I don't know why it failed, but you should try fixing it with

tkregister2 --fstal --s <subjectID>

then run with -notalairach

given how bad it is, you might be better starting from scratch, in which case you should add --regheader to the cmd

doug

Michele Perry wrote:

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? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer