For my project, i need to create connectivity using Brainnetome atlas. I’ve read the batman tutorial,Brainnetome’s manual and this discussion (Brainnetome Atlas on HCP) and done the following steps:
1-mapping lh.cortex.label to subject-50328:
mris_ca_label -l $SUBJECTS_DIR/sub-50328/label/lh.cortex.label sub-50328 lh $SUBJECTS_DIR/sub-50328/surf/lh.sphere.reg $SUBJECTS_DIR/lh.BN_Atlas.gcs $SUBJECTS_DIR/sub-50328/label/lh.BN_Atlas.annot
2- mapping rh.cortex.label to subject-50328
mris_ca_label -l $SUBJECTS_DIR/sub-50328/label/rh.cortex.label sub-50328 lh $SUBJECTS_DIR/sub-50328/surf/rh.sphere.reg $SUBJECTS_DIR/lh.BN_Atlas.gcs $SUBJECTS_DIR/sub-50328/label/rh.BN_Atlas.annot
3-Map the annotation files to the subject:
mri_aparc2aseg --old-ribbon --s sub-50328 --annot BN_Atlas --o BN_batmman.mgz
mrconvert BN_batmman.mgz BN_batmman.mif
4- Replace the random integers of the BN_batmman.mif file with integers that start at 1 and increase by 1.
labelconvert BN_batmman.mif BN_Atlas_246_LUT.txt BN_atlas_ordered.txt BN_parcels_nocoreg.mif
as i read in the the batman tutorial, the resulting image (BN_batmman.mif) in the step 3 will have the adequate atlas-based segmentation, but with more or less random integers assigned and MRtrix requires that the integers start with 1 and increase by 1. for sloving this issue, two look up tables are needed (one with the original integers and the other with the ordered integers) which have been provided in share/mrtrix/lableconvert folder.I saw the folder content and i didn’t find any ordered text file for Brainnetome. how can i find this file or create it?
thanks in advance to your help
Bests,
milad