Hi,
I asked about this question to Mr. Cox earlier in our Guangzhou training, but there seemed to be a problem with this program at the time. I wonder if Mr. Cox has fixed it by now or someone else could give me some help.
I was trying to create a default mode network template from a group of subjects. I did a functional connectivity analysis with each subject-- used 3dDeconvolve to get their coefficients with a PCC seed, and then a r-Z transform. Then I averaged all these Z scores from all subjects, and get the result shown in the snapshot attached in this post. Now see the threshold bar, it’s coded R^2. But that’s not what I’m supposed to get. And there’s no p value setting. I can’t get an proper Z score threshold for my template, and that’s kind of a problem.
Mr. Cox suggested using 3drefit, but it didn’t actually work back then (and frankly I still didn’t quite understand half of what he said…)…So…is Mr. Cox revived from his jet lag yet? Or anyone? Really appreciate it~~~~
I have fixed 3drefit to correctly implement the ‘-substatpar’ option, which did not work when we were in Guangzhou. This fixed code has not yet been compiled into new AFNI binaries, though. I’m working on some other fixes that were suggested while we were in China.
The method to change the sub-brick in question would be something like
where ‘0’ is the sub-brick index. I will post here on the message board when new AFNI binaries are ready – probably Friday (of course, that will be Saturday in China :-()
Thanks so much for the prompt reply! Wow, so good to know there’s a place to ask questions that can actually get answered, cos I’ve got tons of them! Thanks again!!!
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