Hi Conn users and Alfonso, 

In my second level results, I used a two group contrast (Healthy Controls vs CTS) at baseline. There were a few clusters with increased FC in CTS compared to HC, each covering several difference brain regions. In order to assess specific anatomical regions, I went through and picked several coordinates to explore the contrast in specific brain region. I wrote a quick bash script to loop through the BETA files for all the subjects and at the baseline condition and extract BETA values by averaging over 4mm diameter seeds (3dmaskave) that I created at the coordinates of interest. However, when I look at the boxplots of these BETA values, several of them show the HC averages being higher than the CTS averages, even though the group contrast map from which I chose these coordinates showed increased FC in CTS. Any thoughts? I checked the seeds I used and they overlap with the clusters of increased FC I exported from conn with the REX viewer. 

Additionally, while I see very strong group maps, the pre vs post contrasts for CTS show very minimal results, even if I relax the p uncorrected thresholds. Should I try adding more components to the aCompCor denoising? Also because one of the CSF masks was completely eroded, I switched to an erosion setting of proportion of post-erosion voxels (set to .3). Is that sufficient to make sure I'm not removing gray matter signal?

Best,
- Harris