Problems with AAL parcellation

[stellamarissanchez89]

Ok!

Case 1: I want the AAL parcellation in the subject’s space

1. Register the subject’s T1 image into AAL template.
   flirt -in T1_bet.nii -ref aal_template.nii -out T12AAL_nn.nii -omat T12AAL_nn.mat -interp nearestneighbour -dof 12

2. Invert the matrix
   convert_xfm -inverse T12AAL_nn.mat -omat AAL2T1_nn.mat

3. Apply the inverted matrix:
   flirt -in aal_template.nii -ref T1_betnii -applyxfm -init AAL2T1_nn.mat -out AAL2T1_nn.nii
   So here I have the AAL parcellation in the subject’s space, it hasn’t discontinuous areas yet.
   

   

4. labelconvert
   labelconvert AAL2T1_nn.nii aal_mapping.txt aal.txt nodos_AAL_nn.nii
   

   

In the next screenshot I show the AAL2T1_nn.nii with the nodos_AAL_nn.nii overlayed, with the interpolation option off and pointing a specific discontinuity in the node image.

On the other hand, I tried this just to see what happens:

Case 2: Run the labelconvert command directly on the AAL template, without moving it to the subject’s space.
labelconvert aal_template.nii aal_mapping.txt aal.txt nodos_aal_template.nii

No discontinuities at all.

Thanks for your time.