Hi Francois,
I was exporting the maps, modifying them, and reimporting as per your instructions above. Everything was working fine. Then when I went to do it again this evening, something changed and it won't work.
I am now getting an error:
Call stack:
** >bst_memory.m>ReshapeConnectMatrix at 1772
** >bst_memory.m at 72
** >view_connect.m at 124
** >tree_callbacks.m at 380
** >bst_call.m at 28
** >panel_protocols.m>CreatePanel/protocolTreeClicked_Callback at 109
I noticed one peculiar thing that changed when I did: TfMat.TF=R(:);,
That was, the resulting matrix size for TF was larger than it had been when it was working.
I cannot figure out why this is happening. And I think it is difficult for you to figure out. But one workaround maybe is if you can explain how to get the R matrix back into the same shape as the original TF matrix. The extracted R is a 4-D matrix. But the TF matrix is not. In my case the TF matrix was a 1953x1x10 double. Now, after importing the R using the command TfMat.TF=R(:);, the TF matrix is 38440x1 double.
Again, this double matrix shape had worked before, but the size was smaller. I don't know why it has increased. 
Any ideas?
Thank you so much.
Jared