open-discussion > Where is Cortical LUT lookup table
Aug 19, 2019  05:08 AM | Peter Jones - University of cambridge
Where is Cortical LUT lookup table
Thank you for making the BN_Atlas_freesurfer available to all.

I have been successfully using your script mapping_to_subjects.sh (with some edits). However, this does not make an aparc of the cortex, only an aseg of subcortical regions. I used the command
mri_aparc2aseg --s ${sub} --o ${SUBJECTS_DIR}/${sub}/mri/aseg.bn.mgz --annot BN_Atlas
to make an aseg. But the LUT is not correct. The file BN.mgz you provide reuses some values from the FreeSurferColorLUT, e.g. freesurfer value 173 (midbrain) is listed in the insula of BN. If I select the BN_Atlas_246_LUT then this is relabelled dig_L. But in my file created with the command above it has a value 1173. Where can I find the correct LUT for the aseg.bn that matches the --annot BN_Atlas? Then I could do the command,
mri_aparc2aseg --s ${sub} --o ${SUBJECTS_DIR}/${sub}/mri/aseg.bn.mgz --annot BN_Atlas --annot_table NEW_LUT

Thanks for your help.

Simon