Hello Alfonso!
I want to do resting state analysis using Conn software. For my case there is not much requirement of second level analysis. So I want to use the results of 1st Level analysis only. This is what I have done so far.
Set up:
A) ROI:
atlas and DMN are unselected.
csf, White matter and Grey matter files are selected from a standard template ( They are tissue probability maps that I use for segmentation section in SPM. Is it okay to use them?)
New ROI(M) mask file selected
Multiple ROI= not selected
Mask with GM selected for New ROI (M) only.
Subject specific ROI = not selected
session specific ROI= unselected
use ROI source data= not selected for GM,WM, CSF. Selected for new ROI(M)
B)Optional Fields:
task modulation factor= no effect
time frequency decomposition= what to select here???
C) Options:
Analysis Space: same as templates
Analysis mask: explicit mask of brain==> brain mask selected from output of Brain Extraction Tool of FSL (  is this correct???)
Analysis Units= Raw ( I want the average of the intensity values of the ROI, That's why I did not select the percent signal change)


Denoising:
A) Bandpass= 0.009 to 0.08
after regression
B) Additional Steps: linear detrending, No despiking ( what is the effect of despiking?? How will it change my analysis???)


!st level Analysis:
A) Analysis options:
==> functional connectivity- weighted GLM
==> Correlation- No weighting
==>hrf weighting- no Weighting
==> ROI to ROI & seed to voxel


The files that are produced in the folder results/1stlevel are:
1)BETA_Subject1_Condition001_Source001.nii  ==> connectivity maps for each subject/condition/source (e.g. fisher transformed correlation values if using 'bivariate correlation' connectivity measures)
2)corr_Subject1_Condition001_Source001.nii  ==> correlation map

3) p_corr_Subject1_Condition001_Source001.nii  ==> p value map
4)pFDR_corr_Subject1_Condition001_Source001.nii  ==> FDR corrected P value map
5) se_Subject1_Condition001.nii   ==> what is this???

What I understand from the following thread:
http://www.nitrc.org/forum/message.php?m...

is that this step has been already performed if I am using Conn14p. I am attaching my results as a jpeg image. According to the convention, it should be the regions with least p value that are most likely to be correlated with my ROI. So the red regions are the best correlated areas?  

My questions are:
1) Am I doing it in the right way???
2) Is there a way to plot correlated areas according to Z score?

Thanking you,
Sounak