I ran recon-all -stage1 -nomotioncor -subjid <subjectID> It exited with errors during mri_fill:
mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood...
I ran -stage1 again with rh, lh, cc, and pons seed points. It finished without errors but the cc cut was still incorrect (wm in the rh was incorrectly labelled lh wm). I opened "brain" in tkmedit and loaded the talairach transform. The talairach is really off. When I choose "corornal" view, I get horizonal view. Increasing slice numbers go superior to inferior When I choose "horizontal" view, I get an upside-down coronal view, increasing slice numbers go anterior to posterior When I choose "sagittal" view, I get a sagittal view rotated 90 degrees counter-clockwise. Increasing slice numbers go right to left.
How do I fix this?