I am trying to do a cross-subject surface based analysis of data analysed using FSL. I am following the instructions in the following tutorial link. http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer

Each of my subject data comprises of two runs. My question is related to how to use mris_preproc to combine them. Can I combine together each of the runs of multiple subjects as below?

mris_preproc --target fsaverage --hemi lh \

        --out $OUT_DIR/xrun/lh.varcope$c.mgh \

        --iv $subj[1]/run1.feat/stats/varcope$c.nii.gz $subj[1]/run1.feat/reg/freesurfer/anat2exf.register.dat  \

        --iv $subj[1]/run2.feat/stats/varcope$c.nii.gz $subj[1]/run2.feat/reg/freesurfer/anat2exf.register.dat  \

        --iv $subj[2]/run1.feat/stats/varcope$c.nii.gz $subj[2]/run1.feat/reg/freesurfer/anat2exf.register.dat  \

        --iv $subj[2]/run2.feat/stats/varcope$c.nii.gz $subj[2]/run2.feat/reg/freesurfer/anat2exf.register.dat  

I understand that I can combine the gfeat output of each subject using mris_preproc. I am preferring above method as I believe it is more accurate. Please correct me if I am wrong. 