Dear FS team, Thank you for your answers before (email: WmParc). We now realize that we've formulated our question wrong, since our problem is mainly in creating the wmparc.a2009s.mgz file. We ran the following command: mri_aparc2aseg --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz (<subjid> was replaced by our subject and the ribbon command was set to 'noribbon' because we otherwise received the message the that the ribbon command was unknown.)
If we run this command, we can extract grey matter labels with fslmaths (e.g. 11136 for the left planum temporale), but not the white matter labels we are looking for (this is 13136 for the left planum temporale). The problem seems to be in the labelling of the white matter.
Many thanks. Jolijn & Caroline