Thanks for your response. Yes, it is a Siemens scanner from what I was told. I was given a file for each subject which has information taken from the header file (presumably, but using fslhd I cannot access this) about the acquisition parameters and # of slices etc.  Some of the values vary. For one of the subjects the acquisition is even interleaved and the subject has 64 slices whereas all other subjects have odd inter and 61 slices.  Other values in the info file vary as well like volume interval and the timings of the acquisitions vary slightly across subjects. 

For FSL interleaved option, does it automatically take into account the number of slices as you mentioned? It has 0 2 4...1 3 5 7 listed under the option so I had assumed it was even interleaved. But if it will detect the number of slices and do odd interleaved then I will give that a try. But regardless, shouldn't this option give me the same results as the slice order file I mentioned?

edit: I ran the data using the FSL interleaved option and got the same results as with my slice timing file I mentioned.

For all of the slice timing options used so far the data is extremely noisy (resting-state data) and the time series plots at a single voxel come out very similar across slice timing methods. Should this be the case? For example, using no slice timing and regular descending the time series plots are nearly identical.