Hi everyone,
Summary of what happened:
I am running my first PPI analysis with SPM12 and when I extract the VOI.mat using the spm contrast of interest and a sphere with the anatomical ROI coordinates of interest, for some subjects it doesn’t work as no VOI.mat file is created. I have tried adding another mobile sphere as described here (Timeseries extraction - SPM Documentation) and pasted below, that should move to the peak activation for the contrast in the area inside the mask, but it also fails to extract the VOI.mat file or moves far away from the ROI coordinates.
Would it make sense to extract the VOI just using the coordinates from the ROI interest adjusted by the spm contrast? Could anybody explain to me the differences between the methods I just explained?
Command used (and if a helper script was used, a link to the helper script or the command generated):
matlabbatch{1, 1}.spm.util.voi.spmmat = cellstr(spmFile);
matlabbatch{1, 1}.spm.util.voi.adjust = 22; %number of contrast of interest; matlabbatch{1}.spm.util.voi.session = 1; % Session index
matlabbatch{1, 1}.spm.util.voi.name = 'unexnov_vta';
% Define thresholded SPM for finding the subject's local peak response matlabbatch{1}.spm.util.voi.roi{1}.spm.spmmat = {''};
matlabbatch{1}.spm.util.voi.roi{1}.spm.contrast = 21; % Index of contrast for choosing voxels matlabbatch{1}.spm.util.voi.roi{1}.spm.conjunction = 1; matlabbatch{1}.spm.util.voi.roi{1}.spm.threshdesc = 'none'; matlabbatch{1}.spm.util.voi.roi{1}.spm.thresh = 0.05;
matlabbatch{1}.spm.util.voi.roi{1}.spm.extent = 0;
matlabbatch{1}.spm.util.voi.roi{1}.spm.mask = struct('contrast', {}, 'thresh', {}, 'mtype', {})
% Define large fixed outer sphere
matlabbatch{1}.spm.util.voi.roi{2}.sphere.centre = [30 -66 33]; matlabbatch{1}.spm.util.voi.roi{2}.sphere.radius = 6; % Radius (mm) matlabbatch{1}.spm.util.voi.roi{2}.sphere.move.fixed = 1;
% Define smaller inner sphere which jumps to the peak of the outer sphere matlabbatch{1}.spm.util.voi.roi{3}.sphere.centre = [0 0 0]; % Leave this at zero matlabbatch{1}.spm.util.voi.roi{3}.sphere.radius = 6; % Set radius here (mm) matlabbatch{1}.spm.util.voi.roi{3}.sphere.move.global.spm = 21; % Index of SPM within the batch matlabbatch{1}.spm.util.voi.roi{3}.sphere.move.global.mask = 'i2'; % Index of the outer sphere within the batch
% Include voxels in the thresholded SPM (i1) and the mobile inner sphere (i3) matlabbatch{1}.spm.util.voi.expression = 'i1 & i2';