> Thank you for the earlier reply. I updated to the most recent SPM
> available. I still have the same issues with segmentation. The images I
> would like to segments are output images from affine registration using
> FLIRT. I have issues segmenting these images but am able to segment
> other images well. COuld this be a compatibility issue between SPM and
> FLIRT? If it is what can I do to over come this else what could the
> problem be?
It could be a compatibility issue. When FLIRT reslices an image, what value
does it put in those regions where it is unable to sample data from the
original? In SPM, these values are either 0 or NaN - depending on the type
of data. You can check this with Display, and click on one of those regions
to see what the intensity is. If it is something other than zero or NaN,
then it is a compatibility issue, which is to do with there being a sharp
peak (at that value) in the histograms used for the initial affine
registration.
Another possibility is that you may not have re-starting MATLAB before
re-running the segmentation (or cleared the functions that were cached in
MATLAB's memory).
Bye for now,
-John
> On Tue, 2008-08-12 at 11:19 +0100, John Ashburner wrote:
> > Do you have the latest updates installed (Revision 1782). The line
> > numbers in your error message do not appear to match the lines in the
> > latest updates. I think this problem was fixed, and arises because there
> > are a lot of voxels with a value of zero (resliced or skull-stripped
> > data), so there is a sharp peak in the histograms used by the initial
> > affine registration.
> >
> > Best regards,
> > -John
> >
> > On Monday 11 August 2008 20:04, Vidya Rajagopalan wrote:
> > > Hello All,
> > >
> > > I am trying to segment a batch of 66 T1 weighted MR images of the human
> > > brain. I would like to run DARTEL on them. When I try to segment the
> > > images initially, I get the following error for all 66 images:
> > >
> > > Warning: Matrix is singular to working precision.
> > >
> > > > In expm>PadeApproximantOfDegree at 123
> > >
> > > In expm at 39
> > > In spm_maff>P2M at 191
> > > In spm_maff>affreg at 152
> > > In spm_maff at 27
> > > In spm_preproc at 152
> > > In spm_config_preproc>execute at 472
> > > In spm_jobman>run_struct1 at 1585
> > > In spm_jobman>run_struct1 at 1595
> > > In spm_jobman>run_struct1 at 1595
> > > In spm_jobman>run_struct at 1514
> > >
> > > Error running job: Error using ==> schur
> > > Input to SCHUR must not contain NaN or Inf.
> > > In file "/usr/local/matlab/toolbox/matlab/matfun/sqrtm.m" (???),
> > > function "sqrtm" at line 33. In file "/home/scratch/spm5/spm_maff.m"
> > > (v987), function "M2P" at line 160. In file
> > > "/home/scratch/spm5/spm_maff.m" (v987), function "affreg" at line 76.
> > > In file "/home/scratch/spm5/spm_maff.m" (v987), function "spm_maff" at
> > > line 27. In file
> > > "/home/scratch/spm5/spm_preproc.m" (v946), function "spm_preproc" at
> > > line 153. In file "/home/scratch/spm5/spm_config_preproc.m" (v1032),
> > > function "execute" at line 472. --------------------------
> > > Done.
> > >
> > >
> > > What does this error signify and how can I correct it.
> > >
> > > Thank you.
> > > Vidya Rajagopalan
> > > Virginia Tech
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