26 Feb
2008
26 Feb
'08
5:04 p.m.
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-25c704d7d03b1c22e5...
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
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email: jpacheco@mail.utexas.edu
> On Tue, Feb 26, 2008 at 3:29 PM, Michael Harms mharms@conte.wustl.edu
> 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: mharms@wustl.edu
> > --------------------------------------------------------------------
> >
> >
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