Deane, the -no-talcheck flag is your best option now, considering that a manual alignment is no better than the automatic.
What is the age range of your subjects? We're implementing an alternate target consisting of young adults scanned at 3T, which works better for that cohort over the adults in the default target we use. Nick On Fri, 2009-06-12 at 09:43 -0400, Deane Aikins wrote: > > Hello, > > I had a Talairach QA check failure, with the error log indicating a Z = -8 > which > was below the criterion of z =-6. > > I then used tkregister2 to attempt a manual alignment (no surf orig was > available). After visual inspection, the subject and Talairach volumes looked > really closely aligned already. I did some very conservative rotation and > movement in the sagital plane, checked other planes, hit "SAVE REG" and then > executed > > recon-all -all -subjid MYFILENAMEHERE > > in the subj directory. I then get the same error, with the same z score. > I've > tried several alignments (very little adjustment each time) with the same > results. > > I notice that when I hit SAVE REG there is a new 4 x 4 numerical matrix > written > to my xterm screen. The values look very very similar to those prior. > > Is there a way to interpret these values to assist me in my manual alignment? > Should I just bag it and use -notal-check? The majority of my patient set ran > without errors. > > Thank you! > > > Deane Aikins, PhD > Director, Cognitive Neuroscience Laboratory > National Center for PTSD Clinical Neuroscience Division > Assistant Professor, Department of Psychiatry > Yale School of Medicine > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
