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Hi,
I'm trying to use a script to get the maximum T value from a mask I created in
SPM2. The mask is basically a binary mask multiplied by a spmT image. Using a
script, I am able to get the maximum T value and I'm also able to get at what
coordinates in the matrix this T value occurrs, but I'm not sure how to go from
the matrix coordinates into MNI coordinates, which is what I really want to
know. Any help on this matter would be appreciated. See below for the script.
Thank you.
-Saul


%Subjects list
sub_list = str2mat('sub1','sub2','sub3');
%Directory where subjects are located
working_dir = '/study_dir/';
%Directory where mask is located within subjects dir
mask_dir = 'labels/';
%text file containing .img mask
inputfile = 'ROIs.txt';


num_sub = size(sub_list,1);


fid=fopen(inputfile);
c=0;
masks=[];
while 1
    line = fgetl(fid);
    if ~isstr(line), break, end
    if c==0 
       masks=line;
       c=1;
   else
       masks=str2mat(masks,line);
   end
end
fclose(fid);
[nummasks,temp]=size(masks);

fid = fopen('T_values.txt','w');

for i=1:num_sub
    cur_sub = deblank(sub_list(i,:));
    fprintf(fid,['Subject: ',cur_sub,'\n']);
    for j=1:nummasks
        highT = 0;
        x_coord = 0;
        y_coord = 0;
        z_coord = 0;
        mask_name = masks(j,:); 
        m_num = strfind(mask_name,'.');
        mask_label = masks(j,1:m_num-1);
        mask =
spm_read_vols(spm_vol([working_dir,cur_sub,'/',mask_dir,mask_name]));
		for x=1:size(mask,1)
            for y=1:size(mask,2)
                for z=1:size(mask,3)
                    if mask(x,y,z) > highT
                        highT = mask(x,y,z);
                        x_coord = x;
                        y_coord = y;
                        z_coord = z;
                    end
                end
            end
		end
		fprintf(fid,[mask_label,': highest T: ',num2str(highT),'
(',num2str(x_coord),',',num2str(y_coord),',',num2str(z_coord),')','\n']);
    end
end
fclose(fid);