Hi Mike, I've run into the same problem you see in number 1 - the SPLINE_CUBIC_SET - Fatal Error!, with a fine talaraich. I was able to fix this by using the -no1d flag in mri_normalize. You can add this as an xopt to that subject so that it is always run: http://surfer.nmr.mgh.harvard.edu/fswiki/recon_2dall#head-25c704d7d03b1c22e5f712383f6045d2b4156957
I think this occurs when there is a bigger bias field in left-right direction than in the anterior-posterior direction (although, maybe it's I/S, I forget now). I'll leave the other two problems for someone more qualified! Jenni -- Learning and Memory Lab The University of Texas at Austin Department of Psychology 1 University Station A8000 Austin, TX 78712 phone: (512) 471-2727 fax: (512) 471-5935 email: [EMAIL PROTECTED] > On Tue, Feb 26, 2008 at 3:29 PM, Michael Harms <[EMAIL PROTECTED]> > wrote: > > > > > Hello, > > We recently just ran 80 elderly brains through -autorecon1 using FS > > v4.0.2, and encountered 3 different types of errors that we are not > > entirely sure how to handle: > > > > (1) During mri_normalize of 1 subject we encountered: > > SPLINE_CUBIC_SET - Fatal error! > > The number of data points N must be at least 2. > > The input value is 1. > > > > The FS archive indicates to check the talairach transform given this > > error, but the talairach.xfm appears fine for this subject (as assessed > > using tkregister2). > > > > (2) During mri_watershed of 1 subject: > > Sorting... > > mri_watershed Error: > > Problem in the COG calculation > > > > This subject had a slightly warped talaraich.xfm, but I think more > > relevantly, its talairach_with_skull.lta was way off. > > > > (3) During mri_watershed of 5 subjects: > > mri_watershed Error: > > GLOBAL region of the brain empty ! > > > > For all 5 of these subjects, the talairch_with_skull.lta also had > > obvious problems. > > > > RE (1): Any insight would be appreciated. > > > > RE (2) and (3): I suspect that we should try running with the -no- > > wsgcaatlas flag, so that talairach_with_skull.lta is longer used by > > mri_watershed. Should we then substitute the -wsatlas flag instead? > > (Its not clear to me which atlas is used when that particular flag is > > included). > > > > Last, I thought you might be interested in these errors, because they > > directly relate to my recent question regarding the robustness of > > talairach_with_skull.lta. At least during the -autorecon1 (i.e., > > initial) creation of this lta file, it appears that there is some > > possibility of a bad talairach_with_skull registration (6 of 80 in this > > particular subject set). > > > > thanks, > > Mike H. > > -- > > Michael Harms, Ph.D. > > -------------------------------------------------------------------- > > Conte Center for the Neuroscience of Mental Disorders > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > Renard Hospital, Room 6615 Tel: 314-747-6173 > > 660 South Euclid Ave. Fax: 314-747-2182 > > St. Louis, MO 63110 Email: [EMAIL PROTECTED] > > -------------------------------------------------------------------- > > > > > > _______________________________________________ > > 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
