxfm -init norm_2_t1w.mat -out hcpmmp1_labels.nii.gz
then i did
labelconvert hcpmmp1_labels.nii.gz hcpmmp1_original.txt hcpmmp1_ordered.txt hcpmmp2_parcels_nocoreg.mif
now i am getting an error
labelconvert: Image “hcpmmp1_labels.nii.gz” stored with floating-point type; need to check for non-integer or negative values
labelconvert: [100%] uncompressing image “hcpmmp1_labels.nii.gz”
labelconvert: [100%] Verifying parcellation image
labelconvert: [ERROR] Floating-point number detected in image “hcpmmp1_labels.nii.gz”; label images should contain integers only.
Hi,
When you apply a transformation to the labels with flirt, you should add the flag -interp nearestneighbour to the command.
Best regards,
Manuel
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Yes, i have done that but still i have a problem, for the label 120 the streamlines are not assigned
tck2connectome: [100%] Constructing connectome
tck2connectome: [WARNING] The following nodes do not have any streamlines assigned:
tck2connectome: [WARNING] 120
tck2connectome: [WARNING] (This may indicate a poor registration)
Hi,
This could be to several reasons:
- Small number of streamlines, 1million I think is very small number for this parcellation.
- It could be that this area is specially difficult to tract and you need to refine your tractography parameters
- Maybe remains unassigned, because all the area falls inside of the GM, and therefore no tracts are allowed to reach that part. I encountered this problem with some areas for some subjects (neonates).
First I would inspect the image, to see that are aligned and the node 120 is not all covered by GM, then I would create a tractography with 100million streamlines and see if the warning is still there. There is a paper discussing some of these issues.
Best regards,
Manuel
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