open-discussion > Use BioImage Suite to do functionalConnectivityPreprocessing
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Aug 7, 2019  02:08 PM | Yuanhanqing Huang
Use BioImage Suite to do functionalConnectivityPreprocessing
To whom it may concern,

Good day! 

I am doing research about functional connectivity, and I want to implement some fMRI preprocessing suggested in related papers. They used BioImage Suite to do something like
  1) removal of linear components related to motion parameters;
  2) regression of the mean time courses of the white matter and CSF as well as the global signal;
  3) removal of the linear trend;
  4) low-pass filtering;
  5) ...

From the previous discussion here, I guess the procedure is by using some commands like bis_csfwmmotioncorrbis_removetemporaldrift, and so on, as suggested in [url=]this manual[/url].

But this manual is in 2010. I guess the commands here are replaced by the Javascript code published on GitHub ( Please correct me if I am wrong. However, when I ran
./js/bin/bisweb.js -h functionalConnectivityPreprocessing
I could not get any help information.
And then I found out that this function is commented in

And I guess that may be the reason why I could not use it.

So, my questions are
1) May I directly uncomment this line and use this function?
2) Does this function contain the implementation of data preprocessing  mentioned before?
3) If not, what should I do to complete the functional connectivity preprocessing?

I am looking forward to your reply.

Murphy Huang
Aug 26, 2019  01:08 PM | Xenophon Papademetris
Use BioImage Suiteto do functionalConnectivityPreprocessing

Sorry for the delay, this was lost when I was travelling. The module "functionalConnectivityPreprocessing" is unfinished at this point - it is on the todo list for the fall, so do not uncomment. The pieces are all there and tested so you can try them but I would not recommend it as we are not quite done with them.