Hello,

I am working on re-analyzing some fMRI data, which was previously analyzed using SPM. 3dinfo shows that each of my runs are 173 time points. At 2 seconds a TR, I assume this should mean that the runs are 346 seconds each. My output from 3dDeconvolve confirms that the longest run is 346.0 seconds, and all the runs should be the same length. However, 3dDeconvolve appears to be cutting runs off at 344, which is causing the last trial in some of my functional runs to be considered unusable since they consistently onset a little after 344 (e.g. 344.285 or 344.59).

Does anyone have any idea what might be causing this inconsistency in how AFNI is reading my run lengths and how to deal with this problem? I don't think the stim times are wrong because the original analysis yielded decent results, and it doesn't make sense to me that AFNI and SPM would see the runs as being different lengths or that the onset times would be different for different analysis platforms. My scripts were generated using uber_subject.py. No TRs were removed for any of the functional runs and I have checked the length of each scaled run using 3dinfo, so the runs going into 3ddeconvolve are 173 time points.

Here is an example of the warning message I am getting:

*+ WARNING: '-stim_times 6' (LOCAL) run#6 has 1 times outside range 0 .. 344 [PSFB syndrome]
+ dataset TR being used is 2 s -- unusable times follow
344.59

Thanks,

Katelyn