Dear Conn Community, dear Alfonso,

I'm quiet new to CONN and usually I could find all the answers to my questions within this forum - thanks for that!
However, this time I wonder if you could help me solving this problem:

I've uploaded several multiple ROI files in MNI space in the SETUP step. Each of theses files contains multiple ROIs ("Atlas" box is marked).
With the display ROI function, I can see that all ROIs are also uploaded (for example 37 ROIs within one ROI file) and properly coregistered.

But, after running the SETUP pipeline I run into two problems:
First, the individual ROIs of one file are not named by their name as I have named them in an additional txt file (same pattern as the default atlas and network ROIs), but all ROIs of one file have the same name with a number, e.g. "ROI.Cluster001, ROI.Cluster002"

Second, not all ROIs of one file are implemented. For example the file including 37 ROIs lists only 25 "Clusters". I don't know if ROI.Cluster001 represents the first entry of my .txt file. and I don't know how to check what went wrong.

Do you have any suggestions how I could proceed to solve these problems?

Thanks in advance,
Alexandra

Hello,

I found the solution:

some ROIs were overlapping that is probably why some ROIs were missing in the end and why the labeling did not work out. We created separate files to disentangle overlapping ROIs and used fslmaths for creating the ROI files - now everything is working fine.

Greetings,
Alexandra