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Hi Eugenio,

what you want is easily achievable using spm and Matlab functionality. 
The following should work, although the output is only to the Matlab 
command window. Watch out for linebreaks when copying.

% ==== start ====

% get images to analyze
   P = spm_select([Inf],'image','Select image(s)', [],pwd,'.*');


% loop over images
   clc
   for i = 1:size(P,1);


	% get current image, filename
	  sub = deblank(P(i,:));
	  [p, nm, e, v] = spm_fileparts(sub);
	  disp(['... processing image ' nm ' from ' p '...']);
	  V = spm_vol(sub);


	% load, clean data
	  vol = spm_read_vols(V);
	  vol(isnan(vol)) = 0;
	  vol(~isfinite(vol)) = 0;


	% find, loop over clusters
	  [clus_vol,number] = spm_bwlabel(vol,18);
	  for ii = 1:number


		% get coordinates, find center
		  temp = vol .* (clus_vol == ii);
		  coords = find(temp > 0);
		  [out{1:3}] = ind2sub(size(vol),coords);
		  ctr_v = mean(cell2mat(out),1);


		% convert voxel to mm coordinates
		  ctr_mm = (V.mat(1:3,:) * [ ctr_v 1]')';


		% round voxel coordinates
		  ctr_v = round(ctr_v);


		% output to Matlab window
		  disp(['   ... center ' num2str(ii) '/' num2str(number) ' is at voxel 
' num2str(ctr_v(1,1)) '/' num2str(ctr_v(1,2)) '/' num2str(ctr_v(1,3)) ', 
mm = ' sprintf('%02.2f', ctr_mm(1,1)) '/' sprintf('%02.2f', ctr_mm(1,2)) 
'/' sprintf('%02.2f', ctr_mm(1,3)) ]);

	  end;

   end;

% ==== end ====


Hope this helps,
Marko


Eugenio Abela wrote:
> Dear Experts
>
> I have one binary image in native anatomical space that consists of ~80 clusters (locations of intracranial electrodes from an intensity segmented skull stripped CT image). I'd like to find the coordinates of this clusters but do not know how to code that in Matlab. Any hints are greatly appreciated.
>
> Regards
>
> Eugenio Abela, MD
>
> Research Fellow
> Dep. of Neurology
> University Hospital
> 3010 Bern/Switzerland
>

-- 
____________________________________________________
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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  http://www.medizin.uni-tuebingen.de/kinder/epn/
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