Ok, i narrowed it down and it actually is a bug, but we will fix it in the next release.
As a workaround, you can do the following
In your brainsuite installation
1. Rename the file BrainSuite21a/svreg/BCI-DNI_brain_atlas/sulcal_protocol_HD.xml to
BrainSuite21a/svreg/BCI-DNI_brain_atlas/sulcal_protocol_HD.xml.old
2. copy /home/ajoshi/BrainSuite21a/svreg/BCI-DNI_brain_atlas/BCI-DNI_brain.sulcal_protocol_HD.xml to /home/ajoshi/BrainSuite21a/svreg/BCI-DNI_brain_atlas/sulcal_protocol_HD.xml
Now if you reprocess the data, it should work as intended.