Hi Vy,
Well, spm is telling you what the problem is: the images do not all have
the same dimensions. SPM will calculate anyway, but it may be completely
meaningless (e.g., if you combine a native-space and a normalized
image), hence the warning. This message has been discussed several tmes
on the list in the past, and some of the replies may be helpful to you.
In order to see what the problem may be, check the dimensions of all
images. Segmentation may produce images in native space or not, which is
the most likely source of error. BTW, spm_segment is rather old code and
generally not recommended.
Cheers,
Marko
Vy Dinh wrote:
> Hi Marko,
>
> Sorry to bother you again, but I wonder how much spm_preproc_write's
> output segmentations differ from spm_segment's output? The reason why I
> ask is because when I try to use spm_imcalc_ui to apply the white matter
> segment (from spm_preproc_write) to the DTI maps (using the formula i1>
> .5 * i2, i1 is the white matter segment, i2 is the DTI map), I get the
> message:
>
> Warning: images don't all have same dimensions - using those of 1st image
> > In spm_imcalc_ui at 133
>
> However, with the wm segment from spm_segment, I did not get any warning
> message.
>
> Thanks,
>
> Vy
>
>
>
> On Fri, Jul 9, 2010 at 2:11 PM, Vy Dinh <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Thanks a bunch for the code help and the heads up on using the CSF
> segment! So far we have not been using it in our analysis, but we
> anticipate that we might in the future so we decided to write out
> the CSF segment anyway. Again, I really appreciate all your time and
> responsiveness to my issue.
>
> Best,
>
> Vy
>
>
>
> On Fri, Jul 9, 2010 at 1:46 AM, Marko Wilke
> <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Hello,
>
>
> spm_preproc_write(po)
> However, this line only gave me the gm and wm segmentation,
> not the csf.
> I know I have to create an opts structure such that opts.GM
> = flags,
> opts.WM = flags, and opts.CSF = flags. But where do I get
> these flags from?
>
>
> First, CSF segmentation has never been very good in SPM and
> unless you really need it, I would not write it out. The flags
> are described in the file that needs it, i.e.,
> spm_preproc_write. You need to specify and pass them, as for
> example in ...
>
> opts_write = struct('biascor',0,'GM',[0 0 1],'WM',[0 0
> 1],'CSF',[0 0 1],'cleanup',1); % this should be in one line in
> the script!
>
> spm_preproc_write(po,opts_write);
>
> Ech value for GM, WM, CSF stands for one of the options, and you
> can set one, or all, to one in order to write out the respective
> file.
>
>
> Cheers,
> Marko
> --
> =====================================================================
> Marko Wilke
> (Dr.med./M.D.)
> [log in to unmask]
> <mailto:[log in to unmask]>
>
> Universitäts-Kinderklinik University Children's
> Hospital
> Abt. III (Neuropädiatrie) Dept. III (Pediatric
> neurology)
> Hoppe-Seyler-Str. 1, D - 72076 Tübingen
> Tel.: (+49) 07071 29-83416 Fax: (+49) 07071
> 29-5473
> =====================================================================
>
>
>
>
> --
> Vy T.U. Dinh
> Research Assistant, Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853
> Fax: (312) 563-4660
> Email: [log in to unmask] <mailto:[log in to unmask]>
>
>
>
>
>
> --
> Vy T.U. Dinh
> Research Assistant, Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853
> Fax: (312) 563-4660
> Email: [log in to unmask] <mailto:[log in to unmask]>
>
>
--
=====================================================================
Marko Wilke (Dr.med./M.D.)
[log in to unmask]
Universitäts-Kinderklinik University Children's Hospital
Abt. III (Neuropädiatrie) Dept. III (Pediatric neurology)
Hoppe-Seyler-Str. 1, D - 72076 Tübingen
Tel.: (+49) 07071 29-83416 Fax: (+49) 07071 29-5473
=====================================================================
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