Dear all,

I am trying to run some preprocessing steps for a set of PET images (from different subjects) by developing a batch script from the SPM gui. I would like to confirm with you that what I am doing is correct.

Say I want to mask out every image by the same brain mask. I have done the following:

1) Load SPM and the ImCalc gui. Fill all the fields with the appropriate options

2) Click File -> Save batch and scripts (which generates a .m file and a _job.m file)

3) In the .m file I have set the number of runs to 1 and I have left all the rest the same. In the _job.m file I have added a for loop which selects one subject at a time (ie. the image to be masked changes at each iteration and is selected from a folder). For each subject the ImCalc processing is run (at least this is what I would like to obtain).

here is how the _job.m file appears (note this is from SPM8):

files2Mask = dir('Data\*.nii');

for i = 1:length(files2Mask)

matlabbatch{i}.spm.util.imcalc.input = {

strcat('Data\',files2Mask(i).name,',1')

'Maskl.nii,1'

};

matlabbatch{i}.spm.util.imcalc.output = strcat('Masked_',files2Mask(i).name);

matlabbatch{i}.spm.util.imcalc.outdir = {'Masked'};

matlabbatch{i}.spm.util.imcalc.expression = 'i1.*i2';

matlabbatch{i}.spm.util.imcalc.options.dmtx = 0;

matlabbatch{i}.spm.util.imcalc.options.mask = 0;

matlabbatch{i}.spm.util.imcalc.options.interp = 1;

matlabbatch{i}.spm.util.imcalc.options.dtype = 4;

end

Is this correct? My concern is that there is a for loop in the .m file but I am not quite sure on how to use it and by reading the manual, it seems that it is for a multisession analysis of the same subject, while in my case I want to repeate the same processing (ie. masking or normalisation..) for a set of subject stored in a folder.

Hope all this makes some sense,

Could you please give some advice on whether this is correct?

Thank you very much in advanced,

Bianca