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?
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Douglas N. Greve, Ph.D.
MGH-NMR Center
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