Hi Cameron,

Thanks for the extensive explanation! I've ordered the book you suggestion, I look forward to reading it.
It seems much easier to use the timecourses that you already created, so I will proceed with those. But a quick question first: why aren't the mean_xxx consecutive? Or is it arbitrary?

Just to be sure, this is how I think to proceed:
 - import snwmrda1018959_session_1_rest_1_cc400_TCs.1D from CC400 time course (as A) (A is  Nrows x 148 Means)
 - create correlation matrix of A
 - threshold and ceil the data to get a undirected connection matrix => A(A < 0.2) = 0; A(A >= 0.2) = 1;
 - Cluster <- cluster(A)
Cluster will then be a vector indicating the class to which each point (i.e. Mean_xxx) belongs ( e.g. Cluster = [1 1 1 8 2 3 ...]' )

This is the point where I got a bit confused, how do I create the overlay and which file do you mean by `ROI Atlas image files'? Also, how do I convert this vector to a 3d mask?

 - read mask_wmean_mrda1018959_session_1_rest_1.nii and put the class values in the mask data.
 - write the new mask and create display it for example as an overlay on wssd1018959_session_1_anat.nii




I hope you can help me further, I guess i'm almost there to get it working!

Cheers!

 - Niels