I was trying to run the recon-all for one of the subjects. I got following error message:

"ERROR: mritotal failed, see transforms/talairach.log".

The image seems to have some missing hippocampal area. I wonder If we can still run the recon-all?

 I checked previous archive emails (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40166.html). It says tkregister can be used to manually align the image. Can anyone explain properly, how can we use the tkregister to align the image and save so that the freesurfer cannot complain about the "mritotal failed".

Thank you in advance,

Hari