There was some ambiguity in communication from a previous MR technician regarding the slice ordering in our BOLD data.

preproc-sess was applied to our data:

preproc-sess -sf SUBJECTS -surface fsaverage lhrh -per-run -fsd bold -sliceorder up -fwhm 4

I then ran selxavg3-sess on the data, followed by mri_glmfit to produce contrast maps

As an experiment, I deleted the fmcpr.up.* data, and re-ran preproc-sess, this time specifying sliceorder down:

preproc-sess -sf SUBJECTS -surface fsaverage lhrh -per-run -fsd bold -sliceorder down -fwhm 4

After re-running selxavg3-sess and mri_glmfit on the reverse-stc-corrected data, the contrast maps were identical, which seemed peculiar, given that the slice time corrections for a 2-second TR were in the opposite direction.

I note that when I run selxavg3-sess, it generates a set of fmcpr.sm4 files, and I suspect that the GLM is run on those novel non-stc files. Is there a switch I am missing in the call to selxavg3-sess or mkanalysis-sess that will ensure that will allow me to ensure that the GLM is run on fmcpr.[STC].sm4.fsaverage.[rl]h.nii.gz?

Thanks