AAL3 parcellation

1

Hi experts,

Thanks for the amazing tools. I have registered the AAL3 parcellation to individual T1 following the step provided in Problems with AAL parcellation - #14 by stellamarissanchez89. However,I still cannot figure out how to do connectomic analysis in AAL3 atlas. When I tried to run the labelconvert AALtoT1.nii.gz ROI_MNI_V6_vol.txt aal3.txt AALtoT1_relabel.nii.gz
There is no aal3.txt provided in the labelconvert document in mrtrix and the aal3.nii.txt downloaded from the aal3_for_spm12.tar.gz does not apply either.

Is there an approach to solve the issue?

2 Likes
2

I tried to create the aal3.txt by myself following the format of aal2.txt provided in mrtrix. However, it keeps telling me the lut file “aal3.txt” is in unrecognized format: [ text text text]. What’s going on? What else should I do?

4

I realize I don’t need to do labelconvert. Problem solved!

5

Hi Frances,

I am also trying to use the AAL3 atlas for parcellation and connectome construction. I was wondering how you achieved this? Did you register the AAL3 atlas into diffusion space (AAL3 → T1 space → diffusion space)? Also, how did you manage to not use labelconvert?

Thank you for any help!