Hi.

I am trying to use the conn toolbox to analyze within subject resting state data. There is a single group and they have a resting state scan pre / post a treatment.

Please tell me if I am setting up the analysis correctly.
1) BASIC: number of sessions 2 (for each subject). Other entries self-explanatory

2) FUNCTIONAL: Associated resting scans with each session. (There are 196 scans, TR=2.5, duration = 490 seconds).

3) STRUCTURAL: no questions.

4) ROIs: I used all the default ROI's and selected the subject's segmented gray matter, white matter and CSF images. 
  Should I threshold these images? What value? Perhaps this will make each mask more exclusive? 
  The dimensions are set at default of 16 for white matter and csf and regress out covariates is checked. 
  For gray matter, dimensions is 1 and nothing is checked.

5) CONDITIONS:  1 condition called rest, and associated that with each session. Is that correct?

6) COVARIATES: First level: 1 covariate called movement. I associated it with each session and selected the relevant rp*.txt file.

7) COVARIATES: Second level: Not sure what to enter here. It only seems to accept a single number such as 1 or -1. 

8) OPTIONS: I clicked all planned analyses. 

9) PREPROCESSING TAB: I selected white matter, CSF and movement as confounds.

10) FIRST LEVEL ANALYSIS TAB: If I select a region such as PCC as source would my weight be "none". When would I use something like HRF or Hanning?

I'm not sure how to compare session 1 and 2 within each other within subjects and then across subjects?

Thanks
Darren