Hi Martin,

thanks for not taking the scripts for what they are and taking the time to go through them and seeing what they're actually doing :) 

Indeed, we did not include slice-timing correction in the 2_funcpreproc.sh script. The reason for that is that when gathering the data from the sites we did not have access to all imaging parameters. To avoid a delay in sharing the data and putting out the feasability study (Biswal et al., 2010) we decided to go ahead without implementing the slice-timing correction. And yes, there is also the controversy about whether slice time correction has any influence if you're looking at the slow-frequency fluctuations. In terms of the fcon data it would also mean applyin different slice time corrections to different datasets as not all had the same acquisition order. (Since then we added the slice timing information to the table you can find here http://www.nitrc.org/docman/?group_id=296).

However, yes, most people (including us in our papers) implement slice-timing correction. As mentioned in the wiki you are free to add slice time correction to the script, which should be fairly easy. You should do it as one of the first steps, right after removing the first n timepoints.

Let me know if you have any difficulties adding it to your scripts.
Best,
Maarten