... in addition to what Donald said, Matlab's min and max functions
don't handle NaN values all too well:
min([1 2 3 4 5 NaN])
will return NaN. Hence, the values in the image may still make sense,
but the calculation is screwed up. If you do
vol = spm_read_vols(spm_vol(spm_select));
vol(isnan(vol)) = [];
vol(vol==0) = [];
then
min(vol(:))
should give you the "real" minimum value. There are dedicated nanmin and
nanmax functions, but I am not sure they are included in the standard
Matlab installation.
Hope this helps,
Marko
MCLAREN, Donald wrote:
> There are still values in the image; however,the image now contains NaN
> values. This is expected as your new bounding box is larger than the old
> bounding box. With no possible value, the program uses NaN.
>
> If you want to use "subject space", it would be preferable to use
> "native space" which is the size and location of your functional data,
> rather than the size and location of your anatomical data.
>
> Best Regards, Donald McLaren
> =================
> D.G. McLaren, Ph.D.
> Research Fellow, Department of Neurology, Massachusetts General Hospital and
> Harvard Medical School
> Postdoctoral Research Fellow, GRECC, Bedford VA
> Website: http://www.martinos.org/~mclaren
> Office: (773) 406-2464
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> On Fri, Dec 13, 2013 at 8:20 AM, [log in to unmask]
> <mailto:[log in to unmask]> <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Hi all,
> I have an image with zscores obtained after running an ICA (Icasso).
> This
> image is in MNI space and the voxels have different intensities values:
> Zvol:: Size = (121,145,121)
> Zvol:: ROI Size = (121,145,121)
> Zvol:: Dims = (1.5,1.5,1.5)
> Zvol:: Minimum and maximum intensities are: -5.36202 and 11.2541
>
> I need the image to be in subject space, so I run an inverse
> deformation with
> SPM8. After that the intensities values of the voxels became NaN:
> Zvol:: Size = (224,256,192)
> Zvol:: ROI Size = (224,256,192)
> Zvol:: Dims = (0.859375,0.859375,1.1)
> Zvol:: Minimum and maximum intensities are: nan and nan
>
> Is there a way to keep the intensities values? I need these
> informations in
> order to separate the clusters in the image.
>
>
--
____________________________________________________
PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
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