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Hi Brian

I've wrote some stuffs for VBM ; one of the scripts gives you the grey / white / csf volumes ...uses the same kind of code

http://www.sbirc.ed.ac.uk/cyril/cp_download.html

cyril

> Hello,
>
> I'm trying to compute total grey matter volume on modulated segmented grey
> matter images (mwc1.img) to include as a nuisance covariate in a VBM
> analysis. I'm using the new_get_grey matlab script but am getting an error.
>
> I've pasted the new_get_grey script below.
>
> The error is: Syntax error near unexpected token '('
>
> The error relates to line number 35, which reads: fprintf('\n Global 
> grey matter
> volume (ml) for each subject... \n ')
>
> I've tried putting a space between fprintf and the ( and other syntax changes
> like that but nothing has worked.
>
> Help in solving this would be greatly appreciated.
>
> Thanks in advance,
>
> Brian
>
> New Get Grey Script
>
> %       Script modified from John Ashburner's 08/08/2005 post to JISCMAIL
> %            Written by Alastair Reid 22/09/2005
> %
> %            Script to generate total grey matter volumes (in ml) from
> modulated
> %            segmented images (mwc1*.img)
> %
> %            Note: have to specify own vbmdir and img_dir to suit
> %
>
> spm_defaults
> global defaults
> %% Number of subjects
> nsub=30;
>
> %% Directory in which processing occurs
> vbmdir='~/data1/users/bgold/GROUP_ANLYSIS/STRUCTURAL/GM_images/';
>
> %%  Load images volumes
> P=spm_select(nsub,'any','Select Modulated Images','',vbmdir,'.img','');
>
> %% Name of output file
> logname = 'grey_volumes.txt';
>
> if exist(logname,'file');
> %fid = fopen(logname,'a');
> %else
> fprintf('\ndeleting existing grey_volumes.txt\n');
> !rm grey_volumes.txt;
>                 fid = fopen(logname,'w');
>                 %fprintf(fid,'Volume [ml]\tgray');
> end
>
>
> fprintf('\n\n Calculating global tissue volumes for each subject...\n ');
> fprintf('\n Global grey matter volume ml for each subject...\n ');
> img_dir='data1/users/bgold/GROUP_ANLYSIS/STRUCTURAL/GM_images/';
> for sub = 30:nsub
>
>                                 Q = deblank(P(sub,:));
>         [pth,nm,xt,vr] = fileparts(deblank(Q));
>         U = fullfile([vbmdir img_dir],['' nm '' xt vr]);
>         V = spm_vol(U);
>                                 vol=0;
>                                 voxvol=0;
>         for z=1:V.dim(3)
>                                                 
> img=spm_slice_vol(V,spm_matrix([0 0
> z]),V.dim(1:2),0);
>                                                 img=img(finite(img));
>                                                 vol=vol+sum(img(:));
>         end
>         voxvol=abs(det(V.mat(1:3,1:3)))*1e-6;
>         fprintf('%g voxels, %g mlitres\n',vol,1000*vol*voxvol);
>                                 fprintf(fid,'\t%5.3f',1000*vol*voxvol);
>                                 % fprintf ('%g',volml)
>
>         fprintf('\n');
> end
>
>


--
Dr Cyril Pernet,
fMRI Lead Researcher SINAPSE
SFC Brain Imaging Research Center
Division of Clinical Neurosciences
University of Edinburgh
Western General Hospital
Crewe Road
Edinburgh
EH4 2XU
Scotland, UK

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http://www.sbirc.ed.ac.uk/cyril
http://www.dcn.ed.ac.uk/b ic/sinapse/sinapse.asp