Hi,

I am currently facing a problem when performing second-level analysis of fMRI volumes using SPM. 

My population of patients is characterized by stroke lesions. Two patients, in particular, have lesions in both brain hemispheres. For patients with lesions in a single brain hemisphere, I included enantiomorphic lesion filling with the Clinical Toolbox and Dartel normalization within my preprocessing steps. For patients with lesions in both brain hemispheres, since there is no intact hemisphere to mirror using the enantiomorphic lesion filling, I have reset the origin of my volumes considering the position of the anterior commissure and used Old Normalisation including my lesion mask. 

After preprocessing, I can find a good overlap between volumes from different patients in MNI space. Nonetheless, the bounding box of the volumes derived from patients with lesions in both brain hemispheres differ from each other and from those of the other patients.

For reference: I did specify the usual MNI bounding box in Old Normalisation using 'matlabbatch{1}.spm.tools.oldnorm.estwrite.roptions.bb = [-78 -112 -70; 78 76 85];' but the resulting volumes still have different dimensions.

Is there a way to adjust/crop the bounding box for the patients with lesions in both brain hemispheres so that they match the others?

Thanks in advance for any advice,

Gabriele