Hi Gabe,

Thanks for trying out SLOMOCO, its really great once you get it working! So to summarize, you've been running with a different slice acquisition order than the default, and the last part of the script fails, please correct me if thats wrong. I have good news...

Fortunately, SLOMOCO is not as sensitive to slice acquisition order as PESTICA, as long as the same setting is used throughout the script.  Unfortunately the first part of the script just assumes interleaved ascending order, and the last part reads it from the command environment. As long as its the same for both parts (and yes, I need to fix this in the next release, this is not a nice way to leave software), it will run correctly, so please run it with the default original slice order for now (siemens-alt-asc).  In fact, siemens-alt-asc is identical to GE interleaved when you have an odd number of slices (the difference only occurs when you have an even number of slices, then it starts on slice #2 on Siemens, but even in that case you can leave it as the default in this script). I'm sorry I left such a weird hack in the script, it will be fixed in the next release. Once it works, you should get a pair of saved images for the motion parameters, and the motion parameters in the slomoco.combined.reg6dof.txt for every slice.

Erik