Hello all,
I am experiencing an error during the mri_ca_normalize step of
auto-recon-1 using a non-default atlas (for infant brains). Essentially,
"norm.mgz" and "ctrl_pts.mgz" are both outputting as blank files
(completely black). However, brainmask.mgz looks completely fine, which
leads me to believe that skull-stripping and alignment should be OK.
Subsequently, zero control points were found during the
"mri_ca_normalize" step. While mri_ca_normalize does not fail, I believe
the lack of control points causes the following error in the "mri_ca_label"
step:*searching scale 1 Z rot 2.3 * *searching scale 1 Z rot 2.5 * *searching scale 1 Z rot 2.8 * *searching scale 1 Z rot 3.0 * *searching scale 1 Z rot 3.3 * *searching scale 1 Z rot 3.5 * *searching scale 1 Z rot 3.8 * *searching scale 1 Z rot 4.0 * *searching scale 1 Z rot 4.3 * *searching scale 1 Z rot 4.5 * *searching scale 1 Z rot 4.8 * *searching scale 1 Z rot 5.0 * *searching scale 1 Z rot 5.3 * *searching scale 1 Z rot 5.5 * *searching scale 1 Z rot 5.8 * *searching scale 1 Z rot 6.0 * *searching scale 1 Z rot 6.3 * *searching scale 1 Z rot 6.5 * *searching scale 1 Z rot 6.8 global minimum found at slice 0.0, rotations (90.00, -0.00)* *final transformation (x=0.0, yr=90.000, zr=-0.000):* *-0.000 0.000 1.000 128.000;* *-0.000 1.000 -0.000 128.000;* *-1.000 0.000 0.000 128.000;* * 0.000 0.000 0.000 1.000;* *Segmentation fault* I am wondering if anyone knows why the control points would not be found and if there is anyway to solve the problem? I can also attach the .gca atlas that I am using if that would help. I also noticed that the "aseg.auto_noCCseg.mgz" file seems to have shifted significantly from the position of the GCA atlas. In fact, it shifted so far that some of the occipital lobe appears to have been cut out [I attached an image for details]. I am not sure if this is a related problem, but I figured I should mention it. I appreciate the help! Best, Mark
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