Hi Masaki,

The usual FSL/SPM style CSF mask covers the entire brain. I have attached a snapshot as an example. Conn uses SPM segmentation mask by default for each subject. The attached file is the partial volume map; this would be binarized and eroded before time series extraction for regression during denoising.

If you just want to use Conn without the details of denoising, you could specify the bandpass filter as Inf to include the time series as such. You could also remove the WM/CSF masks to prevent their time series from being regressed. Optionally, you could also remove the scrubbing volumes if you do not wish these volumes to be regressed (just specify an empty "R" variable). By default, Conn also includes second order derivatives for the six regression parameters. This can be changed to only include the six parameters.

Hope this helps


Best
Pravesh