Dear Tom,
I'm not sure I fully understand your approach, but one valid (and in my opinion, the best) way to run a conjunction analysis is to simply take the minimum of two thresholded maps. In this way, you end up testing the conjunction null, i.e. which voxels are significant in both contrasts: https://www.sciencedirect.com/science/article/abs/pii/S1053811904007505
You can easily do this using the SPM batch (imcalc):
clear matlabbatch
matlabbatch{1}.spm.util.imcalc.input = {
path_to_image_1;
path_to_image_2
};
matlabbatch{1}.spm.util.imcalc.output = 'conjunction.nii';
matlabbatch{1}.spm.util.imcalc.outdir = {'my_output_folder'};
matlabbatch{1}.spm.util.imcalc.expression = 'min(X)';
matlabbatch{1}.spm.util.imcalc.var = struct('name', {}, 'value', {});
matlabbatch{1}.spm.util.imcalc.options.dmtx = 1;
matlabbatch{1}.spm.util.imcalc.options.mask = -1;
matlabbatch{1}.spm.util.imcalc.options.interp = 0;
matlabbatch{1}.spm.util.imcalc.options.dtype = 16;
spm_jobman('run',matlabbatch);
I hope this helps!
All the best,
Philipp Kuhnke
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