Hi Jack,
It is possible that this is somehow caused by the qform and/or sform differences.
Can you try running fslcpgeom on the input image, to copy the info from the reference image, and then see if the results are different?
It shouldn't revert to the default schedule, but if you want to be sure, just turn on the verbose output with -v and you'll see exactly what schedule lines it is using.
All the best,
Mark
> On 28 May 2017, at 22:43, Jack Grinband <[log in to unmask]> wrote:
>
> Hi Mark,
> Is it possible that if FLIRT encounters an error with the custom schedule, that it reverts to the default schedule instead? I did not encounter any obvious error messages, but I can't think of any other explanations.
> thanks!
>
> jack
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