open-discussion > Use BioImage Suite to do functionalConnectivityPreprocessing
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=https://medicine.yale.edu/bioimaging/suite/Images/BioImage%20Module_tcm501-95808.pdf]this manual[/url].

But this manual is in 2010. I guess the commands here are replaced by the Javascript code published on GitHub (https://github.com/bioimagesuiteweb/bisweb). 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 
https://github.com/bioimagesuiteweb/bisweb/blob/31fe3460cb075497d7633db96908579d6b27ecf5/js/modules/moduleindex.js#L60

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