Hello freesurfers,
I am currently attempting to run recon-all on a set of infant brains with a non-default atlas. I was previously running into a problem where freesurfer was unable to find control points for the various labeled regions of the atlas. It appears as if the “wm_mean” of the atlas and subject are being set to 0. My thought is that the non-deafult atlas was resulting in some sort of null error where everything was just set to zero by default. This resulted in a completely blank “ctrl_points.mgz” and “norm.mgz” files.
However, I recently noticed that the “aseg.auto_noCCseg.mgz” file looks like the atlas is actually mapping the various regions to the subject’s original T1 file. A screenshot of this file is attached to the e-mail.
Does anyone have any ideas why the atlas would map correctly to the aseg file, but then fail to find any control points in those same regions? I attached the log file in case that would help. Thank you!
- Mark
