Hi Matt you can't skip the careg step if you want an automated recon. It's not optional. Sorry. Bruce On Wed, 24 Oct 2012, Matt Leonard wrote:

Hello,

I'm trying to run a simple recon on a single T1 dataset, and am not interested in any quantitative measures (this is just for data presentation and eventual MRI/CT co-registration).  To save time, I tried to skip the CA registration step, but got the following error:

#--------------------------------------

#@# CA Reg Inv Wed Oct 24 14:49:20 PDT 2012

/Applications/freesurfer/subjects/CH/mri

\n mri_ca_register -invert-and-save transforms/talairach.m3z \n

Loading, Inverting, Saving, Exiting ...

Reading transforms/talairach.m3z

ERROR: cannot find or read transforms/talairach.m3z

ERROR: mri_ca_register with non-zero status 0

So then I tried skipping all the steps that appear to need the talairach.m3z file, and used this command:

recon-all -s CH -autorecon2 -nocanorm -nocareg -normneck -noskull-lta -nocalabel -nosegstats

That gave the same error.  What am I doing wrong as far as skipping the careg step?

Thanks,

Matt