Hi Dianne,

Shoot, I'm sorry, I didn't test this on sequential data. You're setting the string correctly but its not getting passed through because its not in the motion param reading command. Can you add $SLOMOCO_SLICE_ORDER to the read_motion_newslicealg() function as the second parameter in the shell script, by changing:

mocoparams=read_motion_newslicealg('tempslmoco_volslc_alg_vol_$epi.slicemocoxy_afni/motion.wholevol_zt');

to

mocoparams=read_motion_newslicealg('tempslmoco_volslc_alg_vol_$epi.slicemocoxy_afni/motion.wholevol_zt',$SLOMOCO_SLICE_ORDER);

This command is repeated several times (different branch logic), if you do a find and replace to get them all, it should work. Can you try this and let me know if it works? I could also create a new slicemoco_newalgorithm.sh file for you, if you like.

Also, its failing on the last 3drefit inside the shell script - can you comment out the last 3drefit (and may as well comment out the 3dNotes command) and re-run? It won't change the data, although it also means it won't pull the full header information across. There's got to be a better way to do this, but the afni_matlab toolbox doesn't have many options. It may be better to simply re-to3d create the dataset, but I'd like try this first if possible.

Erik