Hi Bruce- Agreed. Visual check of talairach looks good and manual correction of slight sagital angle fails to improve z value, hence the current notal-check.
Looking at recon-all.log, there is a statement that The surface validation has detected a possible Error", with a suggestion to use the '-atlas' option if the final seg is not valid. Also, it's saying that brainmask.mgz already exists and that I would need to add -clean-bm to overwrite brainmask.mgz. \n Is any of that information of use? Deane Quoting Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi Deanne, > > something is badly wrong - that step should only take a couple of minutes. > Did you check the talairach visually? It may need to be manually corrected. > > cheers > Bruce > On Fri, 12 Jun 2009, Deane Aikins wrote: > > > 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 > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
