Hi Thang,
running talairach just before running the fill won't necessarily help, as it will added the talairach.xfm transform to the orig/COR-.info, which the fill (mri_fill) doesn't read. You can either add it by hand to the wm/COR-.info file (copies from the orig), or you can specify it directly on the command line using mri_fill -xform \ $SUBJECTS_DIR/$subject/mri/transforms/talairach.xfm ...
cheers, Bruce
On Fri, 22 Oct 2004, Nguyen, Thang Q wrote:
Hi all, I have a few subjects who have angled cutting planes. I ran talairach <subjid> and rerun the mri_fill and there is a very angled cut. A reason for this may be that the pons have been removed during white matter segmentation. The brain images have the pons intact but the wm images don't. I've run recon-all stage1, segment_subject, and process volume from the csurf interface. They all remove the pons. I've also tracked the coordinates of the pons in the brain volumes and used those in the mri_fill command (-P <x> <y> <z>). Is there a reason for this and a way to fix it? Thank you, Thang Nguyen