SPM Volume Extraction Script HELP!

Hello experts:

The script I will post works for SPM5 (running from MATLAB -nojvm). Now on SPM8 that is not supported with -nojvm and possibly other changes to the new version... the script does not work!

Any suggestions would be greatly appreciated.

The volume extractoin script:

1

    clear all;

option=input('What volume do you want to get for grey only enter 1 for grey+white enter 2 for grey+white+csf enter 3: ')
scan_list=spm_select(1, 'any','Select scan list file');
scans = load(scan_list);
reg = spm_select(inf,'image','Select Region Mask Images');
V_regs = spm_vol(reg);
m_len=length(V_regs);
if (option == 1 || option == 2 || option == 3)
for i=1:m_len
    [Y,XYZ]=spm_read_vols(V_regs(i));
    NZ=find(Y);
        [prth,nam,ext]=fileparts(V_regs(i).fname);
        fid1=fopen(nam,'a');
    fprintf(fid1,'%s\n','scans type volume');
    for j=1:length(scans)
        scanid = num2str(scans(j));
        if (5 - length(scanid))==1
            prefix = 'mwc10';
        elseif (5 - length(scanid))==2
            prefix = 'mwc100';
        elseif (5 - length(scanid))==3
            prefix = 'mwc1000';
        else
            prefix = 'mwc1';
        end 
        V=spm_vol(fullfile(pwd,[prefix scanid '.img,1']));
        M=inv(V.mat);
        volume=0;
        %lnam=length(V_regs(i).fname);
        %nam=V_regs(i).fname(53:lnam-4);
        for k=1:length(NZ)
            arr=XYZ(:,NZ(k));
            vox=M(1:3,:)*[arr;ones(1,size(arr,2))];
            intensity=spm_sample_vol(V,vox(1),vox(2),vox(3),1);
            if (isnan(intensity) == 1)
                intensity = 0;
            end
            volume=volume+(intensity*8);
        end
        fprintf(fid1,'%d %s %f\n',scans(j),'gray',volume);
    end
    fclose(fid1);
end
end

if (option == 2 || option == 3)
for i=1:m_len
        [Y,XYZ]=spm_read_vols(V_regs(i));
        NZ=find(Y);
        [prth,nam,ext]=fileparts(V_regs(i).fname);
        fid1=fopen(nam,'a');
        %fprintf(fid1,'%s\n','scans type volume');
        for j=1:length(scans)
                scanid = num2str(scans(j));
                if (5 - length(scanid))==1
                        prefix = 'mwc20';
                elseif (5 - length(scanid))==2
                        prefix = 'mwc200';
        elseif (5 - length(scanid))==3
                        prefix = 'mwc2000';
                else
                        prefix = 'mwc2';
                end
                V=spm_vol(fullfile(pwd,[prefix scanid '.img,1']));
                M=inv(V.mat);
                volume=0;
                %lnam=length(V_regs(i).fname);
                %nam=V_regs(i).fname(53:lnam-4);
                for k=1:length(NZ)
                        arr=XYZ(:,NZ(k));
                        vox=M(1:3,:)*[arr;ones(1,size(arr,2))];
                        intensity=spm_sample_vol(V,vox(1),vox(2),vox(3),1);
                        if (isnan(intensity) == 1)
                                intensity = 0;
                        end
                        volume=volume+(intensity*8);
                end
                fprintf(fid1,'%d %s %f\n',scans(j),'white',volume);
        end
        fclose(fid1);
end
end

if (option == 3)
for i=1:m_len
        [Y,XYZ]=spm_read_vols(V_regs(i));
        NZ=find(Y);
        [prth,nam,ext]=fileparts(V_regs(i).fname);
        fid1=fopen(nam,'a');
        %fprintf(fid1,'%s\n','scans type volume');
        for j=1:length(scans)
                scanid = num2str(scans(j));
                if (5 - length(scanid))==1
                        prefix = 'mwc30';
                elseif (5 - length(scanid))==2
                        prefix = 'mwc300';
        elseif (5 - length(scanid))==3
                        prefix = 'mwc3000';
                else
                        prefix = 'mwc3';
                end
                V=spm_vol(fullfile(pwd,[prefix scanid '.img,1']));
                M=inv(V.mat);
                volume=0;
                %lnam=length(V_regs(i).fname);
                %nam=V_regs(i).fname(53:lnam-4);
                for k=1:length(NZ)
                        arr=XYZ(:,NZ(k));
                        vox=M(1:3,:)*[arr;ones(1,size(arr,2))];
                        intensity=spm_sample_vol(V,vox(1),vox(2),vox(3),1);
                        if (isnan(intensity) == 1)
                                intensity = 0;
                        end
                        volume=volume+(intensity*8);
                end
                fprintf(fid1,'%d %s %f\n',scans(j),'csf',volume);
        end
        fclose(fid1);
end
end

Thank you in advance, Catherine

[Sean de Wolski]

What does "not work mean"? What isn't working? Have you tried using:

dbstop if error

To stop with the debugger at the point of the error?