I'm rerunning it with -no-talcheck. It looks to be hanging on finding control points in the Left_Cerebral_White_matter. Can this one step take more than 24 hrs? The "usual" time for a recon-all was @30 hrs for the other brains.
Thanks, Deane Quoting Nick Schmansky <ni...@nmr.mgh.harvard.edu>: > 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
