Dear FS List,

I recently encountered a couple of issues with some patient data that caused recon-all not to work. Recon.log files attached.

The first error seems to be during the EM alignment step and has an MCSRCH ERROR and applies to 1030813-1, 1030813-3, and P201503416. The T1s look generally fine except that there might be some WM degradation. But I’ve seen worse that worked. Is this because the brain is too far off the center for alignment to the GCA atlas? Would reorienting or manual centering here help?

The second error applies to U200057992 and may be a segmentation problem. For this case, there is a tumor in the WM, along with WM degradation. Is Freesurfer able to handle WM tumors?

Thanks! Josh