Hello,
Hope this message finds you well.
I was beginning to run recon-all on a dataset and was encountering a problem with the talairach registration. I've encountered this error before here and there, but I've been receiving the same error for every scan that I've been trying to run, and I'm not sure why. It's also the first time I've used NIFTI files as the input - not sure if that's a contributing factor. I've also tried the -use-mritotal flag without any luck.
These are the errors I receive:
WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
I would appreciate your help. Thank you!
Warmly, Ariana