Hi John, Uma
This should do it:
taken from http://www.sph.umich.edu/~nichols/JohnsGems.html#Gem2
in matlab type (with adjusted filenames):
VI = spm_vol('original_beta.img');
VO = VI;
VO.fname = 'patched_beta.img';
VO = spm_create_image(VO);
for i=1:VI.dim(3),
img = spm_slice_vol(VI,spm_matrix([0 0
i]),VI.dim(1:2),0);
tmp = find(isnan(img));
img(tmp) = 0;
VO = spm_write_plane(VO,img,i);
end;
Jim
------------------------------------------------------------------------
James C. Thompson, PhD
Research Associate
Center for Advanced Imaging
Department of Radiology
West Virginia University
Robert C Byrd Health Sciences Center South
PO Box 9235
Morgantown WV 26506-9235
USA
Tel: +1 304 293 5050
Fax: +1 304 293 4287
email: [EMAIL PROTECTED]
------------------------------------------------------------------------
>>> [EMAIL PROTECTED] 07/25/05 4:44 PM >>>
Hi Uma,
I am not familiar with the "beta" and "con" volumes. However, when I
searched google, I found a couple of web pages that state that in the
"beta" and "con" volumes, voxels outside the brain are set to Nan (not
a number).
The web page "http://psyphz.psych.wisc.edu/~oakes/spm/spm_how_tos.html";
states " One caveat which you may know if you've followed the list, is
that the con**.img and beta*.img images have the areas outside the
brain values set
to NaN".
Something similar to this is posted on the SPM99 web site
"http://www.fil.ion.ucl.ac.uk/spm/software/spm99/"; that voxels outside
the brain are set to 0 or Nan.
Caret5 expects all voxels in a volume to have valid numerical values.
You will need to find a way to convert the NaN voxels to zeros in your
volumes.
----------------------------------------------------------
John Harwell
[EMAIL PROTECTED]
314-362-3467
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave. Box 8108
St. Louis, MO 63110 USA
On Jul 25, 2005, at 1:08 PM, Uma Sreekumar wrote:
> Hi all,
>
> I am new to Caret. I am trying to map results of my
> group level analysis performed in SPM99 onto the PALS
> atlas in Caret 5.3.
>
> While I am able to map the spmT*.hdr for the
> functional volume (as per the online documentation
> provided), I am unable to map the con*.hdr or
> beta*.hdr. Following around 80% processing, wherein
> both the scaling and descaling ranges are read as -NaN
> -NaN, the programme crashes with the message
> sqrt: domain error.
>
> All required settings (voxel size etc) seem to be
> correct. I have gone through the previous mails in the
> list. Shouldnt it be possible to map any SPM *.hdr
> file through Caret? Help of any kind would be highly
> appreciated.
>
> Best regards,
> Uma Sreekumar
>
>
>
> -----------------------------
> Y. Uma Sreekumar
> NMR Research Centre,
> Institute of Nuclear Medicine and Allied Sciences,
> Delhi- 110 054, INDIA
>
>
>
>
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