Problems with AAL parcellation

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22

Hi Stella,

Thank you for sharing the code and methods.

I have some question about the labelconvert , I want to know what’s the aal.txt and the LUT you used looks like?

Thanks,
Andy

23

Hi Andy,

Please commence a new thread if the labelconvert tutorial does not adequately explain the process.

Thanks
Rob

24

I have follow these steps :
flirt -in T1w_masked.nii -ref $FSL_DIR/data/standard/MNI152_T1_2mm_brain.nii.gz -out T1w_sub_mni -omat T1w_sub_mni.mat -interp nearestneighbour -dof 12

convert_xfm -omat i_T1.mat -inverse T1w_sub_mni.mat

flirt -in /home/pc/Documents/conn_preproc/aal116MNI.nii -ref T1w_masked.nii -out aalt1w.nii.gz -applyxfm -init i_T1.mat -interp nearestneighbour -dof 12

labelconvert /home/pc/Documents/conn_preproc/aal116MNI.nii /home/pc/Documents/conn_preproc/aal_lut116.txt /home/pc/Documents/conn_preproc/aal_lut.txt aal_percilated.mif -force

tck2connectome -symmetric -zero_diagonal -scale_invnodevol -tck_weights_in sift_1M.txt tracks_1M.tck aalt1w.nii.gz sc.csv -force

But still get the error of poor registrations.
tck2connectome: [WARNING] 2111, 2112, 2211, 2212, 2321, 2322, 2611, 2612, 2701, 2702, 8121, 8122, 8211, 8212, 9011, 9012, 9051, 9052, 9062, 9072, 9081, 9082

Please help me.