Hi,

I was trying to use mri_aparc2aseg to convert the BA.annot (or BA.thresh.annot) to segmentation volume, that will be then converted to EPI space for some diffusion data.

I tried both the BA.annot for the individual subject as well as the PALS_B12_Brodmann.annot in fsaverage.

The command line I used was: mri_aparc2aseg --s s1 --annot BA.annot --o BAseg.mgz.

It seems that this command is working, but when I view the BAseg.mgz file in freeview, the index for the BA areas seems wrong. For example, for BA1, the index says 2004 for ctx-rh-corpuscallosum. It seems that the index for BA areas in FreeSurferColorLUT are from 400 to 414.

Is there a way to make the index correct? Or mri_aparc2aseg can only be used for aparc.a2009s.annot or aparc.annot?

Thanks a lot.

Best

QT