Using brain Brainnetome atlas for creating connectivity

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



Hi Milad,

With my own pipeline (which I’ve admittedly not used for connectome construction for some time), for the Brainnetome parcellation it seems from the code that I deemed the labelconvert step unnecessary for this particular parcellation. So I would begin by checking that the contents of image BN_batmman.mgz are in fact not already integers consecutively incrementing from 1. If that’s not the case, then either the altas data have changed since I last used them, or you have acquired those data from some other location and the values contained within are different (which I’ve seen historically for the AAL atlas).

From the forum thread you linked, it looked like it was proposed that such a text file did not yet exist and would need to be created. If nobody has done so / is willing to share such, then as I’m sure I’ve mentioned elsewhere, I can’t really give instructions over and above the content of the labelconvert dedicated documentation page: if you understand the operation of that command, it should be clear what the contents of the requisite file should be.


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Dear Rob

Many thanks for your helps. I manually modified BN_Atlas_246_LUT.tx and created that text file using other ordered text files provided in the /mrtrix/share. I also created a connectivity using brainnetome atlas.